BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 013759
(437 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1DT9|A Chain A, The Crystal Structure Of Human Eukaryotic Release Factor
Erf1-Mechanism Of Stop Codon Recognition And
Peptidyl-Trna Hydrolysis
Length = 437
Score = 624 bits (1609), Expect = e-179, Method: Compositional matrix adjust.
Identities = 306/432 (70%), Positives = 348/432 (80%), Gaps = 2/432 (0%)
Query: 3 DGQETDKNXXXXXXXXXXXXXXXXRGNGTSMISLIMPPRDQVSRVTKMLGDEFGTASNIK 62
D D+N RGNGTSMISLI+PP+DQ+SRV KML DEFGTASNIK
Sbjct: 4 DPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIK 63
Query: 63 SRVNRQSVLGAITSAQQRLKLYNKVPPNGLVLYTGTIVTDDGKEKKVTIDFEPFRPINAS 122
SRVNR SVLGAITS QQRLKLYNKVPPNGLV+Y GTIVT++GKEKKV IDFEPF+PIN S
Sbjct: 64 SRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTS 123
Query: 123 LYLCDNKFHTDALNELLESDDKFGFIVMDGNGTLFGTLSGNTREVLHKFSVDLPKKHGRG 182
LYLCDNKFHT+AL LL D KFGFIV+DG+G LFGTL GNTREVLHKF+VDLPKKHGRG
Sbjct: 124 LYLCDNKFHTEALTALLSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRG 183
Query: 183 GQSALRFARLRMEKRHNYVRKTAELATQFYINPATSQPNVSGLVLAGSADFKTELSQSDM 242
GQSALRFARLRMEKRHNYVRK AE A Q +I + + NV+GLVLAGSADFKTELSQSDM
Sbjct: 184 GQSALRFARLRMEKRHNYVRKVAETAVQLFI--SGDKVNVAGLVLAGSADFKTELSQSDM 241
Query: 243 FDPRLQAKILKVVDVSYGGENGFNQAIELSAESLSNVKFIQEKRLIGKYFEEISQDTGKY 302
FD RLQ+K+LK+VD+SYGGENGFNQAIELS E LSNVKFIQEK+LIG+YF+EISQDTGKY
Sbjct: 242 FDQRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNVKFIQEKKLIGRYFDEISQDTGKY 301
Query: 303 VFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSA 362
FG +DTLKAL+MGAV+ LIV+ENLDI RYVL T E I +L EQE ++++F D
Sbjct: 302 CFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKE 361
Query: 363 TSAELEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQLDMRS 422
T E E+ E LLEWFAN Y++FG TLE VT+KSQEGSQF +GFGGIGGILRY++D +
Sbjct: 362 TGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQG 421
Query: 423 FDEFSDDGEIYD 434
+ D E +D
Sbjct: 422 MEYQGGDDEFFD 433
>pdb|3E1Y|A Chain A, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|B Chain B, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|C Chain C, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|D Chain D, Crystal Structure Of Human Erf1ERF3 COMPLEX
Length = 451
Score = 624 bits (1609), Expect = e-179, Method: Compositional matrix adjust.
