01_look_see_download.r
2015-08-22
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.
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
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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$id), cex=0.8,
ylab="1-Identity", main="Sequence Identity Clustering", fillbox=FALSE)
#dev.off()
# Fit structures
xyz <- pdbfit(aln)
# RMSD (structural distance)
rd <- rmsd(xyz)
## Warning in rmsd(xyz): No indices provided, using the 273 non NA positions
# Clustering
hc.rmsd <- hclust(as.dist(rd), method="ward.D")
#plot(hc.rmsd)
hclustplot(hc.rmsd, k=3, labels=basename.pdb(aln$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