01_look_see_download.r

Date Written:

2015-08-22

Description:

Find out how may transducin-like structures there are in the protein databank (PDB) then:
- download these to disc
- extract sequences
- cluster by sequence identity
- superpose structures and cluster by RMSD
- annotate and assign sequence identity and RMSD cluster groups - compare consistency of clustering patterns with figure for collaborator.

Usage and versions:

Developed in interactive R mode then rendered with rmarkdown (i.e.)
library(rmarkdown); render("01_look_see_download.r")

See sessionInfo() output at end.

# Load required packages
library(bio3d)
library(dendextend)


# Use PDB structure as search seed input
input <- "1GIT"

# Extract sequence from structure and BLAST search PDB
pdb <- read.pdb(input)
##   Note: Accessing on-line PDB file
## Warning in get.pdb(file, path = tempdir(), quiet = TRUE): /var/folders/
## nn/zjfxp9k162vfr0_p6tb75j080000gn/T//Rtmpa4dIsq/1GIT.pdb exists. Skipping
## download
aa1 <- pdbseq(pdb)
blast <- blast.pdb( pdbseq(pdb) )
##  Searching ... please wait (updates every 5 seconds) RID = XHNC7VUZ015 
##  .
##  Reporting 272 hits
# Summarize hit stat profile. 
raw.hits <- plot(blast)
##   * Possible cutoff values:    709 2 
##             Yielding Nhits:    82 272 
## 
##   * Chosen cutoff value of:    709 
##             Yielding Nhits:    82
# Save plot to pdf
#pdf("../results/pdb_blast_plot.pdf")
plot(blast)
##   * Possible cutoff values:    709 2 
##             Yielding Nhits:    82 272 
## 
##   * Chosen cutoff value of:    709 
##             Yielding Nhits:    82

## $hits
##    pdb.id   gi.id       group
## 1  "1GG2_A" "1942391"   "1"  
## 2  "1GIT_A" "157831196" "1"  
## 3  "2ZJY_A" "225733962" "1"  
## 4  "2ZJZ_A" "225733963" "1"  
## 5  "2ZJZ_B" "225733964" "1"  
## 6  "1GP2_A" "1942397"   "1"  
## 7  "1AGR_A" "2392128"   "1"  
## 8  "1AGR_D" "2392129"   "1"  
## 9  "1CIP_A" "4930007"   "1"  
## 10 "1BOF_A" "157830415" "1"  
## 11 "1GDD_A" "157831169" "1"  
## 12 "1GFI_A" "157831179" "1"  
## 13 "1GIA_A" "157831190" "1"  
## 14 "4PAN_A" "672883465" "1"  
## 15 "4PAQ_A" "672883467" "1"  
## 16 "2XNS_A" "335892077" "1"  
## 17 "2XNS_B" "335892078" "1"  
## 18 "1KJY_A" "21465862"  "1"  
## 19 "1KJY_C" "21465864"  "1"  
## 20 "2OM2_A" "152149207" "1"  
## 21 "2OM2_C" "152149209" "1"  
## 22 "3FFA_A" "260656194" "1"  
## 23 "3FFB_A" "260656195" "1"  
## 24 "1Y3A_A" "73535566"  "1"  
## 25 "1Y3A_B" "73535567"  "1"  
## 26 "1Y3A_C" "73535568"  "1"  
## 27 "1Y3A_D" "73535569"  "1"  
## 28 "2IK8_A" "119390199" "1"  
## 29 "2IK8_C" "119390201" "1"  
## 30 "4G5Q_A" "403072215" "1"  
## 31 "4G5Q_B" "403072216" "1"  
## 32 "4G5Q_C" "403072217" "1"  
## 33 "4G5Q_D" "403072218" "1"  
## 34 "1SVK_A" "49259163"  "1"  
## 35 "1SVS_A" "49259164"  "1"  
## 36 "2GTP_A" "109158062" "1"  
## 37 "2GTP_B" "109158063" "1"  
## 38 "4N0D_A" "594147785" "1"  
## 39 "4N0E_A" "594147786" "1"  
## 40 "3UMS_A" "374977750" "1"  
## 41 "1AS0_A" "157830048" "1"  
## 42 "1AS2_A" "157830049" "1"  
## 43 "1AS3_A" "157830050" "1"  
## 44 "1GIL_A" "157831192" "1"  
## 45 "4PAM_A" "672883464" "1"  
## 46 "4PAO_A" "672883466" "1"  
## 47 "3ONW_A" "312597480" "1"  
## 48 "3ONW_B" "312597481" "1"  
## 49 "3QI2_A" "374414490" "1"  
## 50 "3QI2_B" "374414491" "1"  
## 51 "1BH2_A" "157830309" "1"  
## 52 "3D7M_A" "224510607" "1"  
## 53 "3QE0_A" "374074114" "1"  
## 54 "3QE0_B" "374074115" "1"  
## 55 "3QE0_C" "374074116" "1"  
## 56 "3UMR_A" "409973704" "1"  
## 57 "2G83_A" "118137802" "1"  
## 58 "2G83_B" "118137804" "1"  
## 59 "2ODE_A" "126031531" "1"  
## 60 "2ODE_C" "126031533" "1"  
## 61 "2V4Z_A" "211938982" "1"  
## 62 "4G5R_A" "403072223" "1"  
## 63 "4G5R_B" "403072224" "1"  
## 64 "4G5R_C" "403072225" "1"  
## 65 "4G5R_D" "403072226" "1"  
## 66 "4G5S_A" "403072231" "1"  
## 67 "4G5S_B" "403072232" "1"  
## 68 "4G5S_C" "403072233" "1"  
## 69 "4G5S_D" "403072234" "1"  
## 70 "2IHB_A" "119390147" "1"  
## 71 "4G5O_A" "403072207" "1"  
## 72 "4G5O_B" "403072208" "1"  
## 73 "4G5O_C" "403072209" "1"  
## 74 "4G5O_D" "403072210" "1"  
## 75 "1FQJ_A" "13399564"  "1"  
## 76 "1FQJ_D" "13399567"  "1"  
## 77 "1FQK_A" "13399569"  "1"  
## 78 "1FQK_C" "13399571"  "1"  
## 79 "3V00_C" "384482350" "1"  
## 80 "3V00_B" "384482351" "1"  
## 81 "3V00_A" "384482352" "1"  
## 82 "1GOT_A" "1942173"   "1"  
## 
## $pdb.id
##  [1] "1GG2_A" "1GIT_A" "2ZJY_A" "2ZJZ_A" "2ZJZ_B" "1GP2_A" "1AGR_A"
##  [8] "1AGR_D" "1CIP_A" "1BOF_A" "1GDD_A" "1GFI_A" "1GIA_A" "4PAN_A"
## [15] "4PAQ_A" "2XNS_A" "2XNS_B" "1KJY_A" "1KJY_C" "2OM2_A" "2OM2_C"
## [22] "3FFA_A" "3FFB_A" "1Y3A_A" "1Y3A_B" "1Y3A_C" "1Y3A_D" "2IK8_A"
## [29] "2IK8_C" "4G5Q_A" "4G5Q_B" "4G5Q_C" "4G5Q_D" "1SVK_A" "1SVS_A"
## [36] "2GTP_A" "2GTP_B" "4N0D_A" "4N0E_A" "3UMS_A" "1AS0_A" "1AS2_A"
## [43] "1AS3_A" "1GIL_A" "4PAM_A" "4PAO_A" "3ONW_A" "3ONW_B" "3QI2_A"
## [50] "3QI2_B" "1BH2_A" "3D7M_A" "3QE0_A" "3QE0_B" "3QE0_C" "3UMR_A"
## [57] "2G83_A" "2G83_B" "2ODE_A" "2ODE_C" "2V4Z_A" "4G5R_A" "4G5R_B"
## [64] "4G5R_C" "4G5R_D" "4G5S_A" "4G5S_B" "4G5S_C" "4G5S_D" "2IHB_A"
## [71] "4G5O_A" "4G5O_B" "4G5O_C" "4G5O_D" "1FQJ_A" "1FQJ_D" "1FQK_A"
## [78] "1FQK_C" "3V00_C" "3V00_B" "3V00_A" "1GOT_A"
## 
## $gi.id
##  [1] "1942391"   "157831196" "225733962" "225733963" "225733964"
##  [6] "1942397"   "2392128"   "2392129"   "4930007"   "157830415"
## [11] "157831169" "157831179" "157831190" "672883465" "672883467"
## [16] "335892077" "335892078" "21465862"  "21465864"  "152149207"
## [21] "152149209" "260656194" "260656195" "73535566"  "73535567" 
## [26] "73535568"  "73535569"  "119390199" "119390201" "403072215"
## [31] "403072216" "403072217" "403072218" "49259163"  "49259164" 
## [36] "109158062" "109158063" "594147785" "594147786" "374977750"
## [41] "157830048" "157830049" "157830050" "157831192" "672883464"
## [46] "672883466" "312597480" "312597481" "374414490" "374414491"
## [51] "157830309" "224510607" "374074114" "374074115" "374074116"
## [56] "409973704" "118137802" "118137804" "126031531" "126031533"
## [61] "211938982" "403072223" "403072224" "403072225" "403072226"
## [66] "403072231" "403072232" "403072233" "403072234" "119390147"
## [71] "403072207" "403072208" "403072209" "403072210" "13399564" 
## [76] "13399567"  "13399569"  "13399571"  "384482350" "384482351"
## [81] "384482352" "1942173"  
## 
## attr(,"class")
## [1] "blast"
#dev.off()