Identities = 306/432 (70%), Positives = 348/432 (80%), Gaps = 2/432 (0%)
Query: 3 DGQETDKNXXXXXXXXXXXXXXXXRGNGTSMISLIMPPRDQVSRVTKMLGDEFGTASNIK 62
D D+N RGNGTSMISLI+PP+DQ+SRV KML DEFGTASNIK
Sbjct: 18 DPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIK 77
Query: 63 SRVNRQSVLGAITSAQQRLKLYNKVPPNGLVLYTGTIVTDDGKEKKVTIDFEPFRPINAS 122
SRVNR SVLGAITS QQRLKLYNKVPPNGLV+Y GTIVT++GKEKKV IDFEPF+PIN S
Sbjct: 78 SRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTS 137
Query: 123 LYLCDNKFHTDALNELLESDDKFGFIVMDGNGTLFGTLSGNTREVLHKFSVDLPKKHGRG 182
LYLCDNKFHT+AL LL D KFGFIV+DG+G LFGTL GNTREVLHKF+VDLPKKHGRG
Sbjct: 138 LYLCDNKFHTEALTALLSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRG 197
Query: 183 GQSALRFARLRMEKRHNYVRKTAELATQFYINPATSQPNVSGLVLAGSADFKTELSQSDM 242
GQSALRFARLRMEKRHNYVRK AE A Q +I + + NV+GLVLAGSADFKTELSQSDM
Sbjct: 198 GQSALRFARLRMEKRHNYVRKVAETAVQLFI--SGDKVNVAGLVLAGSADFKTELSQSDM 255
Query: 243 FDPRLQAKILKVVDVSYGGENGFNQAIELSAESLSNVKFIQEKRLIGKYFEEISQDTGKY 302
FD RLQ+K+LK+VD+SYGGENGFNQAIELS E LSNVKFIQEK+LIG+YF+EISQDTGKY
Sbjct: 256 FDQRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNVKFIQEKKLIGRYFDEISQDTGKY 315
Query: 303 VFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSA 362
FG +DTLKAL+MGAV+ LIV+ENLDI RYVL T E I +L EQE ++++F D
Sbjct: 316 CFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKE 375
Query: 363 TSAELEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQLDMRS 422
T E E+ E LLEWFAN Y++FG TLE VT+KSQEGSQF +GFGGIGGILRY++D +
Sbjct: 376 TGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQG 435
Query: 423 FDEFSDDGEIYD 434
+ D E +D
Sbjct: 436 MEYQGGDDEFFD 447
>pdb|3J2K|6 Chain 6, Cryo-Em Structure Of The Mammalian Erf1-Erf3-Associated
Termination Complex
Length = 411
Score = 621 bits (1601), Expect = e-178, Method: Compositional matrix adjust.
Identities = 300/395 (75%), Positives = 339/395 (85%), Gaps = 2/395 (0%)
Query: 27 RGNGTSMISLIMPPRDQVSRVTKMLGDEFGTASNIKSRVNRQSVLGAITSAQQRLKLYNK 86
RGNGTSMISLI+PP+DQ+SRV KML DEFGTASNIKSRVNR SVLGAITS QQRLKLYNK
Sbjct: 19 RGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRLSVLGAITSVQQRLKLYNK 78
Query: 87 VPPNGLVLYTGTIVTDDGKEKKVTIDFEPFRPINASLYLCDNKFHTDALNELLESDDKFG 146
VPPNGLV+Y GTIVT++GKEKKV IDFEPF+PIN SLYLCDNKFHT+AL LL D KFG
Sbjct: 79 VPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTALLSDDSKFG 138
Query: 147 FIVMDGNGTLFGTLSGNTREVLHKFSVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAE 206
FIV+DG+G LFGTL GNTREVLHKF+VDLPKKHGRGGQSALRFARLRMEKRHNYVRK AE
Sbjct: 139 FIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAE 198
Query: 207 LATQFYINPATSQPNVSGLVLAGSADFKTELSQSDMFDPRLQAKILKVVDVSYGGENGFN 266
A Q +I + + NV+GLVLAGSADFKTELSQSDMFD RLQ+K+LK+VD+SYGGENGFN
Sbjct: 199 TAVQLFI--SGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDISYGGENGFN 256
Query: 267 QAIELSAESLSNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLKALDMGAVDTLIVWEN 326
QAIELS E LSNVKFIQEK+LIG+YF+EISQDTGKY FG +DTLKAL+MGAV+ LIV+EN
Sbjct: 257 QAIELSTEVLSNVKFIQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYEN 316
Query: 327 LDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFANEYRRF 386
LDI RYVL T E I +L EQE ++++F D T E E+ E LLEWFAN Y++F
Sbjct: 317 LDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKETGQEHELIESMPLLEWFANNYKKF 376
Query: 387 GCTLEFVTNKSQEGSQFCRGFGGIGGILRYQLDMR 421
G TLE VT+KSQEGSQF +GFGGIGGILRY++D +
Sbjct: 377 GATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQ 411
>pdb|3E20|C Chain C, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|B Chain B, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|H Chain H, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|K Chain K, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
Length = 441
Score = 525 bits (1352), Expect = e-149, Method: Compositional matrix adjust.
