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= 042367
(428 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 503 bits (1296), Expect = e-143, Method: Compositional matrix adjust.
Identities = 248/427 (58%), Positives = 322/427 (75%), Gaps = 12/427 (2%)
Query: 5 SETDSNIEMWKMKKLIKTLSAVKGDGTSLISLVVNPRDKIPRVTKMLGEEYQNASKIKKR 64
S D N+E+WK+KKLIK+L A +G+GTS+ISL++ P+D+I RV KML +E+ AS IK R
Sbjct: 20 SAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSR 79
Query: 65 MNRQSVQAAITYAQSRLKLYKNVPSNGLVLFTGTGVTEDGEEKKFAHDLVPFKPINSSLY 124
+NR SV AIT Q RLKLY VP NGLV++ GT VTE+G+EKK D PFKPIN+SLY
Sbjct: 80 VNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLY 139
Query: 125 VCDSSFHTEA----------YGYIIIDGNGTLIGTLCGSSREVVLKFTVDLPKKHGRGGQ 174
+CD+ FHTEA +G+I+IDG+G L GTL G++REV+ KFTVDLPKKHGRGGQ
Sbjct: 140 LCDNKFHTEALTALLSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQ 199
Query: 175 SALRFSRLRVEKRHNYLREAAELATKCFIDPATSQPNVTGLILAGSAEFKTELSQSGMFD 234
SALRF+RLR+EKRHNY+R+ AE A + FI + + NV GL+LAGSA+FKTELSQS MFD
Sbjct: 200 SALRFARLRMEKRHNYVRKVAETAVQLFI--SGDKVNVAGLVLAGSADFKTELSQSDMFD 257
Query: 235 PCLMAKILKVLDISYGGVSGFNQAIELSSDVIANVNVLKEKRVIGKFFEEIGQDTGKFVV 294
L +K+LK++DISYGG +GFNQAIELS++V++NV ++EK++IG++F+EI QDTGK+
Sbjct: 258 QRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNVKFIQEKKLIGRYFDEISQDTGKYCF 317
Query: 295 GVDDSVKALEMGAIHTLIVWEDLDINRYELKQSVTNGIVIKHLNKKQEAEPSNFKDSAAA 354
GV+D++KALEMGA+ LIV+E+LDI RY L T I +L +QE + S+F D
Sbjct: 318 GVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKETG 377
Query: 355 SDLKVEGKMGLLEWLVDHYKQFGCSLEIVTDKSQEGSQFCRGFGGIGGILRYQPDMGSFD 414
+ ++ M LLEW ++YK+FG +LEIVTDKSQEGSQF +GFGGIGGILRY+ D +
Sbjct: 378 QEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQGME 437
Query: 415 EGSGDGE 421
GD E
Sbjct: 438 YQGGDDE 444
>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 = 503 bits (1295), Expect = e-143, Method: Compositional matrix adjust.