# Annotate significant hits
annot <- pdb.annotate(raw.hits$pdb.id, 
                      anno.terms=c("resolution", "source", 
                                   "ligandId", "citation"))
## Warning in pdb.annotate(raw.hits$pdb.id, anno.terms = c("resolution",
## "source", : ids should be standard 4 character PDB-IDs: trying first 4
## characters...
# Print table...
annot
##        resolution                        source       ligandId
## 1GG2_A        2.4             Rattus norvegicus            GDP
## 1GIT_A        2.6             Rattus norvegicus        GDP,PO4
## 2ZJY_A        2.8             Rattus norvegicus     ALF,GDP,MG
## 2ZJZ_A        2.6             Rattus norvegicus            GDP
## 2ZJZ_B        2.6             Rattus norvegicus            GDP
## 1GP2_A        2.3             Rattus norvegicus            GDP
## 1AGR_A        2.8             Rattus norvegicus ALF,CIT,GDP,MG
## 1AGR_D        2.8             Rattus norvegicus ALF,CIT,GDP,MG
## 1CIP_A        1.5             Rattus norvegicus         GNP,MG
## 1BOF_A        2.2             Rattus norvegicus     GDP,MG,SO4
## 1GDD_A        2.2             Rattus norvegicus        GDP,SO4
## 1GFI_A        2.2             Rattus norvegicus     ALF,GDP,MG
## 1GIA_A        2.0             Rattus norvegicus         GSP,MG
## 4PAN_A        2.4             Rattus norvegicus     CL,GDP,SO3
## 4PAQ_A        2.0             Rattus norvegicus         GSP,MG
## 2XNS_A       3.41                  HOMO SAPIENS        GDP,SRT
## 2XNS_B       3.41                  HOMO SAPIENS        GDP,SRT
## 1KJY_A        2.7                  Homo sapiens         CS,GDP
## 1KJY_C        2.7                  Homo sapiens      CS,GDP,MG
## 2OM2_A        2.2                  Homo sapiens         GDP,MG
## 2OM2_C        2.2                  Homo sapiens         GDP,MG
## 3FFA_A        2.3             Rattus norvegicus     GSP,MG,SO4
## 3FFB_A       2.57             Rattus norvegicus        GDP,SO4
## 1Y3A_A        2.5                  Homo sapiens            GDP
## 1Y3A_B        2.5                  Homo sapiens            GDP
## 1Y3A_C        2.5                  Homo sapiens            GDP
## 1Y3A_D        2.5                  Homo sapiens            GDP
## 2IK8_A       2.71                  Homo sapiens ALF,GDP,MG,SO4
## 2IK8_C       2.71                  Homo sapiens ALF,GDP,MG,SO4
## 4G5Q_A        2.9                  Homo sapiens        GDP,SO4
## 4G5Q_B        2.9                  Homo sapiens    CIT,GDP,SO4
## 4G5Q_C        2.9                  Homo sapiens    CIT,GDP,SO4
## 4G5Q_D        2.9                  Homo sapiens    CIT,GDP,SO4
## 1SVK_A        2.0             Rattus norvegicus     ALF,GDP,MG
## 1SVS_A        1.5             Rattus norvegicus         GNP,MG
## 2GTP_A       2.55                  Homo sapiens     ALF,GDP,MG
## 2GTP_B       2.55                  Homo sapiens     ALF,GDP,MG
## 4N0D_A       1.55             Rattus norvegicus     GSP,MG,SO3
## 4N0E_A        2.1             Rattus norvegicus        GDP,SO4
## 3UMS_A       2.34                  Homo sapiens     CL,GDP,SO4
## 1AS0_A        2.0             Rattus norvegicus     GSP,MG,SO4
## 1AS2_A        2.8             Rattus norvegicus        GDP,PO4
## 1AS3_A        2.4             Rattus norvegicus        GDP,SO4
## 1GIL_A        2.3             Rattus norvegicus         GSP,MG
## 4PAM_A        2.1             Rattus norvegicus     CL,GDP,SO3
## 4PAO_A        2.0             Rattus norvegicus         GSP,MG
## 3ONW_A       2.38                  Homo sapiens        GDP,SO4
## 3ONW_B       2.38                  Homo sapiens        GDP,SO4
## 3QI2_A        2.8                  Homo sapiens    GDP,GOL,SO4
## 3QI2_B        2.8                  Homo sapiens        GDP,SO4
## 1BH2_A        2.1             Rattus norvegicus         GSP,MG
## 3D7M_A        2.9             Rattus norvegicus     ALF,GDP,MG
## 3QE0_A        3.0                  Homo sapiens         GDP,MG
## 3QE0_B        3.0                  Homo sapiens         GDP,MG
## 3QE0_C        3.0                  Homo sapiens         GDP,MG
## 3UMR_A       2.04                  Homo sapiens CL,GDP,GOL,SO4
## 2G83_A        2.8                  Homo sapiens     ALF,GDP,MG
## 2G83_B        2.8                  Homo sapiens     ALF,GDP,MG
## 2ODE_A        1.9                  Homo sapiens     ALF,GDP,MG
## 2ODE_C        1.9                  Homo sapiens     ALF,GDP,MG
## 2V4Z_A        2.8                  HOMO SAPIENS     ALF,GDP,MG
## 4G5R_A       3.48                  Homo sapiens        GDP,SO4
## 4G5R_B       3.48                  Homo sapiens    CIT,GDP,SO4
## 4G5R_C       3.48                  Homo sapiens    CIT,GDP,SO4
## 4G5R_D       3.48                  Homo sapiens            GDP
## 4G5S_A       3.62                  Homo sapiens        CIT,GDP
## 4G5S_B       3.62                  Homo sapiens            GDP
## 4G5S_C       3.62                  Homo sapiens        CIT,GDP
## 4G5S_D       3.62                  Homo sapiens           <NA>
## 2IHB_A       2.71                  Homo sapiens     ALF,GDP,MG
## 4G5O_A        2.9                  Homo sapiens    CIT,GDP,SO4
## 4G5O_B        2.9                  Homo sapiens        GDP,SO4
## 4G5O_C        2.9                  Homo sapiens    CIT,GDP,SO4
## 4G5O_D        2.9                  Homo sapiens    CIT,GDP,SO4
## 1FQJ_A       2.02 Bos taurus, Rattus norvegicus     ALF,GDP,MG
## 1FQJ_D       2.02 Bos taurus, Rattus norvegicus     ALF,GDP,MG
## 1FQK_A        2.3 Bos taurus, Rattus norvegicus     ALF,GDP,MG
## 1FQK_C        2.3 Bos taurus, Rattus norvegicus     ALF,GDP,MG
## 3V00_C        2.9 Bos taurus, Rattus norvegicus            GDP
## 3V00_B        2.9 Bos taurus, Rattus norvegicus            GDP
## 3V00_A        2.9 Bos taurus, Rattus norvegicus            GDP
## 1GOT_A        2.0                    Bos taurus            MSE
##                                                  citation
## 1GG2_A                            Wall et al. Cell (1995)
## 1GIT_A                   Berghuis et al. Structure (1996)
## 2ZJY_A             Morikawa et al. To be Published (null)
## 2ZJZ_A             Morikawa et al. To be Published (null)
## 2ZJZ_B             Morikawa et al. To be Published (null)
## 1GP2_A                            Wall et al. Cell (1995)
## 1AGR_A                          Tesmer et al. Cell (1997)
## 1AGR_D                          Tesmer et al. Cell (1997)
## 1CIP_A                 Coleman et al. J.Biol.Chem. (1999)
## 1BOF_A                 Coleman et al. Biochemistry (1998)
## 1GDD_A                        Mixon et al. Science (1995)
## 1GFI_A                      Coleman et al. Science (1994)
## 1GIA_A                      Coleman et al. Science (1994)
## 4PAN_A                    Kaya et al. J.Biol.Chem. (2014)
## 4PAQ_A                    Kaya et al. J.Biol.Chem. (2014)
## 2XNS_A               Sammond et al. J.Am.Chem.Soc. (2011)
## 2XNS_B               Sammond et al. J.Am.Chem.Soc. (2011)
## 1KJY_A                        Kimple et al. Nature (2002)
## 1KJY_C                        Kimple et al. Nature (2002)
## 2OM2_A                  Sammond et al. J.Mol.Biol. (2007)
## 2OM2_C                  Sammond et al. J.Mol.Biol. (2007)
## 3FFA_A                   Kapoor et al. J.Mol.Biol. (2009)
## 3FFB_A                   Kapoor et al. J.Mol.Biol. (2009)
## 1Y3A_A                   Johnston et al. Structure (2005)
## 1Y3A_B                   Johnston et al. Structure (2005)
## 1Y3A_C                   Johnston et al. Structure (2005)
## 1Y3A_D                   Johnston et al. Structure (2005)
## 2IK8_A Soundararajan et al. Proc.Natl.Acad.Sci.Usa (2008)
## 2IK8_C Soundararajan et al. Proc.Natl.Acad.Sci.Usa (2008)
## 4G5Q_A                  Jia et al. To be Published (null)
## 4G5Q_B                  Jia et al. To be Published (null)
## 4G5Q_C                  Jia et al. To be Published (null)
## 4G5Q_D                  Jia et al. To be Published (null)
## 1SVK_A        Thomas et al. Proc.Natl.Acad.Sci.USA (2004)
## 1SVS_A        Thomas et al. Proc.Natl.Acad.Sci.USA (2004)
## 2GTP_A Soundararajan et al. Proc.Natl.Acad.Sci.Usa (2008)
## 2GTP_B Soundararajan et al. Proc.Natl.Acad.Sci.Usa (2008)
## 4N0D_A                  Thaker et al. J.Biol.Chem. (2014)
## 4N0E_A                  Thaker et al. J.Biol.Chem. (2014)
## 3UMS_A       Lambert et al. Proc.Natl.Acad.Sci.USA (2012)
## 1AS0_A                     Raw et al. Biochemistry (1997)
## 1AS2_A                     Raw et al. Biochemistry (1997)
## 1AS3_A                     Raw et al. Biochemistry (1997)
## 1GIL_A                      Coleman et al. Science (1994)
## 4PAM_A                    Kaya et al. J.Biol.Chem. (2014)
## 4PAO_A                    Kaya et al. J.Biol.Chem. (2014)
## 3ONW_A                   Bosch et al. J.Biol.Chem. (2011)
## 3ONW_B                   Bosch et al. J.Biol.Chem. (2011)
## 3QI2_A                   Bosch et al. Plos Pathog. (2012)
## 3QI2_B                   Bosch et al. Plos Pathog. (2012)
## 1BH2_A                  Posner et al. J.Biol.Chem. (1998)
## 3D7M_A              Preininger et al. Biochemistry (2009)
## 3QE0_A                   Bosch et al. Plos Pathog. (2012)
## 3QE0_B                   Bosch et al. Plos Pathog. (2012)
## 3QE0_C                   Bosch et al. Plos Pathog. (2012)
## 3UMR_A             Johnston et al. To be Published (null)
## 2G83_A                Johnston et al. Biochemistry (2006)
## 2G83_B                Johnston et al. Biochemistry (2006)
## 2ODE_A Soundararajan et al. Proc.Natl.Acad.Sci.Usa (2008)
## 2ODE_C Soundararajan et al. Proc.Natl.Acad.Sci.Usa (2008)
## 2V4Z_A                  Kimple et al. J.Biol.Chem. (2009)
## 4G5R_A                  Jia et al. To be Published (null)
## 4G5R_B                  Jia et al. To be Published (null)
## 4G5R_C                  Jia et al. To be Published (null)
## 4G5R_D                  Jia et al. To be Published (null)
## 4G5S_A                  Jia et al. To be Published (null)
## 4G5S_B                  Jia et al. To be Published (null)
## 4G5S_C                  Jia et al. To be Published (null)
## 4G5S_D                  Jia et al. To be Published (null)
## 2IHB_A Soundararajan et al. Proc.Natl.Acad.Sci.Usa (2008)
## 4G5O_A                  Jia et al. To be Published (null)
## 4G5O_B                  Jia et al. To be Published (null)
## 4G5O_C                  Jia et al. To be Published (null)
## 4G5O_D                  Jia et al. To be Published (null)
## 1FQJ_A                          Slep et al. Nature (2001)
## 1FQJ_D                          Slep et al. Nature (2001)
## 1FQK_A                          Slep et al. Nature (2001)
## 1FQK_C                          Slep et al. Nature (2001)
## 3V00_C                   Singh et al. Biochemistry (2012)
## 3V00_B                   Singh et al. Biochemistry (2012)
## 3V00_A                   Singh et al. Biochemistry (2012)
## 1GOT_A                     Lambright et al. Nature (1996)
# Save annotated hit table 
write.table(annot, sep="\t", quote=FALSE, file="../results/pdb_blast_hits.tbl")