Identities = 257/414 (62%), Positives = 324/414 (78%), Gaps = 8/414 (1%)
Query: 27 RGNGTSMISLIMPPRDQVSRVTKMLGDEFGTASNIKSRVNRQSVLGAITSAQQRLKLYNK 86
GNGTSMI+LI+PP +Q+SR + ML +E+GTASNIKSRVNR SVL AITS ++RLKLYNK
Sbjct: 33 HGNGTSMITLIIPPGEQISRYSNMLAEEYGTASNIKSRVNRLSVLSAITSTRERLKLYNK 92
Query: 87 VPPNGLVLYTGTIVTDDGKEKKVTIDFEPFRPINASLYLCDNKFHTDALNELLESDDKFG 146
VP NGLV+Y G ++ + K +K+ IDFEPF+PIN S YLCDNKFHT+AL ELLESD +FG
Sbjct: 93 VPDNGLVIYCGEVIMEGNKTRKLNIDFEPFKPINTSQYLCDNKFHTEALAELLESDQRFG 152
Query: 147 FIVMDGNGTLFGTLSGNTREVLHKFSVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAE 206
FIVMDG+ TL+G +SG+ REVL +F+VDLPKKHGRGGQSALRFARLR EKRHNYVRK AE
Sbjct: 153 FIVMDGHQTLYGVVSGSAREVLQRFTVDLPKKHGRGGQSALRFARLRDEKRHNYVRKVAE 212
Query: 207 LATQFYINPATSQPNVSGLVLAGSADFKTELSQSDMFDPRLQAKILKVVDVSYGGENGFN 266
A Q +I +PNV+G+VLAGSADFKTEL QSD+FD RLQ++I+K VDVSYGG+ GFN
Sbjct: 213 GAVQHFI--TDDKPNVAGIVLAGSADFKTELGQSDLFDQRLQSRIIKTVDVSYGGDAGFN 270
Query: 267 QAIELSAESLSNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLKALDMGAVDTLIVWEN 326
QAIEL+A++LSNVK++QEK+LI ++F+EIS D+GKY FG DT+ AL GAV+TL+ + +
Sbjct: 271 QAIELAADTLSNVKYVQEKKLIQRFFDEISLDSGKYCFGVVDTMNALQEGAVETLLCFAD 330
Query: 327 LDITRYVLKNTVTGEIVIKHLNREQET--NQNNF-RDSATSAELEVQEKSSLLEWFANEY 383
LD+ RY KN+ G VI ++ +EQE + N+F D T AE+E+ L EW A Y
Sbjct: 331 LDMIRYEFKNS-EGNPVITYMTKEQEEKDSTNSFLLDKDTGAEMELVSSMLLSEWLAEHY 389
Query: 384 RRFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQLDMRSFDEFSDDGEIYDDSE 437
+ +G LEFV+++SQEG QF +GFGGIG ++RYQLD+ D SD E Y DS+
Sbjct: 390 KDYGANLEFVSDRSQEGMQFVKGFGGIGAVMRYQLDLSMLDPESD--EFYSDSD 441
>pdb|2HST|A Chain A, Solution Structure Of The Middle Domain Of Human
Eukaryotic Translation Termination Factor Erf1
Length = 143
Score = 227 bits (579), Expect = 8e-60, Method: Compositional matrix adjust.
Identities = 110/138 (79%), Positives = 121/138 (87%), Gaps = 2/138 (1%)
Query: 139 LESDDKFGFIVMDGNGTLFGTLSGNTREVLHKFSVDLPKKHGRGGQSALRFARLRMEKRH 198
L D KFGFIV+DG+G LFGTL GNTREVLHKF+VDLPKKHGRGGQSALRFARLRMEKRH
Sbjct: 1 LSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRH 60
Query: 199 NYVRKTAELATQFYINPATSQPNVSGLVLAGSADFKTELSQSDMFDPRLQAKILKVVDVS 258
NYVRK AE A Q +I+ + NV+GLVLAGSADFKTELSQSDMFD RLQ+K+LK+VD+S
Sbjct: 61 NYVRKVAETAVQLFISG--DKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDIS 118
Query: 259 YGGENGFNQAIELSAESL 276
YGGENGFNQAIELS E L
Sbjct: 119 YGGENGFNQAIELSTEVL 136
>pdb|2LLX|A Chain A, Solution Structure Of The N-Terminal Domain Of Human
Polypeptide Chain Release Factor Erf1
Length = 150
Score = 209 bits (533), Expect = 2e-54, Method: Compositional matrix adjust.