Identities = 248/427 (58%), Positives = 322/427 (75%), Gaps = 12/427 (2%)
Query: 5 SETDSNIEMWKMKKLIKTLSAVKGDGTSLISLVVNPRDKIPRVTKMLGEEYQNASKIKKR 64
S D N+E+WK+KKLIK+L A +G+GTS+ISL++ P+D+I RV KML +E+ AS IK R
Sbjct: 6 SAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSR 65
Query: 65 MNRQSVQAAITYAQSRLKLYKNVPSNGLVLFTGTGVTEDGEEKKFAHDLVPFKPINSSLY 124
+NR SV AIT Q RLKLY VP NGLV++ GT VTE+G+EKK D PFKPIN+SLY
Sbjct: 66 VNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLY 125
Query: 125 VCDSSFHTEA----------YGYIIIDGNGTLIGTLCGSSREVVLKFTVDLPKKHGRGGQ 174
+CD+ FHTEA +G+I+IDG+G L GTL G++REV+ KFTVDLPKKHGRGGQ
Sbjct: 126 LCDNKFHTEALTALLSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQ 185
Query: 175 SALRFSRLRVEKRHNYLREAAELATKCFIDPATSQPNVTGLILAGSAEFKTELSQSGMFD 234
SALRF+RLR+EKRHNY+R+ AE A + FI + + NV GL+LAGSA+FKTELSQS MFD
Sbjct: 186 SALRFARLRMEKRHNYVRKVAETAVQLFI--SGDKVNVAGLVLAGSADFKTELSQSDMFD 243
Query: 235 PCLMAKILKVLDISYGGVSGFNQAIELSSDVIANVNVLKEKRVIGKFFEEIGQDTGKFVV 294
L +K+LK++DISYGG +GFNQAIELS++V++NV ++EK++IG++F+EI QDTGK+
Sbjct: 244 QRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNVKFIQEKKLIGRYFDEISQDTGKYCF 303
Query: 295 GVDDSVKALEMGAIHTLIVWEDLDINRYELKQSVTNGIVIKHLNKKQEAEPSNFKDSAAA 354
GV+D++KALEMGA+ LIV+E+LDI RY L T I +L +QE + S+F D
Sbjct: 304 GVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKETG 363
Query: 355 SDLKVEGKMGLLEWLVDHYKQFGCSLEIVTDKSQEGSQFCRGFGGIGGILRYQPDMGSFD 414
+ ++ M LLEW ++YK+FG +LEIVTDKSQEGSQF +GFGGIGGILRY+ D +
Sbjct: 364 QEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQGME 423
Query: 415 EGSGDGE 421
GD E
Sbjct: 424 YQGGDDE 430
>pdb|3J2K|6 Chain 6, Cryo-Em Structure Of The Mammalian Erf1-Erf3-Associated
Termination Complex
Length = 411
Score = 497 bits (1279), Expect = e-141, Method: Compositional matrix adjust.
Identities = 243/411 (59%), Positives = 316/411 (76%), Gaps = 12/411 (2%)
Query: 10 NIEMWKMKKLIKTLSAVKGDGTSLISLVVNPRDKIPRVTKMLGEEYQNASKIKKRMNRQS 69
N+E+WK+KKLIK+L A +G+GTS+ISL++ P+D+I RV KML +E+ AS IK R+NR S
Sbjct: 2 NVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRLS 61
Query: 70 VQAAITYAQSRLKLYKNVPSNGLVLFTGTGVTEDGEEKKFAHDLVPFKPINSSLYVCDSS 129
V AIT Q RLKLY VP NGLV++ GT VTE+G+EKK D PFKPIN+SLY+CD+
Sbjct: 62 VLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLYLCDNK 121
Query: 130 FHTEA----------YGYIIIDGNGTLIGTLCGSSREVVLKFTVDLPKKHGRGGQSALRF 179
FHTEA +G+I+IDG+G L GTL G++REV+ KFTVDLPKKHGRGGQSALRF
Sbjct: 122 FHTEALTALLSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRF 181
Query: 180 SRLRVEKRHNYLREAAELATKCFIDPATSQPNVTGLILAGSAEFKTELSQSGMFDPCLMA 239
+RLR+EKRHNY+R+ AE A + FI + + NV GL+LAGSA+FKTELSQS MFD L +
Sbjct: 182 ARLRMEKRHNYVRKVAETAVQLFI--SGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQS 239
Query: 240 KILKVLDISYGGVSGFNQAIELSSDVIANVNVLKEKRVIGKFFEEIGQDTGKFVVGVDDS 299
K+LK++DISYGG +GFNQAIELS++V++NV ++EK++IG++F+EI QDTGK+ GV+D+
Sbjct: 240 KVLKLVDISYGGENGFNQAIELSTEVLSNVKFIQEKKLIGRYFDEISQDTGKYCFGVEDT 299
Query: 300 VKALEMGAIHTLIVWEDLDINRYELKQSVTNGIVIKHLNKKQEAEPSNFKDSAAASDLKV 359
+KALEMGA+ LIV+E+LDI RY L T I +L +QE + S+F D + ++
Sbjct: 300 LKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKETGQEHEL 359
Query: 360 EGKMGLLEWLVDHYKQFGCSLEIVTDKSQEGSQFCRGFGGIGGILRYQPDM 410
M LLEW ++YK+FG +LEIVTDKSQEGSQF +GFGGIGGILRY+ D
Sbjct: 360 IESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDF 410
>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 = 435 bits (1118), Expect = e-122, Method: Compositional matrix adjust.