# Extract and align sequences of all hits
raw.files <- get.pdb(raw.hits$pdb.id, split=TRUE, path="../data/")
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1GG2.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1GIT.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//2ZJY.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//2ZJZ.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1GP2.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1AGR.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1CIP.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1BOF.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1GDD.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1GFI.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1GIA.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//4PAN.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//4PAQ.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//2XNS.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1KJY.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//2OM2.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//3FFA.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//3FFB.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1Y3A.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//2IK8.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//4G5Q.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1SVK.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1SVS.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//2GTP.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//4N0D.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//4N0E.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//3UMS.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1AS0.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1AS2.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1AS3.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1GIL.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//4PAM.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//4PAO.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//3ONW.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//3QI2.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1BH2.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//3D7M.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//3QE0.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//3UMR.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//2G83.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//2ODE.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//2V4Z.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//4G5R.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//4G5S.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//2IHB.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//4G5O.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1FQJ.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1FQK.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//3V00.pdb exists. Skipping download
## Warning in get.pdb(raw.hits$pdb.id, split = TRUE, path = "../data/"): ../
## data//1GOT.pdb exists. Skipping download
## 
  |                                                                       
  |                                                                 |   0%
  |                                                                       
  |=                                                                |   2%
  |                                                                       
  |===                                                              |   4%
  |                                                                       
  |====                                                             |   6%
  |                                                                       
  |=====                                                            |   7%
  |                                                                       
  |=====                                                            |   8%
  |                                                                       
  |======                                                           |  10%
  |                                                                       
  |=======                                                          |  11%
  |                                                                       
  |========                                                         |  12%
  |                                                                       
  |=========                                                        |  14%
  |                                                                       
  |==========                                                       |  16%
  |                                                                       
  |============                                                     |  18%
  |                                                                       
  |=============                                                    |  20%
  |                                                                       
  |==============                                                   |  22%
  |                                                                       
  |================                                                 |  24%
  |                                                                       
  |=================                                                |  26%
  |                                                                       
  |==================                                               |  27%
  |                                                                       
  |==================                                               |  28%
  |                                                                       
  |===================                                              |  29%
  |                                                                       
  |====================                                             |  30%
  |                                                                       
  |====================                                             |  31%
  |                                                                       
  |=====================                                            |  32%
  |                                                                       
  |======================                                           |  34%
  |                                                                       
  |=======================                                          |  36%
  |                                                                       
  |========================                                         |  36%
  |                                                                       
  |========================                                         |  37%
  |                                                                       
  |========================                                         |  38%
  |                                                                       
  |=========================                                        |  38%
  |                                                                       
  |=========================                                        |  39%
  |                                                                       
  |==========================                                       |  40%
  |                                                                       
  |===========================                                      |  41%
  |                                                                       
  |===========================                                      |  42%
  |                                                                       
  |=============================                                    |  44%
  |                                                                       
  |==============================                                   |  46%
  |                                                                       
  |===============================                                  |  47%
  |                                                                       
  |===============================                                  |  48%
  |                                                                       
  |================================                                 |  50%
  |                                                                       
  |==================================                               |  52%
  |                                                                       
  |===================================                              |  54%
  |                                                                       
  |====================================                             |  56%
  |                                                                       
  |======================================                           |  58%
  |                                                                       
  |=======================================                          |  60%
  |                                                                       
  |========================================                         |  62%
  |                                                                       
  |==========================================                       |  64%
  |                                                                       
  |===========================================                      |  66%
  |                                                                       
  |============================================                     |  67%
  |                                                                       
  |============================================                     |  68%
  |                                                                       
  |=============================================                    |  69%
  |                                                                       
  |==============================================                   |  70%
  |                                                                       
  |===============================================                  |  72%
  |                                                                       
  |================================================                 |  74%
  |                                                                       
  |=================================================                |  75%
  |                                                                       
  |=================================================                |  76%
  |                                                                       
  |===================================================              |  78%
  |                                                                       
  |===================================================              |  79%
  |                                                                       
  |====================================================             |  80%
  |                                                                       
  |=====================================================            |  81%
  |                                                                       
  |=====================================================            |  82%
  |                                                                       
  |=======================================================          |  84%
  |                                                                       
  |=======================================================          |  85%
  |                                                                       
  |========================================================         |  86%
  |                                                                       
  |=========================================================        |  87%
  |                                                                       
  |=========================================================        |  88%
  |                                                                       
  |==========================================================       |  90%
  |                                                                       
  |===========================================================      |  90%
  |                                                                       
  |===========================================================      |  91%
  |                                                                       
  |===========================================================      |  92%
  |                                                                       
  |============================================================     |  92%
  |                                                                       
  |============================================================     |  93%
  |                                                                       
  |=============================================================    |  94%
  |                                                                       
  |==============================================================   |  95%
  |                                                                       
  |==============================================================   |  96%
  |                                                                       
  |===============================================================  |  97%
  |                                                                       
  |================================================================ |  98%
  |                                                                       
  |=================================================================| 100%
aln <- pdbaln( raw.files )