Identities = 99/137 (72%), Positives = 108/137 (78%)
Query: 3 DGQETDKNXXXXXXXXXXXXXXXXRGNGTSMISLIMPPRDQVSRVTKMLGDEFGTASNIK 62
D D+N RGNGTSMISLI+PP+DQ+SRV KML DEFGTASNIK
Sbjct: 4 DPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIK 63
Query: 63 SRVNRQSVLGAITSAQQRLKLYNKVPPNGLVLYTGTIVTDDGKEKKVTIDFEPFRPINAS 122
SRVNR SVLGAITS QQRLKLYNKVPPNGLV+Y GTIVT++GKEKKV IDFEPF+PIN S
Sbjct: 64 SRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTS 123
Query: 123 LYLCDNKFHTDALNELL 139
LYLCDNKFHT+AL LL
Sbjct: 124 LYLCDNKFHTEALTALL 140
>pdb|2LGT|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For
Qfm(Y)f
Length = 144
Score = 204 bits (518), Expect = 1e-52, Method: Compositional matrix adjust.
Identities = 96/137 (70%), Positives = 106/137 (77%)
Query: 3 DGQETDKNXXXXXXXXXXXXXXXXRGNGTSMISLIMPPRDQVSRVTKMLGDEFGTASNIK 62
D D+N RGNGTSMISLI+PP+DQ+SRV KML DEFGTASNIK
Sbjct: 4 DPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIK 63
Query: 63 SRVNRQSVLGAITSAQQRLKLYNKVPPNGLVLYTGTIVTDDGKEKKVTIDFEPFRPINAS 122
SRVNR SVLGAITS QQRLKLYNKVPPNGLV+Y GTIVT++GKEKKV IDFEPF+PIN
Sbjct: 64 SRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINQF 123
Query: 123 LYLCDNKFHTDALNELL 139
+Y CDNKFHT+AL LL
Sbjct: 124 MYFCDNKFHTEALTALL 140
>pdb|2KTU|A Chain A, Human Erf1 C-Domain, "closed" Conformer
pdb|2KTV|A Chain A, Human Erf1 C-Domain, "open" Conformer
Length = 170
Score = 196 bits (499), Expect = 1e-50, Method: Compositional matrix adjust.
Identities = 98/158 (62%), Positives = 120/158 (75%)
Query: 277 SNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLKALDMGAVDTLIVWENLDITRYVLKN 336
SNVKFIQEK+LIG+YF+EISQDTGKY FG +DTLKAL+MGAV+ LIV+ENLDI RYVL
Sbjct: 1 SNVKFIQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHC 60
Query: 337 TVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFANEYRRFGCTLEFVTNK 396
T E I +L EQE ++++F D T E E+ E LLEWFAN Y++FG TLE VT+K
Sbjct: 61 QGTEEEKILYLTPEQEKDKSHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDK 120
Query: 397 SQEGSQFCRGFGGIGGILRYQLDMRSFDEFSDDGEIYD 434
SQEGSQF +GFGGIGGILRY++D + + D E +D
Sbjct: 121 SQEGSQFVKGFGGIGGILRYRVDFQGMEYQGGDDEFFD 158
>pdb|3AGK|A Chain A, Crystal Structure Of Archaeal Translation Termination
Factor, Arf1
pdb|3VMF|B Chain B, Archaeal Protein
Length = 373
Score = 152 bits (384), Expect = 3e-37, Method: Compositional matrix adjust.