Identities = 215/427 (50%), Positives = 301/427 (70%), Gaps = 17/427 (3%)
Query: 5 SET-DSNIEMWKMKKLIKTLSAVKGDGTSLISLVVNPRDKIPRVTKMLGEEYQNASKIKK 63
SET + IE+WK+++L+K L G+GTS+I+L++ P ++I R + ML EEY AS IK
Sbjct: 10 SETAEKAIEIWKIRRLVKQLINCHGNGTSMITLIIPPGEQISRYSNMLAEEYGTASNIKS 69
Query: 64 RMNRQSVQAAITYAQSRLKLYKNVPSNGLVLFTGTGVTEDGEEKKFAHDLVPFKPINSSL 123
R+NR SV +AIT + RLKLY VP NGLV++ G + E + +K D PFKPIN+S
Sbjct: 70 RVNRLSVLSAITSTRERLKLYNKVPDNGLVIYCGEVIMEGNKTRKLNIDFEPFKPINTSQ 129
Query: 124 YVCDSSFHTEA----------YGYIIIDGNGTLIGTLCGSSREVVLKFTVDLPKKHGRGG 173
Y+CD+ FHTEA +G+I++DG+ TL G + GS+REV+ +FTVDLPKKHGRGG
Sbjct: 130 YLCDNKFHTEALAELLESDQRFGFIVMDGHQTLYGVVSGSAREVLQRFTVDLPKKHGRGG 189
Query: 174 QSALRFSRLRVEKRHNYLREAAELATKCFIDPATSQPNVTGLILAGSAEFKTELSQSGMF 233
QSALRF+RLR EKRHNY+R+ AE A + FI +PNV G++LAGSA+FKTEL QS +F
Sbjct: 190 QSALRFARLRDEKRHNYVRKVAEGAVQHFI--TDDKPNVAGIVLAGSADFKTELGQSDLF 247
Query: 234 DPCLMAKILKVLDISYGGVSGFNQAIELSSDVIANVNVLKEKRVIGKFFEEIGQDTGKFV 293
D L ++I+K +D+SYGG +GFNQAIEL++D ++NV ++EK++I +FF+EI D+GK+
Sbjct: 248 DQRLQSRIIKTVDVSYGGDAGFNQAIELAADTLSNVKYVQEKKLIQRFFDEISLDSGKYC 307
Query: 294 VGVDDSVKALEMGAIHTLIVWEDLDINRYELKQSVTNGIVIKHLNKKQEAEPSN---FKD 350
GV D++ AL+ GA+ TL+ + DLD+ RYE K S N VI ++ K+QE + S D
Sbjct: 308 FGVVDTMNALQEGAVETLLCFADLDMIRYEFKNSEGNP-VITYMTKEQEEKDSTNSFLLD 366
Query: 351 SAAASDLKVEGKMGLLEWLVDHYKQFGCSLEIVTDKSQEGSQFCRGFGGIGGILRYQPDM 410
+++++ M L EWL +HYK +G +LE V+D+SQEG QF +GFGGIG ++RYQ D+
Sbjct: 367 KDTGAEMELVSSMLLSEWLAEHYKDYGANLEFVSDRSQEGMQFVKGFGGIGAVMRYQLDL 426
Query: 411 GSFDEGS 417
D S
Sbjct: 427 SMLDPES 433
>pdb|2HST|A Chain A, Solution Structure Of The Middle Domain Of Human
Eukaryotic Translation Termination Factor Erf1
Length = 143
Score = 188 bits (477), Expect = 6e-48, Method: Compositional matrix adjust.