## Reading PDB files:
## ../data//split_chain/1GG2_A.pdb
## ../data//split_chain/1GIT_A.pdb
## ../data//split_chain/2ZJY_A.pdb
## ../data//split_chain/2ZJZ_A.pdb
## ../data//split_chain/2ZJZ_B.pdb
## ../data//split_chain/1GP2_A.pdb
## ../data//split_chain/1AGR_A.pdb
## ../data//split_chain/1AGR_D.pdb
## ../data//split_chain/1CIP_A.pdb
## ../data//split_chain/1BOF_A.pdb
## ../data//split_chain/1GDD_A.pdb
## ../data//split_chain/1GFI_A.pdb
## ../data//split_chain/1GIA_A.pdb
## ../data//split_chain/4PAN_A.pdb
## ../data//split_chain/4PAQ_A.pdb
## ../data//split_chain/2XNS_A.pdb
## ../data//split_chain/2XNS_B.pdb
## ../data//split_chain/1KJY_A.pdb
## ../data//split_chain/1KJY_C.pdb
## ../data//split_chain/2OM2_A.pdb
## ../data//split_chain/2OM2_C.pdb
## ../data//split_chain/3FFA_A.pdb
## ../data//split_chain/3FFB_A.pdb
## ../data//split_chain/1Y3A_A.pdb
## ../data//split_chain/1Y3A_B.pdb
## ../data//split_chain/1Y3A_C.pdb
## ../data//split_chain/1Y3A_D.pdb
## ../data//split_chain/2IK8_A.pdb
## ../data//split_chain/2IK8_C.pdb
## ../data//split_chain/4G5Q_A.pdb
## ../data//split_chain/4G5Q_B.pdb
## ../data//split_chain/4G5Q_C.pdb
## ../data//split_chain/4G5Q_D.pdb
## ../data//split_chain/1SVK_A.pdb
## ../data//split_chain/1SVS_A.pdb
## ../data//split_chain/2GTP_A.pdb
## ../data//split_chain/2GTP_B.pdb
## ../data//split_chain/4N0D_A.pdb
## ../data//split_chain/4N0E_A.pdb
## ../data//split_chain/3UMS_A.pdb
## ../data//split_chain/1AS0_A.pdb
## ../data//split_chain/1AS2_A.pdb
## ../data//split_chain/1AS3_A.pdb
## ../data//split_chain/1GIL_A.pdb
## ../data//split_chain/4PAM_A.pdb
## ../data//split_chain/4PAO_A.pdb
## ../data//split_chain/3ONW_A.pdb
## ../data//split_chain/3ONW_B.pdb
## ../data//split_chain/3QI2_A.pdb
## ../data//split_chain/3QI2_B.pdb
## ../data//split_chain/1BH2_A.pdb
## ../data//split_chain/3D7M_A.pdb
## ../data//split_chain/3QE0_A.pdb
## ../data//split_chain/3QE0_B.pdb
## ../data//split_chain/3QE0_C.pdb
## ../data//split_chain/3UMR_A.pdb
## ../data//split_chain/2G83_A.pdb
## ../data//split_chain/2G83_B.pdb
## ../data//split_chain/2ODE_A.pdb
## ../data//split_chain/2ODE_C.pdb
## ../data//split_chain/2V4Z_A.pdb
## ../data//split_chain/4G5R_A.pdb
## ../data//split_chain/4G5R_B.pdb
## ../data//split_chain/4G5R_C.pdb
## ../data//split_chain/4G5R_D.pdb
## ../data//split_chain/4G5S_A.pdb
## ../data//split_chain/4G5S_B.pdb
## ../data//split_chain/4G5S_C.pdb
## ../data//split_chain/4G5S_D.pdb
## ../data//split_chain/2IHB_A.pdb
## ../data//split_chain/4G5O_A.pdb
## ../data//split_chain/4G5O_B.pdb
## ../data//split_chain/4G5O_C.pdb
## ../data//split_chain/4G5O_D.pdb
## ../data//split_chain/1FQJ_A.pdb
## ../data//split_chain/1FQJ_D.pdb
## ../data//split_chain/1FQK_A.pdb
## ../data//split_chain/1FQK_C.pdb
## ../data//split_chain/3V00_C.pdb
## ../data//split_chain/3V00_B.pdb
## ../data//split_chain/3V00_A.pdb
## ../data//split_chain/1GOT_A.pdb
## ..............   PDB has ALT records, taking A only, rm.alt=TRUE
## .   PDB has ALT records, taking A only, rm.alt=TRUE
## .   PDB has ALT records, taking A only, rm.alt=TRUE
## .............   PDB has ALT records, taking A only, rm.alt=TRUE
## .   PDB has ALT records, taking A only, rm.alt=TRUE
## ..   PDB has ALT records, taking A only, rm.alt=TRUE
## .   PDB has ALT records, taking A only, rm.alt=TRUE
## ....   PDB has ALT records, taking A only, rm.alt=TRUE
## .   PDB has ALT records, taking A only, rm.alt=TRUE
## .   PDB has ALT records, taking A only, rm.alt=TRUE
## ......   PDB has ALT records, taking A only, rm.alt=TRUE
## ..........   PDB has ALT records, taking A only, rm.alt=TRUE
## ...   PDB has ALT records, taking A only, rm.alt=TRUE
## .   PDB has ALT records, taking A only, rm.alt=TRUE
## ...........   PDB has ALT records, taking A only, rm.alt=TRUE
## .   PDB has ALT records, taking A only, rm.alt=TRUE
## ..   PDB has ALT records, taking A only, rm.alt=TRUE
## .........
## 
## Extracting sequences
## 
## pdb/seq: 1   name: ../data//split_chain/1GG2_A.pdb 
## pdb/seq: 2   name: ../data//split_chain/1GIT_A.pdb 
## pdb/seq: 3   name: ../data//split_chain/2ZJY_A.pdb 
## pdb/seq: 4   name: ../data//split_chain/2ZJZ_A.pdb 
## pdb/seq: 5   name: ../data//split_chain/2ZJZ_B.pdb 
## pdb/seq: 6   name: ../data//split_chain/1GP2_A.pdb 
## pdb/seq: 7   name: ../data//split_chain/1AGR_A.pdb 
## pdb/seq: 8   name: ../data//split_chain/1AGR_D.pdb 
## pdb/seq: 9   name: ../data//split_chain/1CIP_A.pdb 
## pdb/seq: 10   name: ../data//split_chain/1BOF_A.pdb 
## pdb/seq: 11   name: ../data//split_chain/1GDD_A.pdb 
## pdb/seq: 12   name: ../data//split_chain/1GFI_A.pdb 
## pdb/seq: 13   name: ../data//split_chain/1GIA_A.pdb 
## pdb/seq: 14   name: ../data//split_chain/4PAN_A.pdb 
## pdb/seq: 15   name: ../data//split_chain/4PAQ_A.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 16   name: ../data//split_chain/2XNS_A.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 17   name: ../data//split_chain/2XNS_B.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 18   name: ../data//split_chain/1KJY_A.pdb 
## pdb/seq: 19   name: ../data//split_chain/1KJY_C.pdb 
## pdb/seq: 20   name: ../data//split_chain/2OM2_A.pdb 
## pdb/seq: 21   name: ../data//split_chain/2OM2_C.pdb 
## pdb/seq: 22   name: ../data//split_chain/3FFA_A.pdb 
## pdb/seq: 23   name: ../data//split_chain/3FFB_A.pdb 
## pdb/seq: 24   name: ../data//split_chain/1Y3A_A.pdb 
## pdb/seq: 25   name: ../data//split_chain/1Y3A_B.pdb 
## pdb/seq: 26   name: ../data//split_chain/1Y3A_C.pdb 
## pdb/seq: 27   name: ../data//split_chain/1Y3A_D.pdb 
## pdb/seq: 28   name: ../data//split_chain/2IK8_A.pdb 
## pdb/seq: 29   name: ../data//split_chain/2IK8_C.pdb 
## pdb/seq: 30   name: ../data//split_chain/4G5Q_A.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 31   name: ../data//split_chain/4G5Q_B.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 32   name: ../data//split_chain/4G5Q_C.pdb 
## pdb/seq: 33   name: ../data//split_chain/4G5Q_D.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 34   name: ../data//split_chain/1SVK_A.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 35   name: ../data//split_chain/1SVS_A.pdb 
## pdb/seq: 36   name: ../data//split_chain/2GTP_A.pdb 
## pdb/seq: 37   name: ../data//split_chain/2GTP_B.pdb 
## pdb/seq: 38   name: ../data//split_chain/4N0D_A.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 39   name: ../data//split_chain/4N0E_A.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 40   name: ../data//split_chain/3UMS_A.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 41   name: ../data//split_chain/1AS0_A.pdb 
## pdb/seq: 42   name: ../data//split_chain/1AS2_A.pdb 
## pdb/seq: 43   name: ../data//split_chain/1AS3_A.pdb 
## pdb/seq: 44   name: ../data//split_chain/1GIL_A.pdb 
## pdb/seq: 45   name: ../data//split_chain/4PAM_A.pdb 
## pdb/seq: 46   name: ../data//split_chain/4PAO_A.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 47   name: ../data//split_chain/3ONW_A.pdb 
## pdb/seq: 48   name: ../data//split_chain/3ONW_B.pdb 
## pdb/seq: 49   name: ../data//split_chain/3QI2_A.pdb 
## pdb/seq: 50   name: ../data//split_chain/3QI2_B.pdb 
## pdb/seq: 51   name: ../data//split_chain/1BH2_A.pdb 
## pdb/seq: 52   name: ../data//split_chain/3D7M_A.pdb 
## pdb/seq: 53   name: ../data//split_chain/3QE0_A.pdb 
## pdb/seq: 54   name: ../data//split_chain/3QE0_B.pdb 
## pdb/seq: 55   name: ../data//split_chain/3QE0_C.pdb 
## pdb/seq: 56   name: ../data//split_chain/3UMR_A.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 57   name: ../data//split_chain/2G83_A.pdb 
## pdb/seq: 58   name: ../data//split_chain/2G83_B.pdb 
## pdb/seq: 59   name: ../data//split_chain/2ODE_A.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 60   name: ../data//split_chain/2ODE_C.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 61   name: ../data//split_chain/2V4Z_A.pdb 
## pdb/seq: 62   name: ../data//split_chain/4G5R_A.pdb 
## pdb/seq: 63   name: ../data//split_chain/4G5R_B.pdb 
## pdb/seq: 64   name: ../data//split_chain/4G5R_C.pdb 
## pdb/seq: 65   name: ../data//split_chain/4G5R_D.pdb 
## pdb/seq: 66   name: ../data//split_chain/4G5S_A.pdb 
## pdb/seq: 67   name: ../data//split_chain/4G5S_B.pdb 
## pdb/seq: 68   name: ../data//split_chain/4G5S_C.pdb 
## pdb/seq: 69   name: ../data//split_chain/4G5S_D.pdb 
## pdb/seq: 70   name: ../data//split_chain/2IHB_A.pdb 
## pdb/seq: 71   name: ../data//split_chain/4G5O_A.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 72   name: ../data//split_chain/4G5O_B.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 73   name: ../data//split_chain/4G5O_C.pdb 
## pdb/seq: 74   name: ../data//split_chain/4G5O_D.pdb 
##    PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 75   name: ../data//split_chain/1FQJ_A.pdb 
## pdb/seq: 76   name: ../data//split_chain/1FQJ_D.pdb 
## pdb/seq: 77   name: ../data//split_chain/1FQK_A.pdb 
## pdb/seq: 78   name: ../data//split_chain/1FQK_C.pdb 
## pdb/seq: 79   name: ../data//split_chain/3V00_C.pdb 
## pdb/seq: 80   name: ../data//split_chain/3V00_B.pdb 
## pdb/seq: 81   name: ../data//split_chain/3V00_A.pdb 
## pdb/seq: 82   name: ../data//split_chain/1GOT_A.pdb
# Print alignment
aln
##                                 1        .         .         .         40 
## [Truncated_Name:1]1GG2_A.pdb    ---LSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGA
## [Truncated_Name:2]1GIT_A.pdb    ------------------------------REVKLLLLGA
## [Truncated_Name:3]2ZJY_A.pdb    ------------------------------REVKLLLLGA
## [Truncated_Name:4]2ZJZ_A.pdb    ----------------------------AAREVKLLLLGA
## [Truncated_Name:5]2ZJZ_B.pdb    -------------------------------EVKLLLLGA
## [Truncated_Name:6]1GP2_A.pdb    ---LSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGA
## [Truncated_Name:7]1AGR_A.pdb    ---LSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGA
## [Truncated_Name:8]1AGR_D.pdb    ---------AAVERSKMIDRNLREDGEKAAREVKLLLLGA
## [Truncated_Name:9]1CIP_A.pdb    ------------------------------REVKLLLLGA
## [Truncated_Name:10]1BOF_A.pdb   --------KAAVERSKMIDRNLREDGEKAAREVKLLLLGA
## [Truncated_Name:11]1GDD_A.pdb   -------DKAAVERSKMIDRNLREDGEKAAREVKLLLLGA
## [Truncated_Name:12]1GFI_A.pdb   -------------------------------EVKLLLLGA
## [Truncated_Name:13]1GIA_A.pdb   --------------------------------VKLLLLGA
## [Truncated_Name:14]4PAN_A.pdb   -------DKAAVERSKMIDRNLREDGEKAAREVKLLLLGA
## [Truncated_Name:15]4PAQ_A.pdb   -------------------------------EVKLLLLGA
## [Truncated_Name:16]2XNS_A.pdb   ------------------------------REVKLLLLGA
## [Truncated_Name:17]2XNS_B.pdb   ------------------------------REVKLLLLGA
## [Truncated_Name:18]1KJY_A.pdb   ----------------------------GAREVKLLLLGA
## [Truncated_Name:19]1KJY_C.pdb   ----------------------------GAREVKLLLLGA
## [Truncated_Name:20]2OM2_A.pdb   ----------------------------GAREVKLLLLGA
## [Truncated_Name:21]2OM2_C.pdb   ----------------------------GAREVKLLLLGA
## [Truncated_Name:22]3FFA_A.pdb   -------------------------------EVKLLLLGA
## [Truncated_Name:23]3FFB_A.pdb   ----SAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGA
## [Truncated_Name:24]1Y3A_A.pdb   --------------------------------VKLLLLGA
## [Truncated_Name:25]1Y3A_B.pdb   --------------------------------VKLLLLGA
## [Truncated_Name:26]1Y3A_C.pdb   --------------------------------VKLLLLGA
## [Truncated_Name:27]1Y3A_D.pdb   --------------------------------VKLLLLGA
## [Truncated_Name:28]2IK8_A.pdb   ------------------------------REVKLLLLGA
## [Truncated_Name:29]2IK8_C.pdb   -------------------------------EVKLLLLGA
## [Truncated_Name:30]4G5Q_A.pdb   -----------------------------AREVKLLLLGA
## [Truncated_Name:31]4G5Q_B.pdb   ------------------------------REVKLLLLGA
## [Truncated_Name:32]4G5Q_C.pdb   -----------------------------AREVKLLLLGA
## [Truncated_Name:33]4G5Q_D.pdb   -----------------------------AREVKLLLLGA
## [Truncated_Name:34]1SVK_A.pdb   -------------------------------EVKLLLLGA
## [Truncated_Name:35]1SVS_A.pdb   ------------------------------REVKLLLLGA
## [Truncated_Name:36]2GTP_A.pdb   ------------------------------REVKLLLLGA
## [Truncated_Name:37]2GTP_B.pdb   ------------------------------REVKLLLLGA
## [Truncated_Name:38]4N0D_A.pdb   ------------------------------REVKLLLLGA
## [Truncated_Name:39]4N0E_A.pdb   -------DKAAVERSKMIDRNLREDGEKAAREVKLLLLGA
## [Truncated_Name:40]3UMS_A.pdb   ----SAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGA
## [Truncated_Name:41]1AS0_A.pdb   ------------------------------REVKLLLLGA
## [Truncated_Name:42]1AS2_A.pdb   ------------------------------REVKLLLLGA
## [Truncated_Name:43]1AS3_A.pdb   -------DKAAVERSKMIDRNLREDGEKAAREVKLLLLGA
## [Truncated_Name:44]1GIL_A.pdb   --------------------------------VKLLLLGA
## [Truncated_Name:45]4PAM_A.pdb   -------DKAAVERSKMIDRNLREDGEKAAREVKLLLLGA
## [Truncated_Name:46]4PAO_A.pdb   -------------------------------EVKLLLLGA
## [Truncated_Name:47]3ONW_A.pdb   ------------------------------REVKLLLLGA
## [Truncated_Name:48]3ONW_B.pdb   ------------------------------REVKLLLLGA
## [Truncated_Name:49]3QI2_A.pdb   ----------------------------GAREVKLLLLGA
## [Truncated_Name:50]3QI2_B.pdb   --------------------------------VKLLLLGA
## [Truncated_Name:51]1BH2_A.pdb   ------------------------------REVKLLLLGA
## [Truncated_Name:52]3D7M_A.pdb   --------------------------------VKLLLLGA
## [Truncated_Name:53]3QE0_A.pdb   ------------------------------AEVKLLLLGA
## [Truncated_Name:54]3QE0_B.pdb   ------------------------------AEVKLLLLGA
## [Truncated_Name:55]3QE0_C.pdb   --------------------------------VKLLLLGA
## [Truncated_Name:56]3UMR_A.pdb   ------EDKAAVERSKMIDRNLREDGEKAAREVKLLLLGA
## [Truncated_Name:57]2G83_A.pdb   -------------------------------EVKLLLLGA
## [Truncated_Name:58]2G83_B.pdb   -------------------------------EVKLLLLGA
## [Truncated_Name:59]2ODE_A.pdb   -------------------------------EVKLLLLGA
## [Truncated_Name:60]2ODE_C.pdb   -----------------------------AKEVKLLLLGA
## [Truncated_Name:61]2V4Z_A.pdb   ------------------------------KEVKLLLLGA
## [Truncated_Name:62]4G5R_A.pdb   ------------------------------KEVKLLLLGA
## [Truncated_Name:63]4G5R_B.pdb   ------------------------------KEVKLLLLGA
## [Truncated_Name:64]4G5R_C.pdb   -------------------------------EVKLLLLGA
## [Truncated_Name:65]4G5R_D.pdb   ------------------------------KEVKLLLLGA
## [Truncated_Name:66]4G5S_A.pdb   ------------------------------KEVKLLLLGA
## [Truncated_Name:67]4G5S_B.pdb   ------------------------------KEVKLLLLGA
## [Truncated_Name:68]4G5S_C.pdb   -----------------------------AKEVKLLLLGA
## [Truncated_Name:69]4G5S_D.pdb   -----------------------------AKEVKLLLLGA
## [Truncated_Name:70]2IHB_A.pdb   -------------------------------EVKLLLLGA
## [Truncated_Name:71]4G5O_A.pdb   -----------------------------AKEVKLLLLGA
## [Truncated_Name:72]4G5O_B.pdb   ------------------------------KEVKLLLLGA
## [Truncated_Name:73]4G5O_C.pdb   -----------------------------AKEVKLLLLGA
## [Truncated_Name:74]4G5O_D.pdb   -----------------------------AKEVKLLLLGA
## [Truncated_Name:75]1FQJ_A.pdb   ------------------------------RTVKLLLLGA
## [Truncated_Name:76]1FQJ_D.pdb   ------------------------------RTVKLLLLGA
## [Truncated_Name:77]1FQK_A.pdb   ------------------------------RTVKLLLLGA
## [Truncated_Name:78]1FQK_C.pdb   -------------------------------TVKLLLLGA
## [Truncated_Name:79]3V00_C.pdb   HHHMGAGASAEEKHSRELEKKLKEDAEKDARTVKLLLLGA
## [Truncated_Name:80]3V00_B.pdb   -----------EKHSRELEKKLKEDAEKDARTVKLLLLGA
## [Truncated_Name:81]3V00_A.pdb   --HMGAGASAEEKHSRELEKKLKEDAEKDARTVKLLLLGA
## [Truncated_Name:82]1GOT_A.pdb   --------SAEEKHSRELEKKLKEDAEKDARTVKLLLLGA
##                                                                 ******** 
##                                 1        .         .         .         40 
## 
##                                41        .         .         .         80 
## [Truncated_Name:1]1GG2_A.pdb    GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:2]1GIT_A.pdb    GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:3]2ZJY_A.pdb    GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:4]2ZJZ_A.pdb    GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:5]2ZJZ_B.pdb    GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:6]1GP2_A.pdb    GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:7]1AGR_A.pdb    GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:8]1AGR_D.pdb    GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:9]1CIP_A.pdb    GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:10]1BOF_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:11]1GDD_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:12]1GFI_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:13]1GIA_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:14]4PAN_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:15]4PAQ_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:16]2XNS_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:17]2XNS_B.