Identities = 111/392 (28%), Positives = 181/392 (46%), Gaps = 55/392 (14%)
Query: 30 GTSMISLIMPPRDQVSRVTKMLGDEFGTASNIKSRVNRQSVLGAITSAQQRLKLYNKVPP 89
T ++SL +PP +S V +L E+ NIK + RQ+V A+++A RL++ PP
Sbjct: 31 ATVLLSLYIPPGRPLSDVMTLLRQEYSITDNIKLKRTRQAVKRALSAAMDRLQMLTSTPP 90
Query: 90 NGLVLYTGTIVTDDGKEKKVTIDFEPFRPINASLYLCDNKFHTDALNELLESDDKFGFIV 149
NGLVL+ G D K F P PI Y D +F TD L +++E ++ G I+
Sbjct: 91 NGLVLFCGE---DMSTGKFECFMFSPPEPIRVFYYRTDKRFITDFLEDMVEDNNAIGIII 147
Query: 150 MDGNGTLFGTLSGNTREVLHKFSVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELAT 209
++ + G L G EVL + +P KH GGQS R+ R+ + + +K E A+
Sbjct: 148 VERDQATIGLLKGARLEVLKELEGFVPGKHKMGGQSQRRYERIIEQMVDEFFKKVGEEAS 207
Query: 210 QFYINPATSQPNVSGLVLAGSADFKTELSQSDMFDPRLQAKIL--KVVDVSYGGENGFNQ 267
+ P + + G+++AG K E + + D RL+ KIL ++VDV+Y G G +
Sbjct: 208 NLLV-PLAEKGVLKGVIVAGPGLAKQEFVEGNYLDYRLK-KILAPELVDVAYQGLQGLKE 265
Query: 268 AIELSAESLSNVKFIQEKRLIGKYFE-EISQDTGKYVFGADDTLKALDMGAVDTLIVWEN 326
A+ + AE + + ++ + F+ +++ TG V+G D AL+MGAV TL++
Sbjct: 266 AV-MKAEKVVEAQMYRDAVNAMEEFKLHLAKGTGMIVYGEKDVEAALEMGAVKTLLI--- 321
Query: 327 LDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFANEYRRF 386
H +RE LE + + +
Sbjct: 322 -------------------HESRED------------------------LEEWVEKAKSS 338
Query: 387 GCTLEFVTNKSQEGSQFCRGFGGIGGILRYQL 418
G + V E F + FGG+ GILR+++
Sbjct: 339 GAQVIVVPESLAEAEWFLKTFGGLAGILRFRI 370
>pdb|3IR9|A Chain A, C-Terminal Domain Of Peptide Chain Release Factor From
Methanosarcina Mazei.
pdb|3IR9|B Chain B, C-Terminal Domain Of Peptide Chain Release Factor From
Methanosarcina Mazei
Length = 166
Score = 65.1 bits (157), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 43/162 (26%), Positives = 78/162 (48%), Gaps = 5/162 (3%)
Query: 258 SYGGENGFNQAIELSAESLSNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLKALDMGA 317
+Y E+G ++ + + E L +++ +K + +F+E+ D+GK +G L++ +
Sbjct: 3 AYTDESGLSELVNAAGEKLQDLELXGQKNAVRDFFKELIADSGKVAYGESQVRANLEINS 62
Query: 318 VDTLIVWENLDITRYVLKNTVTG---EIVIKHLNREQETNQNNFRDSATSAELEVQEKSS 374
VD L++ E+L R K +V G + + E N +S LEV + +
Sbjct: 63 VDVLLLSEDLRAERVTTKCSVCGYENKWTRRWKPGEPAPAAGNCPKCGSS--LEVTDVTD 120
Query: 375 LLEWFANEYRRFGCTLEFVTNKSQEGSQFCRGFGGIGGILRY 416
+++ F+ + + FV+ EGSQ FGGI ILRY
Sbjct: 121 IVDEFSELADKSNAKVVFVSTDFDEGSQLXNAFGGIAAILRY 162
>pdb|3MCA|B Chain B, Structure Of The Dom34-Hbs1 Complex And Implications For
Its Role In No-Go Decay
Length = 390
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 47/76 (61%), Gaps = 2/76 (2%)
Query: 254 VVDVSYGGENGFNQAIELSA--ESLSNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLK 311
++ S G + N+ ++ A L++ K++QE R++ K+++ +++D K +G + LK
Sbjct: 242 ILHSSTGHIHSLNEILKDPAVESKLADTKYVQEIRVLNKFYDVMNEDDRKAWYGPNHVLK 301
Query: 312 ALDMGAVDTLIVWENL 327
A ++GA+ L++ ++L