Identities = 89/132 (67%), Positives = 113/132 (85%), Gaps = 2/132 (1%)
Query: 135 YGYIIIDGNGTLIGTLCGSSREVVLKFTVDLPKKHGRGGQSALRFSRLRVEKRHNYLREA 194
+G+I+IDG+G L GTL G++REV+ KFTVDLPKKHGRGGQSALRF+RLR+EKRHNY+R+
Sbjct: 7 FGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKV 66
Query: 195 AELATKCFIDPATSQPNVTGLILAGSAEFKTELSQSGMFDPCLMAKILKVLDISYGGVSG 254
AE A + FI + + NV GL+LAGSA+FKTELSQS MFD L +K+LK++DISYGG +G
Sbjct: 67 AETAVQLFI--SGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDISYGGENG 124
Query: 255 FNQAIELSSDVI 266
FNQAIELS++V+
Sbjct: 125 FNQAIELSTEVL 136
>pdb|2LLX|A Chain A, Solution Structure Of The N-Terminal Domain Of Human
Polypeptide Chain Release Factor Erf1
Length = 150
Score = 171 bits (433), Expect = 7e-43, Method: Compositional matrix adjust.
Identities = 80/137 (58%), Positives = 103/137 (75%)
Query: 5 SETDSNIEMWKMKKLIKTLSAVKGDGTSLISLVVNPRDKIPRVTKMLGEEYQNASKIKKR 64
S D N+E+WK+KKLIK+L A +G+GTS+ISL++ P+D+I RV KML +E+ AS IK R
Sbjct: 6 SAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSR 65
Query: 65 MNRQSVQAAITYAQSRLKLYKNVPSNGLVLFTGTGVTEDGEEKKFAHDLVPFKPINSSLY 124
+NR SV AIT Q RLKLY VP NGLV++ GT VTE+G+EKK D PFKPIN+SLY
Sbjct: 66 VNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLY 125
Query: 125 VCDSSFHTEAYGYIIID 141
+CD+ FHTEA ++ D
Sbjct: 126 LCDNKFHTEALTALLSD 142
>pdb|2LGT|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For
Qfm(Y)f
Length = 144
Score = 166 bits (421), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 78/137 (56%), Positives = 100/137 (72%)
Query: 5 SETDSNIEMWKMKKLIKTLSAVKGDGTSLISLVVNPRDKIPRVTKMLGEEYQNASKIKKR 64
S D N+E+WK+KKLIK+L A +G+GTS+ISL++ P+D+I RV KML +E+ AS IK R
Sbjct: 6 SAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSR 65
Query: 65 MNRQSVQAAITYAQSRLKLYKNVPSNGLVLFTGTGVTEDGEEKKFAHDLVPFKPINSSLY 124
+NR SV AIT Q RLKLY VP NGLV++ GT VTE+G+EKK D PFKPIN +Y
Sbjct: 66 VNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINQFMY 125
Query: 125 VCDSSFHTEAYGYIIID 141
CD+ FHTEA ++ D
Sbjct: 126 FCDNKFHTEALTALLSD 142
>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 = 161 bits (407), Expect = 7e-40, Method: Compositional matrix adjust.