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:18]1KJY_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:19]1KJY_C.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:20]2OM2_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:21]2OM2_C.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:22]3FFA_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:23]3FFB_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:24]1Y3A_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:25]1Y3A_B.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:26]1Y3A_C.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:27]1Y3A_D.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:28]2IK8_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:29]2IK8_C.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:30]4G5Q_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:31]4G5Q_B.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:32]4G5Q_C.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:33]4G5Q_D.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:34]1SVK_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:35]1SVS_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:36]2GTP_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:37]2GTP_B.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:38]4N0D_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:39]4N0E_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:40]3UMS_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:41]1AS0_A.pdb   VESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:42]1AS2_A.pdb   VESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:43]1AS3_A.pdb   VESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:44]1GIL_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:45]4PAM_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:46]4PAO_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:47]3ONW_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:48]3ONW_B.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:49]3QI2_A.pdb   RESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:50]3QI2_B.pdb   RESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:51]1BH2_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:52]3D7M_A.pdb   GESGKSTIVKQMKICHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:53]3QE0_A.pdb   RESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:54]3QE0_B.pdb   RESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:55]3QE0_C.pdb   RESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:56]3UMR_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:57]2G83_A.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:58]2G83_B.pdb   GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSI
## [Truncated_Name:59]2ODE_A.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:60]2ODE_C.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:61]2V4Z_A.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:62]4G5R_A.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:63]4G5R_B.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:64]4G5R_C.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:65]4G5R_D.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:66]4G5S_A.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:67]4G5S_B.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:68]4G5S_C.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:69]4G5S_D.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:70]2IHB_A.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:71]4G5O_A.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:72]4G5O_B.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:73]4G5O_C.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:74]4G5O_D.pdb   GESGKSTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSI
## [Truncated_Name:75]1FQJ_A.pdb   GESGKSTIVKQMKIIHQDGYSLEECLEFIAIIYGNTLQSI
## [Truncated_Name:76]1FQJ_D.pdb   GESGKSTIVKQMKIIHQDGYSLEECLEFIAIIYGNTLQSI
## [Truncated_Name:77]1FQK_A.pdb   GESGKSTIVKQMKIIHQDGYSLEECLEFIAIIYGNTLQSI
## [Truncated_Name:78]1FQK_C.pdb   GESGKSTIVKQMKIIHQDGYSLEECLEFIAIIYGNTLQSI
## [Truncated_Name:79]3V00_C.pdb   GESGKSTIVKQMKIIHQDPYSLEECLEFIAIIYGNTLQSI
## [Truncated_Name:80]3V00_B.pdb   GESGKSTIVKQMKIIHQDPYSLEECLEFIAIIYGNTLQSI
## [Truncated_Name:81]3V00_A.pdb   GESGKSTIVKQMKIIHQDPYSLEECLEFIAIIYGNTLQSI
## [Truncated_Name:82]1GOT_A.pdb   GESGKSTIVKQMKIIHQDGYSLEECLEFIAIIYGNTLQSI
##                                  ************* *   ** ^**  ^  ^^* **^*** 
##                                41        .         .         .         80 
## 
##                                81        .         .         .         120 
## [Truncated_Name:1]1GG2_A.pdb    IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:2]1GIT_A.pdb    IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:3]2ZJY_A.pdb    IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:4]2ZJZ_A.pdb    IAIIRAMGRLKIDFGDAARADDARQLFVLA-------MTA
## [Truncated_Name:5]2ZJZ_B.pdb    IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:6]1GP2_A.pdb    IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:7]1AGR_A.pdb    IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:8]1AGR_D.pdb    IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:9]1CIP_A.pdb    IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:10]1BOF_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:11]1GDD_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:12]1GFI_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:13]1GIA_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:14]4PAN_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:15]4PAQ_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:16]2XNS_A.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:17]2XNS_B.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:18]1KJY_A.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:19]1KJY_C.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:20]2OM2_A.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:21]2OM2_C.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:22]3FFA_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:23]3FFB_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:24]1Y3A_A.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLA-------MTA
## [Truncated_Name:25]1Y3A_B.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAG----GFMTA
## [Truncated_Name:26]1Y3A_C.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLA-------MTA
## [Truncated_Name:27]1Y3A_D.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLA-------MTA
## [Truncated_Name:28]2IK8_A.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLA-------MTA
## [Truncated_Name:29]2IK8_C.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLA-------MTA
## [Truncated_Name:30]4G5Q_A.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:31]4G5Q_B.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:32]4G5Q_C.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLA------FMTA
## [Truncated_Name:33]4G5Q_D.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:34]1SVK_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:35]1SVS_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:36]2GTP_A.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLA-------MTA
## [Truncated_Name:37]2GTP_B.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:38]4N0D_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:39]4N0E_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:40]3UMS_A.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:41]1AS0_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:42]1AS2_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:43]1AS3_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:44]1GIL_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:45]4PAM_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:46]4PAO_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:47]3ONW_A.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:48]3ONW_B.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:49]3QI2_A.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:50]3QI2_B.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:51]1BH2_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:52]3D7M_A.pdb   IAIIRAMGRLKIDFGDAARADDARQLFVLA---------A
## [Truncated_Name:53]3QE0_A.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGA----FMTA
## [Truncated_Name:54]3QE0_B.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLA--AEEGFMTA
## [Truncated_Name:55]3QE0_C.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAG----GFMTA
## [Truncated_Name:56]3UMR_A.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
## [Truncated_Name:57]2G83_A.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLA----------
## [Truncated_Name:58]2G83_B.pdb   IAIIRAMGRLKIDFGDSARADDARQLFVLA----------
## [Truncated_Name:59]2ODE_A.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMTP
## [Truncated_Name:60]2ODE_C.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMTP
## [Truncated_Name:61]2V4Z_A.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMTP
## [Truncated_Name:62]4G5R_A.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMTP
## [Truncated_Name:63]4G5R_B.pdb   IAIIRAMGRLKIDFG-AARADDARQLFVLAGSA---VMTP
## [Truncated_Name:64]4G5R_C.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMTP
## [Truncated_Name:65]4G5R_D.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMTP
## [Truncated_Name:66]4G5S_A.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEE-VMTP
## [Truncated_Name:67]4G5S_B.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMTP
## [Truncated_Name:68]4G5S_C.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLA-------MTP
## [Truncated_Name:69]4G5S_D.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLAGSAE--VMTP
## [Truncated_Name:70]2IHB_A.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMTP
## [Truncated_Name:71]4G5O_A.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMTP
## [Truncated_Name:72]4G5O_B.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMTP
## [Truncated_Name:73]4G5O_C.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLA-----GVMTP
## [Truncated_Name:74]4G5O_D.pdb   IAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMTP
## [Truncated_Name:75]1FQJ_A.pdb   LAIVRAMTTLNIQYGDSARQDDARKLMHMADTIEEGTMPK
## [Truncated_Name:76]1FQJ_D.pdb   LAIVRAMTTLNIQYGDSARQDDARKLMHMADTIEEGTMPK
## [Truncated_Name:77]1FQK_A.pdb   LAIVRAMTTLNIQYGDSARQDDARKLMHMADTIEEGTMPK
## [Truncated_Name:78]1FQK_C.pdb   LAIVRAMTTLNIQYGDSARQDDARKLMHMADTIEEGTMPK
## [Truncated_Name:79]3V00_C.pdb   LAIVRAMTTLNIQYGDSARQDDARKLMHMADTIEEGTMPK
## [Truncated_Name:80]3V00_B.pdb   LAIVRAMTTLNIQYGDSARQDDARKLMHMADTIEEGTMPK
## [Truncated_Name:81]3V00_A.pdb   LAIVRAMTTLNIQYGDSARQDDARKLMHMADTIEEGTMPK
## [Truncated_Name:82]1GOT_A.pdb   LAIVRAMTTLNIQYGDSARQDDARKLMHMADTIEEGTMPK
##                                 ^**^***  * * ^*  ** **** *  ^*           
##                                81        .         .         .         120 
## 
##                               121        .         .         .         160 
## [Truncated_Name:1]1GG2_A.pdb    ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:2]1GIT_A.pdb    ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:3]2ZJY_A.pdb    ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:4]2ZJZ_A.pdb    ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:5]2ZJZ_B.pdb    ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:6]1GP2_A.pdb    ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:7]1AGR_A.pdb    ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:8]1AGR_D.pdb    ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:9]1CIP_A.pdb    ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:10]1BOF_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:11]1GDD_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:12]1GFI_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:13]1GIA_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:14]4PAN_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:15]4PAQ_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:16]2XNS_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:17]2XNS_B.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:18]1KJY_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:19]1KJY_C.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:20]2OM2_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:21]2OM2_C.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:22]3FFA_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:23]3FFB_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:24]1Y3A_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:25]1Y3A_B.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:26]1Y3A_C.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:27]1Y3A_D.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:28]2IK8_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:29]2IK8_C.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:30]4G5Q_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:31]4G5Q_B.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:32]4G5Q_C.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:33]4G5Q_D.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:34]1SVK_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:35]1SVS_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:36]2GTP_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:37]2GTP_B.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:38]4N0D_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:39]4N0E_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:40]3UMS_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:41]1AS0_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:42]1AS2_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:43]1AS3_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:44]1GIL_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:45]4PAM_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:46]4PAO_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:47]3ONW_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYLLNDSAAYYLNDLDR
## [Truncated_Name:48]3ONW_B.pdb   ELAGVIKRLWKDSGVQACFNRSREYLLNDSAAYYLNDLDR
## [Truncated_Name:49]3QI2_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:50]3QI2_B.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:51]1BH2_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:52]3D7M_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:53]3QE0_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:54]3QE0_B.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:55]3QE0_C.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:56]3UMR_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:57]2G83_A.