Sbjct: 302 AFELGAIGELLISDSL 317
>pdb|3J15|A Chain A, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 357
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 37/144 (25%), Positives = 70/144 (48%), Gaps = 18/144 (12%)
Query: 196 KRHNYVRKTAELATQFYINPATS------QPNVSGLVLAGSA----DFKTELSQSDMFDP 245
KR+N R++ E+ +F+ + A + + NV ++AG DF L + P
Sbjct: 169 KRYNTDRESEEM--KFFHDVAKTMEEVMKRENVEKAIVAGPGFVKEDFYKFLKEKY---P 223
Query: 246 RLQAKILKVVDVSYGGENGFNQAIE--LSAESLSNVKFIQEKRLIGKYFEEISQDTGKYV 303
L K++ + D S G G + I+ + + +E +L+ K E I+++ G
Sbjct: 224 ELAKKVV-IEDTSVTGRTGIYEVIKRGVVDRVYQENRVAKEVQLVEKVLENIARNNGLVA 282
Query: 304 FGADDTLKALDMGAVDTLIVWENL 327
+G + +A++ GAV+TL+V + L
Sbjct: 283 YGLKEVEEAVNYGAVETLLVLDEL 306
>pdb|3AGJ|B Chain B, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|D Chain D, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|F Chain F, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|H Chain H, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
Length = 358
Score = 36.2 bits (82), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 42/176 (23%), Positives = 72/176 (40%), Gaps = 25/176 (14%)
Query: 157 FGTLSGNTREVLHKFSVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFYINPA 216
L+G+ ++L S LP K R V K + A + + A
Sbjct: 143 LAVLAGHGMKILEDTSARLPGKDD--------------PSREQEVEKYVDRAAKRIVEEA 188
Query: 217 TSQPNVSGLVLAGSADFKTELSQS-DMFDPRLQAKILKVVDVSYGGENGFNQAI--ELSA 273
+ V+AG KT +++ P L+ + VD S GG G +A+ E
Sbjct: 189 ARHRSPIA-VIAGPGQLKTSVAEKVQRAMPSLK---VATVDTSMGGVAGVREALRRESVT 244
Query: 274 ESLSNVKFIQEKRLIGKYFEEI--SQDTGKYVFGADDTLKALDMGAVDTLIVWENL 327
L + ++ + ++ ++ I S+DT Y G + L MGAVDT+++ + L
Sbjct: 245 RILRELSIVEAEGVLEEFLRRIAKSRDTVAYTPG--EVLAVARMGAVDTVLLVDTL 298
>pdb|2QI2|A Chain A, Crystal Structure Of The Thermoplasma Acidophilum Pelota
Protein
Length = 347
Score = 36.2 bits (82), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 33/148 (22%), Positives = 57/148 (38%), Gaps = 46/148 (31%)
Query: 273 AESLSNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLKALDMGAVDTLIVWENLDITRY 332
A+ LSN + ++K ++ ++ + +D G V+G D T AL MGA+ LI+ + +
Sbjct: 239 AKLLSNERIARDKEIVDEFLVAVKKDMG--VYGRDQTESALQMGALSDLIITDEM----- 291
Query: 333 VLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFANEYRRFGCTLEF 392
FR L + + G +
Sbjct: 292 -------------------------FRTEDGRRSLSIAQT-------------VGTRIHI 313
Query: 393 VTNKSQEGSQFCRGFGGIGGILRYQLDM 420
V+ + G Q + FGG GILRY++ +
Sbjct: 314 VSVSNDPG-QIVKKFGGFAGILRYRVQL 340
>pdb|3OBW|A Chain A, Crystal Structure Of Two Archaeal Pelotas Reveal
Inter-Domain Structural Plasticity
Length = 364
Score = 32.3 bits (72), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 28/124 (22%), Positives = 63/124 (50%), Gaps = 6/124 (4%)