Identities = 80/155 (51%), Positives = 109/155 (70%)
Query: 267 ANVNVLKEKRVIGKFFEEIGQDTGKFVVGVDDSVKALEMGAIHTLIVWEDLDINRYELKQ 326
+NV ++EK++IG++F+EI QDTGK+ GV+D++KALEMGA+ LIV+E+LDI RY L
Sbjct: 1 SNVKFIQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHC 60
Query: 327 SVTNGIVIKHLNKKQEAEPSNFKDSAAASDLKVEGKMGLLEWLVDHYKQFGCSLEIVTDK 386
T I +L +QE + S+F D + ++ M LLEW ++YK+FG +LEIVTDK
Sbjct: 61 QGTEEEKILYLTPEQEKDKSHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDK 120
Query: 387 SQEGSQFCRGFGGIGGILRYQPDMGSFDEGSGDGE 421
SQEGSQF +GFGGIGGILRY+ D + GD E
Sbjct: 121 SQEGSQFVKGFGGIGGILRYRVDFQGMEYQGGDDE 155
>pdb|3AGK|A Chain A, Crystal Structure Of Archaeal Translation Termination
Factor, Arf1
pdb|3VMF|B Chain B, Archaeal Protein
Length = 373
Score = 132 bits (333), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 111/406 (27%), Positives = 177/406 (43%), Gaps = 65/406 (16%)
Query: 15 KMKKLIKTLSAVKGDGTSLISLVVNPRDKIPRVTKMLGEEYQNASKIKKRMNRQSVQAAI 74
++ +L+K L T L+SL + P + V +L +EY IK + RQ+V+ A+
Sbjct: 16 ELARLLKELKKWSAPATVLLSLYIPPGRPLSDVMTLLRQEYSITDNIKLKRTRQAVKRAL 75
Query: 75 TYAQSRLKLYKNVPSNGLVLFTGTGVTEDGEEKKF-AHDLVPFKPINSSLYVCDSSFHTE 133
+ A RL++ + P NGLVLF G ED KF P +PI Y D F T+
Sbjct: 76 SAAMDRLQMLTSTPPNGLVLFCG----EDMSTGKFECFMFSPPEPIRVFYYRTDKRFITD 131
Query: 134 ----------AYGYIIIDGNGTLIGTLCGSSREVVLKFTVDLPKKHGRGGQSALRFSRLR 183
A G II++ + IG L G+ EV+ + +P KH GGQS R+ R+
Sbjct: 132 FLEDMVEDNNAIGIIIVERDQATIGLLKGARLEVLKELEGFVPGKHKMGGQSQRRYERII 191
Query: 184 VEKRHNYLREAAELATKCFIDPATSQPNVTGLILAGSAEFKTELSQSGMFDPCLMAKIL- 242
+ + ++ E A+ + P + + G+I+AG K E + D L KIL
Sbjct: 192 EQMVDEFFKKVGEEASNLLV-PLAEKGVLKGVIVAGPGLAKQEFVEGNYLDYRL-KKILA 249
Query: 243 -KVLDISYGGVSGFNQAIELSSDVIANVNVLKEKRVIGKFFEEIGQDTGKFVVGVDDSVK 301
+++D++Y G+ G +A+ + V+ + +F + + TG V G D
Sbjct: 250 PELVDVAYQGLQGLKEAVMKAEKVVEAQMYRDAVNAMEEFKLHLAKGTGMIVYGEKDVEA 309
Query: 302 ALEMGAIHTLIVWEDLDINRYELKQSVTNGIVIKHLNKKQEAEPSNFKDSAAASDLKVEG 361
ALEMGA+ TL++ E + DL+
Sbjct: 310 ALEMGAVKTLLIHE-------------------------------------SREDLE--- 329
Query: 362 KMGLLEWLVDHYKQFGCSLEIVTDKSQEGSQFCRGFGGIGGILRYQ 407
EW V+ K G + +V + E F + FGG+ GILR++
Sbjct: 330 -----EW-VEKAKSSGAQVIVVPESLAEAEWFLKTFGGLAGILRFR 369
>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 = 54.7 bits (130), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 41/162 (25%), Positives = 73/162 (45%), Gaps = 3/162 (1%)
Query: 248 SYGGVSGFNQAIELSSDVIANVNVLKEKRVIGKFFEEIGQDTGKFVVGVDDSVKALEMGA 307
+Y SG ++ + + + + ++ + +K + FF+E+ D+GK G LE+ +
Sbjct: 3 AYTDESGLSELVNAAGEKLQDLELXGQKNAVRDFFKELIADSGKVAYGESQVRANLEINS 62
Query: 308 IHTLIVWEDLDINRYELKQSVTNGIVIKHLNKKQEAEPSNFKDSA--AASDLKVEGKMGL 365
+ L++ EDL R K SV G K + + EP+ + S L+V +
Sbjct: 63 VDVLLLSEDLRAERVTTKCSVC-GYENKWTRRWKPGEPAPAAGNCPKCGSSLEVTDVTDI 121
Query: 366 LEWLVDHYKQFGCSLEIVTDKSQEGSQFCRGFGGIGGILRYQ 407
++ + + + V+ EGSQ FGGI ILRY
Sbjct: 122 VDEFSELADKSNAKVVFVSTDFDEGSQLXNAFGGIAAILRYN 163