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:58]2G83_B.pdb   ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
## [Truncated_Name:59]2ODE_A.pdb   ELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDR
## [Truncated_Name:60]2ODE_C.pdb   ELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDR
## [Truncated_Name:61]2V4Z_A.pdb   ELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDR
## [Truncated_Name:62]4G5R_A.pdb   ELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDR
## [Truncated_Name:63]4G5R_B.pdb   ELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDR
## [Truncated_Name:64]4G5R_C.pdb   ELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDR
## [Truncated_Name:65]4G5R_D.pdb   ELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDR
## [Truncated_Name:66]4G5S_A.pdb   ELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDR
## [Truncated_Name:67]4G5S_B.pdb   ELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDR
## [Truncated_Name:68]4G5S_C.pdb   ELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDR
## [Truncated_Name:69]4G5S_D.pdb   ELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDR
## [Truncated_Name:70]2IHB_A.pdb   ELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDR
## [Truncated_Name:71]4G5O_A.pdb   ELAGVIKRLWRDGGVQACFSRSREYLLNDSASYYLNDLDR
## [Truncated_Name:72]4G5O_B.pdb   ELAGVIKRLWRDGGVQACFSRSREYLLNDSASYYLNDLDR
## [Truncated_Name:73]4G5O_C.pdb   ELAGVIKRLWRDGGVQACFSRSREYLLNDSASYYLNDLDR
## [Truncated_Name:74]4G5O_D.pdb   ELAGVIKRLWRDGGVQACFSRSREYLLNDSASYYLNDLDR
## [Truncated_Name:75]1FQJ_A.pdb   EMSDIIQRLWKDSGIQACFDRASEYQLNDSAGYYLSDLER
## [Truncated_Name:76]1FQJ_D.pdb   EMSDIIQRLWKDSGIQACFDRASEYQLNDSAGYYLSDLER
## [Truncated_Name:77]1FQK_A.pdb   EMSDIIQRLWKDSGIQACFDRASEYQLNDSAGYYLSDLER
## [Truncated_Name:78]1FQK_C.pdb   EMSDIIQRLWKDSGIQACFDRASEYQLNDSAGYYLSDLER
## [Truncated_Name:79]3V00_C.pdb   EMSDIIQRLWKDSGIQACFDRASEYQLNDSAGYYLSDLER
## [Truncated_Name:80]3V00_B.pdb   EMSDIIQRLWKDSGIQACFDRASEYQLNDSAGYYLSDLER
## [Truncated_Name:81]3V00_A.pdb   EMSDIIQRLWKDSGIQACFDRASEYQLNDSAGYYLSDLER
## [Truncated_Name:82]1GOT_A.pdb   EMSDIIQRLWKDSGIQACFDRASEYQLNDSAGYYLSDLER
##                                 *^  ^* ***^* *^**** *  ** ***** *** **^* 
##                               121        .         .         .         160 
## 
##                               161        .         .         .         200 
## [Truncated_Name:1]1GG2_A.pdb    IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:2]1GIT_A.pdb    IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:3]2ZJY_A.pdb    IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:4]2ZJZ_A.pdb    IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:5]2ZJZ_B.pdb    IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:6]1GP2_A.pdb    IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:7]1AGR_A.pdb    IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:8]1AGR_D.pdb    IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:9]1CIP_A.pdb    IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:10]1BOF_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:11]1GDD_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:12]1GFI_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:13]1GIA_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:14]4PAN_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:15]4PAQ_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:16]2XNS_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:17]2XNS_B.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:18]1KJY_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:19]1KJY_C.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:20]2OM2_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:21]2OM2_C.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:22]3FFA_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:23]3FFB_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFD-
## [Truncated_Name:24]1Y3A_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:25]1Y3A_B.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:26]1Y3A_C.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:27]1Y3A_D.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:28]2IK8_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:29]2IK8_C.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:30]4G5Q_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:31]4G5Q_B.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:32]4G5Q_C.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:33]4G5Q_D.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:34]1SVK_A.pdb   IAQPNYIPTQQDVLRTRVPTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:35]1SVS_A.pdb   IAQPNYIPTQQDVLRTRVPTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:36]2GTP_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:37]2GTP_B.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:38]4N0D_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:39]4N0E_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:40]3UMS_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:41]1AS0_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:42]1AS2_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:43]1AS3_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:44]1GIL_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:45]4PAM_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:46]4PAO_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:47]3ONW_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:48]3ONW_B.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:49]3QI2_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:50]3QI2_B.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:51]1BH2_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:52]3D7M_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:53]3QE0_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:54]3QE0_B.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:55]3QE0_C.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:56]3UMR_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:57]2G83_A.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:58]2G83_B.pdb   IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDV
## [Truncated_Name:59]2ODE_A.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:60]2ODE_C.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:61]2V4Z_A.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:62]4G5R_A.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:63]4G5R_B.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:64]4G5R_C.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:65]4G5R_D.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:66]4G5S_A.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:67]4G5S_B.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:68]4G5S_C.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:69]4G5S_D.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:70]2IHB_A.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:71]4G5O_A.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:72]4G5O_B.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:73]4G5O_C.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:74]4G5O_D.pdb   ISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDV
## [Truncated_Name:75]1FQJ_A.pdb   LVTPGYVPTEQDVLRSRVKTTGIIETQFSFKDLNFRMFDV
## [Truncated_Name:76]1FQJ_D.pdb   LVTPGYVPTEQDVLRSRVKTTGIIETQFSFKDLNFRMFDV
## [Truncated_Name:77]1FQK_A.pdb   LVTPGYVPTEQDVLRSRVKTTGIIETQFSFKDLNFRMFDV
## [Truncated_Name:78]1FQK_C.pdb   LVTPGYVPTEQDVLRSRVKTTGIIETQFSFKDLNFRMFDV
## [Truncated_Name:79]3V00_C.pdb   LVTPGYVPTEQDVLRSRVKTTGIIETQFSFKDLNFRMFDV
## [Truncated_Name:80]3V00_B.pdb   LVTPGYVPTEQDVLRSRVKTTGIIETQFSFKDLNFRMFDV
## [Truncated_Name:81]3V00_A.pdb   LVTPGYVPTEQDVLRSRVKTTGIIETQFSFKDLNFRMFDV
## [Truncated_Name:82]1GOT_A.pdb   LVTPGYVPTEQDVLRSRVKTTGIIETQFSFKDLNFRMFDV
##                                 ^    *^** *****^** ****^** *^**** *^***  
##                               161        .         .         .         200 
## 
##                               201        .         .         .         240 
## [Truncated_Name:1]1GG2_A.pdb    GAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:2]1GIT_A.pdb    GAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:3]2ZJY_A.pdb    GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:4]2ZJZ_A.pdb    G----ERKKWIHCFEGVTAIIFCVALSDYDL--AEDEEMN
## [Truncated_Name:5]2ZJZ_B.pdb    GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVL-----MN
## [Truncated_Name:6]1GP2_A.pdb    GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:7]1AGR_A.pdb    GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:8]1AGR_D.pdb    GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:9]1CIP_A.pdb    GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:10]1BOF_A.pdb   G--------------GVTAIIFCVALSDYDL-------MN
## [Truncated_Name:11]1GDD_A.pdb   ----------------VTAIIFCVALSDYDLV------MN
## [Truncated_Name:12]1GFI_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:13]1GIA_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:14]4PAN_A.pdb   ---------------GVTAIIFCVALSDYDL--------N
## [Truncated_Name:15]4PAQ_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:16]2XNS_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:17]2XNS_B.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:18]1KJY_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:19]1KJY_C.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:20]2OM2_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:21]2OM2_C.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:22]3FFA_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:23]3FFB_A.pdb   --------------GGVTAIIFCVALSDYDL-------MN
## [Truncated_Name:24]1Y3A_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLV------MN
## [Truncated_Name:25]1Y3A_B.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:26]1Y3A_C.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLV------MN
## [Truncated_Name:27]1Y3A_D.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:28]2IK8_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:29]2IK8_C.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:30]4G5Q_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:31]4G5Q_B.pdb   GG--SERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:32]4G5Q_C.pdb   G-QRSERKKWIHCFEGVTAIIFCVALSDYDLVLA-DEEMN
## [Truncated_Name:33]4G5Q_D.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:34]1SVK_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:35]1SVS_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:36]2GTP_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:37]2GTP_B.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:38]4N0D_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:39]4N0E_A.pdb   ------------CFEGVTAIIFCVALSDYDLVLA----MN
## [Truncated_Name:40]3UMS_A.pdb   ------------AFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:41]1AS0_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:42]1AS2_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:43]1AS3_A.pdb   GGQ----------FEGVTAIIFCVALSDYDLV------MN
## [Truncated_Name:44]1GIL_A.pdb   GGLRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:45]4PAM_A.pdb   G---------IHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:46]4PAO_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:47]3ONW_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:48]3ONW_B.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:49]3QI2_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:50]3QI2_B.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:51]1BH2_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:52]3D7M_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:53]3QE0_A.pdb   G---SERKKWIHCFEGVTAIIFCVALSDYDLVLA--EEMN
## [Truncated_Name:54]3QE0_B.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:55]3QE0_C.pdb   GGQRS-----IHCFEGVTAIIFCVALSDYDLV------MN
## [Truncated_Name:56]3UMR_A.pdb   D------------FEGVTAIIFCVALSDYDLV----EEMN
## [Truncated_Name:57]2G83_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:58]2G83_B.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:59]2ODE_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:60]2ODE_C.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:61]2V4Z_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:62]4G5R_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:63]4G5R_B.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:64]4G5R_C.pdb   --QRSERKKWIHCFEGVTAIIFCVALSDYDLVL--DEEMN
## [Truncated_Name:65]4G5R_D.pdb   -----ERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:66]4G5S_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:67]4G5S_B.pdb   GG--SERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:68]4G5S_C.pdb   G-----RKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:69]4G5S_D.pdb   G-----RKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:70]2IHB_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:71]4G5O_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:72]4G5O_B.pdb   GG--SERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:73]4G5O_C.pdb   G--RSERKKWIHCFEGVTAIIFCVALSDYDLVLA-DEEMN
## [Truncated_Name:74]4G5O_D.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:75]1FQJ_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:76]1FQJ_D.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:77]1FQK_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:78]1FQK_C.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:79]3V00_C.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:80]3V00_B.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:81]3V00_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
## [Truncated_Name:82]1GOT_A.pdb   GGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
##                                                 ***************        * 
##                               201        .         .         .         240 
## 
##                               241        .         .         .         280 
## [Truncated_Name:1]1GG2_A.pdb    RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:2]1GIT_A.pdb    RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:3]2ZJY_A.pdb    RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:4]2ZJZ_A.pdb    RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:5]2ZJZ_B.pdb    RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:6]1GP2_A.pdb    RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:7]1AGR_A.pdb    RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:8]1AGR_D.pdb    RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:9]1CIP_A.pdb    RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:10]1BOF_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:11]1GDD_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:12]1GFI_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:13]1GIA_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:14]4PAN_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:15]4PAQ_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:16]2XNS_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:17]2XNS_B.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:18]1KJY_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:19]1KJY_C.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:20]2OM2_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:21]2OM2_C.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:22]3FFA_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:23]3FFB_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:24]1Y3A_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:25]1Y3A_B.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:26]1Y3A_C.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:27]1Y3A_D.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:28]2IK8_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:29]2IK8_C.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:30]4G5Q_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:31]4G5Q_B.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:32]4G5Q_C.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:33]4G5Q_D.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:34]1SVK_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:35]1SVS_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:36]2GTP_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:37]2GTP_B.