Query: 206 ELATQFYINPATSQPNVSGLVLAGSADFKTELSQSDMFDPRLQAKILKVVDVSYGGENGF 265
E+AT+ + Q + ++LAG FK E+S+ + L+ K + + VS G
Sbjct: 192 EIATE--LAEYVKQYDPDAILLAGPGFFKEEVSKK--VNAILKNKKIYIDSVSSATRAGL 247
Query: 266 NQAI--ELSAESLSNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLKALDMGAVDTLIV 323
++ + ++ + +++ + + + K E +++ +G + A++MGAV+T++V
Sbjct: 248 HEVLKRDIIDKIMTDYEIAIGAKKMEKAMELLAKQPELVTYGLEQVKNAIEMGAVETVLV 307
Query: 324 WENL 327
E+L
Sbjct: 308 IEDL 311
>pdb|3KYH|A Chain A, Saccharomyces Cerevisiae Cet1-Ceg1 Capping Apparatus
pdb|3KYH|B Chain B, Saccharomyces Cerevisiae Cet1-Ceg1 Capping Apparatus
Length = 310
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 13/82 (15%)
Query: 347 LNREQETNQNN-FRDSATSAELEVQ-EKSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFC 404
+ + + NQN+ R S T+ E+E++ +LL F N +TN S+E +
Sbjct: 233 ITKVENHNQNSKSRQSETTHEVELEINTPALLNAFDN-----------ITNDSKEYASLI 281
Query: 405 RGFGGIGGILRYQLDMRSFDEF 426
R F G I+R +L S++ F
Sbjct: 282 RTFLNNGTIIRRKLSSLSYEIF 303
>pdb|1D8H|A Chain A, X-Ray Crystal Structure Of Yeast Rna Triphosphatase In
Complex With Sulfate And Manganese Ions.
pdb|1D8H|B Chain B, X-Ray Crystal Structure Of Yeast Rna Triphosphatase In
Complex With Sulfate And Manganese Ions.
pdb|1D8H|C Chain C, X-Ray Crystal Structure Of Yeast Rna Triphosphatase In
Complex With Sulfate And Manganese Ions.
pdb|1D8I|A Chain A, X-Ray Crystal Structure Of Yeast Rna Triphosphatase In
Complex With A Sulfate Ion.
pdb|1D8I|B Chain B, X-Ray Crystal Structure Of Yeast Rna Triphosphatase In
Complex With A Sulfate Ion.
pdb|1D8I|C Chain C, X-Ray Crystal Structure Of Yeast Rna Triphosphatase In
Complex With A Sulfate Ion
Length = 311
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 13/82 (15%)
Query: 347 LNREQETNQNN-FRDSATSAELEVQ-EKSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFC 404
+ + + NQN+ R S T+ E+E++ +LL F N +TN S+E +
Sbjct: 234 ITKVENHNQNSKSRQSETTHEVELEINTPALLNAFDN-----------ITNDSKEYASLI 282
Query: 405 RGFGGIGGILRYQLDMRSFDEF 426
R F G I+R +L S++ F
Sbjct: 283 RTFLNNGTIIRRKLSSLSYEIF 304
>pdb|3IDO|A Chain A, Crystal Structure Of Protein Tyrosine Phosphatase From
Entamoeba Histolytica With A Phosphotyrosine Crude Mimic
Hepes Molecule In The Active Site
pdb|3IDO|B Chain B, Crystal Structure Of Protein Tyrosine Phosphatase From
Entamoeba Histolytica With A Phosphotyrosine Crude Mimic
Hepes Molecule In The Active Site
pdb|3ILY|A Chain A, Apo Crystal Structure Of Protein Tyrosine Phosphatase From
Entamoeba Histolytica Featuring A Disordered Active Site
pdb|3ILY|B Chain B, Apo Crystal Structure Of Protein Tyrosine Phosphatase From
Entamoeba Histolytica Featuring A Disordered Active Site
pdb|3JS5|A Chain A, Crystal Structure Of Protein Tyrosine Phosphatase From
Entamoeba Histolytica With Hepes In The Active Site.