>pdb|3J15|A Chain A, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 357
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 39/140 (27%), Positives = 67/140 (47%), Gaps = 10/140 (7%)
Query: 186 KRHNYLREAAELATKCFIDPATS------QPNVTGLILAGSAEFKTELSQSGMFDPCLMA 239
KR+N RE+ E+ K F D A + + NV I+AG K + + +A
Sbjct: 169 KRYNTDRESEEM--KFFHDVAKTMEEVMKRENVEKAIVAGPGFVKEDFYKFLKEKYPELA 226
Query: 240 KILKVLDISYGGVSGFNQAIE--LSSDVIANVNVLKEKRVIGKFFEEIGQDTGKFVVGVD 297
K + + D S G +G + I+ + V V KE +++ K E I ++ G G+
Sbjct: 227 KKVVIEDTSVTGRTGIYEVIKRGVVDRVYQENRVAKEVQLVEKVLENIARNNGLVAYGLK 286
Query: 298 DSVKALEMGAIHTLIVWEDL 317
+ +A+ GA+ TL+V ++L
Sbjct: 287 EVEEAVNYGAVETLLVLDEL 306
>pdb|3MCA|B Chain B, Structure Of The Dom34-Hbs1 Complex And Implications For
Its Role In No-Go Decay
Length = 390
Score = 35.8 bits (81), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 244 VLDISYGGVSGFNQAIELSS--DVIANVNVLKEKRVIGKFFEEIGQDTGKFVVGVDDSVK 301
+L S G + N+ ++ + +A+ ++E RV+ KF++ + +D K G + +K
Sbjct: 242 ILHSSTGHIHSLNEILKDPAVESKLADTKYVQEIRVLNKFYDVMNEDDRKAWYGPNHVLK 301
Query: 302 ALEMGAIHTLIVWEDL 317
A E+GAI L++ + L
Sbjct: 302 AFELGAIGELLISDSL 317
>pdb|1PXW|A Chain A, Crystal Structure Of L7ae Srnp Core Protein From
Pyrococcus Abyssii
pdb|1PXW|B Chain B, Crystal Structure Of L7ae Srnp Core Protein From
Pyrococcus Abyssii
Length = 128
Score = 33.9 bits (76), Expect = 0.20, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 284 EIGQDTGKFVVGVDDSVKALEMGAIHTLIVWEDLD 318
EI +DTGK G +++ KA+E G +I+ ED+D
Sbjct: 29 EIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVD 63
>pdb|2CZW|A Chain A, Crystal Structure Analysis Of Protein Component Ph1496p Of
P.Horikoshii Ribonuclease P
Length = 124
Score = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 284 EIGQDTGKFVVGVDDSVKALEMGAIHTLIVWEDLD 318
EI +DTGK G +++ KA+E G +I+ ED+D
Sbjct: 25 EIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVD 59
>pdb|3OBW|A Chain A, Crystal Structure Of Two Archaeal Pelotas Reveal
Inter-Domain Structural Plasticity
Length = 364
Score = 33.5 bits (75), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 35/134 (26%), Positives = 59/134 (44%), Gaps = 14/134 (10%)
Query: 188 HNYLREAAELATKCFIDPATSQPNVTGLILAGSAEFKTELSQSGMFDPCLMAKILKVLDI 247
N L A ELA Q + ++LAG FK E+S+ + L K + + +
Sbjct: 188 QNALEIATELAEYV------KQYDPDAILLAGPGFFKEEVSKK--VNAILKNKKIYIDSV 239
Query: 248 SYGGVSGFNQAIELSSDVIANVNVLKEKRV----IGKFFEEIGQDTGKFVVGVDDSVKAL 303
S +G ++ L D+I + E + + K E + + G++ A+
Sbjct: 240 SSATRAGLHEV--LKRDIIDKIMTDYEIAIGAKKMEKAMELLAKQPELVTYGLEQVKNAI 297
Query: 304 EMGAIHTLIVWEDL 317
EMGA+ T++V EDL
Sbjct: 298 EMGAVETVLVIEDL 311
>pdb|3HJW|C Chain C, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
Length = 120
Score = 33.5 bits (75), Expect = 0.23, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 284 EIGQDTGKFVVGVDDSVKALEMGAIHTLIVWEDLD 318
EI +DTGK G +++ KA+E G +I+ ED+D
Sbjct: 22 EIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVD 56
>pdb|3LWO|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRU