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:38]4N0D_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:39]4N0E_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:40]3UMS_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:41]1AS0_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:42]1AS2_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:43]1AS3_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:44]1GIL_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:45]4PAM_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:46]4PAO_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:47]3ONW_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:48]3ONW_B.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:49]3QI2_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:50]3QI2_B.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:51]1BH2_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:52]3D7M_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:53]3QE0_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:54]3QE0_B.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:55]3QE0_C.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:56]3UMR_A.pdb   RMHESMKLFDSICNNKCFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:57]2G83_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:58]2G83_B.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:59]2ODE_A.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:60]2ODE_C.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:61]2V4Z_A.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:62]4G5R_A.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:63]4G5R_B.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:64]4G5R_C.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:65]4G5R_D.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:66]4G5S_A.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:67]4G5S_B.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:68]4G5S_C.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:69]4G5S_D.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:70]2IHB_A.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:71]4G5O_A.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:72]4G5O_B.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:73]4G5O_C.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:74]4G5O_D.pdb   RMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRS
## [Truncated_Name:75]1FQJ_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:76]1FQJ_D.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:77]1FQK_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:78]1FQK_C.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:79]3V00_C.pdb   RMHESMHLFNSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:80]3V00_B.pdb   RMHESMHLFNSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:81]3V00_A.pdb   RMHESMHLFNSICNNKWFTDTSIILFLNKKDLFEEKIKKS
## [Truncated_Name:82]1GOT_A.pdb   RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
##                                 ******^** ****** **^******************^* 
##                               241        .         .         .         280 
## 
##                               281        .         .         .         320 
## [Truncated_Name:1]1GG2_A.pdb    PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:2]1GIT_A.pdb    PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:3]2ZJY_A.pdb    PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:4]2ZJZ_A.pdb    PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:5]2ZJZ_B.pdb    PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:6]1GP2_A.pdb    PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:7]1AGR_A.pdb    PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:8]1AGR_D.pdb    PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:9]1CIP_A.pdb    PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:10]1BOF_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:11]1GDD_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:12]1GFI_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:13]1GIA_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:14]4PAN_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:15]4PAQ_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:16]2XNS_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:17]2XNS_B.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:18]1KJY_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:19]1KJY_C.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:20]2OM2_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:21]2OM2_C.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:22]3FFA_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:23]3FFB_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:24]1Y3A_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:25]1Y3A_B.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:26]1Y3A_C.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:27]1Y3A_D.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:28]2IK8_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:29]2IK8_C.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:30]4G5Q_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:31]4G5Q_B.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:32]4G5Q_C.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:33]4G5Q_D.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:34]1SVK_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:35]1SVS_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:36]2GTP_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:37]2GTP_B.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:38]4N0D_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:39]4N0E_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:40]3UMS_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:41]1AS0_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:42]1AS2_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:43]1AS3_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:44]1GIL_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:45]4PAM_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:46]4PAO_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:47]3ONW_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:48]3ONW_B.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:49]3QI2_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:50]3QI2_B.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDT-EIYT
## [Truncated_Name:51]1BH2_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:52]3D7M_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:53]3QE0_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:54]3QE0_B.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:55]3QE0_C.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:56]3UMR_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:57]2G83_A.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:58]2G83_B.pdb   PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYT
## [Truncated_Name:59]2ODE_A.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:60]2ODE_C.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:61]2V4Z_A.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:62]4G5R_A.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:63]4G5R_B.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:64]4G5R_C.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:65]4G5R_D.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:66]4G5S_A.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:67]4G5S_B.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:68]4G5S_C.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:69]4G5S_D.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:70]2IHB_A.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:71]4G5O_A.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:72]4G5O_B.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:73]4G5O_C.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:74]4G5O_D.pdb   PLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYT
## [Truncated_Name:75]1FQJ_A.pdb   PLTICYPEYAGSNTYEEAGNYIKVQFLELNMRRDVKEIYS
## [Truncated_Name:76]1FQJ_D.pdb   PLTICYPEYAGSNTYEEAGNYIKVQFLELNMRRDVKEIYS
## [Truncated_Name:77]1FQK_A.pdb   PLTICYPEYAGSNTYEEAGNYIKVQFLELNMRRDVKEIYS
## [Truncated_Name:78]1FQK_C.pdb   PLTICYPEYAGSNTYEEAGNYIKVQFLELNMRRDVKEIYS
## [Truncated_Name:79]3V00_C.pdb   PLTICYPEYAGSNTYEEAGNYIKVQFLELNMRRDVKEIYS
## [Truncated_Name:80]3V00_B.pdb   PLTICYPEYAGSNTYEEAGNYIKVQFLELNMRRDVKEIYS
## [Truncated_Name:81]3V00_A.pdb   PLTICYPEYAGSNTYEEAGNYIKVQFLELNMRRDVKEIYS
## [Truncated_Name:82]1GOT_A.pdb   PLTICYPEYAGSNTYEEAGNYIKVQFLELNMRRDVKEIYS
##                                 ********* ********^ **  ** ^** *^*  ***^ 
##                               281        .         .         .         320 
## 
##                               321        .         .         .  353 
## [Truncated_Name:1]1GG2_A.pdb    HFTCATDTKNVQFVFDAVTDVIIKNNL------
## [Truncated_Name:2]1GIT_A.pdb    HFTCATDTKNVQFVFDAVTDVIIKNNL------
## [Truncated_Name:3]2ZJY_A.pdb    HFTCATDTKNVQFVFDAVTDVIIKNNL------
## [Truncated_Name:4]2ZJZ_A.pdb    HFTCATDTKNVQFVFDAVTDVIIKNNLPDCGLF
## [Truncated_Name:5]2ZJZ_B.pdb    HFTCATDTKNVQFVFDAVTDVIIKNN-------
## [Truncated_Name:6]1GP2_A.pdb    HFTCATDTKNVQFVFDAVTDVIIKNNL------
## [Truncated_Name:7]1AGR_A.pdb    HFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
## [Truncated_Name:8]1AGR_D.pdb    HFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
## [Truncated_Name:9]1CIP_A.pdb    HFTCATDTKNVQFVFDAVTDVIIKNN-------
## [Truncated_Name:10]1BOF_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
## [Truncated_Name:11]1GDD_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
## [Truncated_Name:12]1GFI_A.pdb   HFTCATDTKNVQFVFDAVTDVIIK---------
## [Truncated_Name:13]1GIA_A.pdb   HFTCATDTKNVQFVFDAVTDVI-----------
## [Truncated_Name:14]4PAN_A.pdb   HFTCATDTKNVQFVYDAVTDVIIKNNLKDCGLF
## [Truncated_Name:15]4PAQ_A.pdb   HFTCATDTKNVQFVYDAVTDVIIKNNL------
## [Truncated_Name:16]2XNS_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNN-------
## [Truncated_Name:17]2XNS_B.pdb   HFTCATDTKNVQFVFDAVTDVIIKNN-------
## [Truncated_Name:18]1KJY_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLK-----
## [Truncated_Name:19]1KJY_C.pdb   HFTCATDTKNVQFVFDAVTDVIIKNN-------
## [Truncated_Name:20]2OM2_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLK-----
## [Truncated_Name:21]2OM2_C.pdb   HFTCATDTKNVQFVFDAVTDVIIKNN-------
## [Truncated_Name:22]3FFA_A.pdb   HFTCATDAKNVQFVFDAVTDVIIKNNL------
## [Truncated_Name:23]3FFB_A.pdb   HFTCATDAKNVQFVFDAVTDVIIKNNLKDCGLF
## [Truncated_Name:24]1Y3A_A.pdb   HFTCATDTKNVQFVFDAVTDVIIK---------
## [Truncated_Name:25]1Y3A_B.pdb   HFTCATDTKNVQFVFDAVTDVII----------
## [Truncated_Name:26]1Y3A_C.pdb   HFTCATDTKNVQFVFDAVTDVII----------
## [Truncated_Name:27]1Y3A_D.pdb   HFTCATDTKNVQFVFDAVTDVII----------
## [Truncated_Name:28]2IK8_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNL------
## [Truncated_Name:29]2IK8_C.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNL------
## [Truncated_Name:30]4G5Q_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKD----
## [Truncated_Name:31]4G5Q_B.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLK-----
## [Truncated_Name:32]4G5Q_C.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
## [Truncated_Name:33]4G5Q_D.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
## [Truncated_Name:34]1SVK_A.pdb   HFTCATDTKNVQFVFDAVTDVIIK---------
## [Truncated_Name:35]1SVS_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNN-------
## [Truncated_Name:36]2GTP_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNL------
## [Truncated_Name:37]2GTP_B.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNL------
## [Truncated_Name:38]4N0D_A.pdb   HFTCATDTKNVQFVFDAVTDVIILNNLKDC---
## [Truncated_Name:39]4N0E_A.pdb   HFTCATDTKNVQFVFDAVTDVIILNNLKDCGLF
## [Truncated_Name:40]3UMS_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
## [Truncated_Name:41]1AS0_A.pdb   HFTCATDTKNVQFVFDAVTDVII----------
## [Truncated_Name:42]1AS2_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKN--------
## [Truncated_Name:43]1AS3_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
## [Truncated_Name:44]1GIL_A.pdb   HFTCATDTKNVQFVFDAVTDVI-----------
## [Truncated_Name:45]4PAM_A.pdb   HFTCATDTKNVQFVCDAVTDVIIKNNLKDCGLF
## [Truncated_Name:46]4PAO_A.pdb   HFTCATDTKNVQFVCDAVTDVIIKNNL------
## [Truncated_Name:47]3ONW_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNN-------
## [Truncated_Name:48]3ONW_B.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNL------
## [Truncated_Name:49]3QI2_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNN-------
## [Truncated_Name:50]3QI2_B.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNL------
## [Truncated_Name:51]1BH2_A.pdb   HFTCSTDTKNVQFVFDAVTDVIIKN--------
## [Truncated_Name:52]3D7M_A.pdb   HFTCATDTKNVCFVFDAVTDVIIKNN-------
## [Truncated_Name:53]3QE0_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
## [Truncated_Name:54]3QE0_B.pdb   HFTCATDTKNVQFVFDAVTDVIIKNN-------
## [Truncated_Name:55]3QE0_C.pdb   HFTCATDTKNVQFVFDAVTDVIIKNN-------
## [Truncated_Name:56]3UMR_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
## [Truncated_Name:57]2G83_A.pdb   HFTCATDTKNVQFVFDAVTDVIIK---------
## [Truncated_Name:58]2G83_B.pdb   HFTCATDTKNVQFVFDAVTDVIIK---------
## [Truncated_Name:59]2ODE_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNL------
## [Truncated_Name:60]2ODE_C.pdb   HFTCATDTKNVQFVFDAVTDVIIKNN-------
## [Truncated_Name:61]2V4Z_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNN-------
## [Truncated_Name:62]4G5R_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKE----
## [Truncated_Name:63]4G5R_B.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNL------
## [Truncated_Name:64]4G5R_C.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKECGL-
## [Truncated_Name:65]4G5R_D.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKECGL-
## [Truncated_Name:66]4G5S_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLK-----
## [Truncated_Name:67]4G5S_B.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLK-----
## [Truncated_Name:68]4G5S_C.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKECGL-
## [Truncated_Name:69]4G5S_D.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKECGL-
## [Truncated_Name:70]2IHB_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLK-----
## [Truncated_Name:71]4G5O_A.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKE----
## [Truncated_Name:72]4G5O_B.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNL------
## [Truncated_Name:73]4G5O_C.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKECGLY
## [Truncated_Name:74]4G5O_D.pdb   HFTCATDTKNVQFVFDAVTDVIIKNNLKECGLY
## [Truncated_Name:75]1FQJ_A.pdb   HMTCATDTQNVKFVFDAVTDIIIKENL------
## [Truncated_Name:76]1FQJ_D.pdb   HMTCATDTQNVKFVFDAVTDIIIKE--------
## [Truncated_Name:77]1FQK_A.pdb   HMTCATDTQNVKFVFDAVTDIIIKENLK-----
## [Truncated_Name:78]1FQK_C.pdb   HMTCATDTQNVKFVFDAVTDIIIKENLK-----
## [Truncated_Name:79]3V00_C.pdb   HMTCATDTQNVKFVFDAVTDIIIKENLKDCGLF
## [Truncated_Name:80]3V00_B.pdb   HMTCATDTQNVKFVFDAVTDIIIKENLKDCGLF
## [Truncated_Name:81]3V00_A.pdb   HMTCATDTQNVKFVFDAVTDIIIKENLKDCGLF
## [Truncated_Name:82]1GOT_A.pdb   HMTCATDTQNVKFVFDAVTDIIIKEN-------
##                                 * ** **  ** ** *****^*            
##                               321        .         .         .  353 
## 
## Call:
##   pdbaln(files = raw.files)
## 
## Class:
##   pdbs, fasta
## 
## Alignment dimensions:
##   82 sequence rows; 353 position columns (273 non-gap, 80 gap) 
## 
## + attr: xyz, resno, b, chain, id, ali, resid, sse, call
# Save alignment FASTA file
write.fasta(aln, file="../results/pdb_alignment.fa")