High Resolution, Alternative Crystal Form With 1
Molecule In Asymmetric Unit
Length = 178
Score = 28.9 bits (63), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 242 MFDPRLQAKILKVVDVSYGGENGFNQAIELSAESLSNVKF-IQEKRLI 288
M D K +V D YGGE GF++ I++ ++ N+ ++E +LI
Sbjct: 130 MVDFCTTIKTTEVPDPYYGGEKGFHRVIDILEDACENLIIKLEEGKLI 177
>pdb|3JVI|A Chain A, Product State Mimic Crystal Structure Of Protein Tyrosine
Phosphatase From Entamoeba Histolytica
Length = 161
Score = 28.9 bits (63), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 242 MFDPRLQAKILKVVDVSYGGENGFNQAIELSAESLSNVKF-IQEKRLI 288
M D K +V D YGGE GF++ I++ ++ N+ ++E +LI
Sbjct: 113 MVDFCTTIKTTEVPDPYYGGEKGFHRVIDILEDACENLIIKLEEGKLI 160
>pdb|3N4Z|A Chain A, Crystal Structure Of Quintuple Arg-To-Lys Variant Of T.
Celer L30e
pdb|3N4Z|B Chain B, Crystal Structure Of Quintuple Arg-To-Lys Variant Of T.
Celer L30e
Length = 101
Score = 28.9 bits (63), Expect = 6.1, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 296 SQDTGKYVFGADDTLKALDMGAVDTLIVWEN 326
+QDTGK V GA +++ MG +IV N
Sbjct: 11 AQDTGKIVMGAKKSIQYAKMGGAKLIIVARN 41
>pdb|3EQ2|A Chain A, Structure Of Hexagonal Crystal Form Of Pseudomonas
Aeruginosa Rssb
pdb|3EQ2|B Chain B, Structure Of Hexagonal Crystal Form Of Pseudomonas
Aeruginosa Rssb
Length = 394
Score = 28.9 bits (63), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 47/99 (47%), Gaps = 9/99 (9%)
Query: 308 DTLKALDMGAVDTLI-VWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366
D ++AL +GA D LI E+L VL+++V + +L E + +RD +A
Sbjct: 91 DAVEALRLGAADYLIKPLEDL----AVLEHSVRRALDRAYLRVENQ----RYRDKLEAAN 142
Query: 367 LEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFCR 405
E+Q +LL+ N R+ VT S EG +F
Sbjct: 143 RELQASLNLLQEDQNAGRQVQXNXLPVTPWSIEGLEFSH 181
>pdb|3F7A|A Chain A, Structure Of Orthorhombic Crystal Form Of Pseudomonas
Aeruginosa Rssb
pdb|3F7A|B Chain B, Structure Of Orthorhombic Crystal Form Of Pseudomonas
Aeruginosa Rssb
Length = 394
Score = 28.9 bits (63), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 47/99 (47%), Gaps = 9/99 (9%)
Query: 308 DTLKALDMGAVDTLI-VWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366
D ++AL +GA D LI E+L VL+++V + +L E + +RD +A
Sbjct: 91 DAVEALRLGAADYLIKPLEDL----AVLEHSVRRALDRAYLRVENQ----RYRDKLEAAN 142
Query: 367 LEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFCR 405
E+Q +LL+ N R+ VT S EG +F
Sbjct: 143 RELQASLNLLQEDQNAGRQVQXNXLPVTPWSIEGLEFSH 181
>pdb|2XR7|A Chain A, Crystal Structure Of Nicotiana Tabacum Malonyltransferase
(Ntmat1) Complexed With Malonyl-Coa
Length = 453
Score = 28.1 bits (61), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 37/89 (41%), Gaps = 2/89 (2%)
Query: 231 ADFKTELSQSDMFDPRLQAKILKVVDVSYGGENGFNQAIELSAESLSNVKFIQEKRLIGK 290
A F L S F L + + V G+ GF A+EL E++ +E L G
Sbjct: 308 AQFNPPLPPS-YFGNALVGYVARTRQVDLAGKEGFTIAVELIGEAIRKRXKDEEWILSGS 366
Query: 291 YFEEISQDTGKYVFGADDTLKALDMGAVD 319
+F+E + K + K LD+ A D
Sbjct: 367 WFKEYDKVDAKRSLSVAGSPK-LDLYAAD 394
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.134 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,429,439
Number of Sequences: 62578
Number of extensions: 508843
Number of successful extensions: 1321
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1296
Number of HSP's gapped (non-prelim): 27
length of query: 437
length of database: 14,973,337
effective HSP length: 102
effective length of query: 335
effective length of database: 8,590,381
effective search space: 2877777635
effective search space used: 2877777635
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)