pdb|3LWP|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRDU
pdb|3LWQ|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
3MU
pdb|3LWR|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
4SU
pdb|3LWV|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
2'- Deoxyuridine
pdb|3J20|3 Chain 3, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
pdb|3J21|G Chain G, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
pdb|3J21|4 Chain 4, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 123
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 284 EIGQDTGKFVVGVDDSVKALEMGAIHTLIVWEDLD 318
EI +DTGK G +++ KA+E G +I+ ED+D
Sbjct: 24 EIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVD 58
>pdb|3NMU|C Chain C, Crystal Structure Of Substrate-Bound Halfmer Box CD RNP
pdb|3NMU|G Chain G, Crystal Structure Of Substrate-Bound Halfmer Box CD RNP
pdb|3NVI|B Chain B, Structure Of N-Terminal Truncated Nop5658 BOUND WITH L7AE
AND BOX CD Rna
pdb|3NVI|D Chain D, Structure Of N-Terminal Truncated Nop5658 BOUND WITH L7AE
AND BOX CD Rna
pdb|3NVK|E Chain E, Structural Basis For Substrate Placement By An Archaeal
Box CD Ribonucleoprotein Particle
pdb|3NVK|H Chain H, Structural Basis For Substrate Placement By An Archaeal
Box CD Ribonucleoprotein Particle
Length = 129
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 284 EIGQDTGKFVVGVDDSVKALEMGAIHTLIVWEDLD 318
EI +DTGK G +++ KA+E G +I+ ED+D
Sbjct: 30 EIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVD 64
>pdb|2HVY|D Chain D, Crystal Structure Of An HACA BOX RNP FROM PYROCOCCUS
FURIOSUS
pdb|3HAX|D Chain D, Crystal Structure Of A Substrate-Bound Gar1-Minus HACA RNP
FROM Pyrococcus Furiosus
pdb|3HAY|D Chain D, Crystal Structure Of A Substrate-Bound Full HACA RNP FROM
Pyrococcus Furiosus
Length = 130
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 284 EIGQDTGKFVVGVDDSVKALEMGAIHTLIVWEDLD 318
EI +DTGK G +++ KA+E G +I+ ED+D
Sbjct: 25 EIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVD 59
>pdb|2QI2|A Chain A, Crystal Structure Of The Thermoplasma Acidophilum Pelota
Protein
Length = 347
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 30/143 (20%), Positives = 56/143 (39%), Gaps = 46/143 (32%)
Query: 265 VIANVNVLKEKRVIGKFFEEIGQDTGKFVVGVDDSVKALEMGAIHTLIVWEDLDINRYEL 324
+++N + ++K ++ +F + +D G V G D + AL+MGA+ LI+ +++
Sbjct: 241 LLSNERIARDKEIVDEFLVAVKKDMG--VYGRDQTESALQMGALSDLIITDEM------- 291
Query: 325 KQSVTNGIVIKHLNKKQEAEPSNFKDSAAASDLKVEGKMGLLEWLVDHYKQFGCSLEIVT 384
F+ L + + G + IV+
Sbjct: 292 -----------------------FRTEDGRRSLSIA-------------QTVGTRIHIVS 315
Query: 385 DKSQEGSQFCRGFGGIGGILRYQ 407
+ G Q + FGG GILRY+
Sbjct: 316 VSNDPG-QIVKKFGGFAGILRYR 337
>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 = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 27/109 (24%), Positives = 57/109 (52%), Gaps = 14/109 (12%)
Query: 216 ILAGSAEFKTELS---QSGMFDPCLMAKILKVLDISYGGVSGFNQAI--ELSSDVIANVN 270