# Produce a nice colored HTML file for this alignment
aln2html(aln, append=FALSE, file="../results/pdb_alignment.html")
aln2html(aln, colorscheme="ent", file="../results/pdb_alignment.html")


# Sequence identity analysis
ide <- seqidentity(aln)
hc <- hclust(as.dist(1-ide), method="ward.D")

#plot(hc)

# Save plot
#pdf("../results/sequence_clustering.pdf")
hclustplot(hc, k=3, labels=basename.pdb(aln$id), cex=0.8,
             ylab="1-Identity", main="Sequence Identity Clustering", fillbox=FALSE)

#dev.off()

Structure analysis

# Fit structures
xyz <- pdbfit(aln)

# RMSD (structural distance)
rd <- rmsd(xyz)
## Warning in rmsd(xyz): No indices provided, using the 273 non NA positions
# Clustering
hc.rmsd <- hclust(as.dist(rd), method="ward.D")
#plot(hc.rmsd)



hclustplot(hc.rmsd, k=3, labels=basename.pdb(aln$id), cex=0.8,
             ylab="RMSD (Ã…)", main="RMSD Cluster Dendrogram", fillbox=FALSE)

# Save both plots to PDF file
pdf("../results/clustering.pdf")
hclustplot(hc, k=3, labels=basename.pdb(aln$id), cex=0.6,
             ylab="1-Identity", main="Sequence Identity Cluster Dendrogram", fillbox=FALSE)

hclustplot(hc.rmsd, k=3, labels=basename.pdb(aln$id), cex=0.6,
             ylab="RMSD (Ã…)", main="RMSD Cluster Dendrogram", fillbox=FALSE)
dev.off()
## quartz_off_screen 
##                 2
# Shorten labels for tanglegram plot
hc$labels=basename.pdb(aln$id)
hc.rmsd$labels=hc$labels
tanglegram(hc, hc.rmsd, lab.cex=0.7)

# Save plot
pdf("../results/cluster_compare.pdf")
tanglegram(hc, hc.rmsd)
dev.off()
## quartz_off_screen 
##                 2
# Save all data
save.image(file="../data/01_store.RData")


# Report on software versions
sessionInfo()
## R version 3.1.2 (2014-10-31)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] dendextend_1.1.0  bio3d_2.2-2.9000  rmarkdown_0.5.3.1
## 
## loaded via a namespace (and not attached):
##  [1] bitops_1.0-6     colorspace_1.2-6 digest_0.6.8     evaluate_0.7    
##  [5] grid_3.1.2       htmltools_0.2.6  knitr_1.10.5     magrittr_1.5    
##  [9] parallel_3.1.2   Rcpp_0.11.6      RCurl_1.95-4.6   stringi_0.4-1   
## [13] stringr_1.0.0    tools_3.1.2      whisker_0.3-2    XML_3.98-1.2