++AG + KT ++ Q M P L + +D S GGV+G +A+ E + ++ ++
Sbjct: 197 VIAGPGQLKTSVAEKVQRAM--PSLK---VATVDTSMGGVAGVREALRRESVTRILRELS 251
Query: 271 VLKEKRVIGKFFEEIG--QDTGKFVVGVDDSVKALEMGAIHTLIVWEDL 317
+++ + V+ +F I +DT + G + + MGA+ T+++ + L
Sbjct: 252 IVEAEGVLEEFLRRIAKSRDTVAYTPG--EVLAVARMGAVDTVLLVDTL 298
>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 = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 232 MFDPCLMAKILKVLDISYGGVSGFNQAIELSSDVIANVNV-LKEKRVI 278
M D C K +V D YGG GF++ I++ D N+ + L+E ++I
Sbjct: 130 MVDFCTTIKTTEVPDPYYGGEKGFHRVIDILEDACENLIIKLEEGKLI 177
>pdb|3JVI|A Chain A, Product State Mimic Crystal Structure Of Protein Tyrosine
Phosphatase From Entamoeba Histolytica
Length = 161
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 232 MFDPCLMAKILKVLDISYGGVSGFNQAIELSSDVIANVNV-LKEKRVI 278
M D C K +V D YGG GF++ I++ D N+ + L+E ++I
Sbjct: 113 MVDFCTTIKTTEVPDPYYGGEKGFHRVIDILEDACENLIIKLEEGKLI 160
>pdb|2VGM|A Chain A, Structure Of Yeast Dom34 : A Protein Related To
Translation Termination Factor Erf1 And Involved In
No-Go Decay.
pdb|3IZQ|0 Chain 0, Structure Of The Dom34-Hbs1-Gdpnp Complex Bound To A
Translating Ribosome
pdb|3J16|A Chain A, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 386
Score = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 20/107 (18%)
Query: 227 LSQSGMFDPCLMAKIL---------KVLD---------ISYGGVSGFNQAIE--LSSDVI 266
L G + LM KI K+LD S G + G N+ ++ L + +
Sbjct: 213 LCSPGFYAKILMDKIFQYAEEEHNKKILDNKGMFFIAHCSTGYLQGINEVLKNPLYASKL 272
Query: 267 ANVNVLKEKRVIGKFFEEIGQDTGKFVVGVDDSVKALEMGAIHTLIV 313
+ KE V+ +F + +D K G + VKA E GAI L++
Sbjct: 273 QDTKYSKEIMVMDEFLLHLNKDDDKAWYGEKEVVKAAEYGAISYLLL 319
>pdb|2XA8|H Chain H, Crystal Structure Of The Fab Domain Of Omalizumab At 2.41a
Length = 219
Score = 28.5 bits (62), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 28/134 (20%), Positives = 52/134 (38%), Gaps = 19/134 (14%)
Query: 100 VTEDGEEKKFAHDLVPFKPINSSLYVCDSSFHTEAYGYIIIDGNGTLIGTLCGSSREVVL 159
++ D + F + + ++++Y C H + + + G GTL+ T+ +S +
Sbjct: 70 ISRDDSKNTFYLQMNSLRAEDTAVYYCARGSHYFGHWHFAVWGQGTLV-TVSSASTKGPS 128
Query: 160 KFTVDLPKKHGRGGQSALRFSRLRVEKRHNYLREAAELATKCFIDPATSQPNVTGLILAG 219
F + K GG +AL L F +P T N +G + +G
Sbjct: 129 VFPLAPSSKSTSGGTAAL-----------------GCLVKDYFPEPVTVSWN-SGALTSG 170
Query: 220 SAEFKTELSQSGMF 233
F L SG++
Sbjct: 171 VHTFPAVLQSSGLY 184
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 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,911,327
Number of Sequences: 62578
Number of extensions: 556390
Number of successful extensions: 1730
Number of sequences better than 100.0: 34
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1692
Number of HSP's gapped (non-prelim): 37
length of query: 428
length of database: 14,973,337
effective HSP length: 102
effective length of query: 326
effective length of database: 8,590,381
effective search space: 2800464206
effective search space used: 2800464206
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)