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= 014874
(416 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2B64|Y Chain Y, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf1
From A Crystal Structure Of The Whole Ribosomal Complex.
This File Contains The 30s Subunit, Trnas, Mrna And
Release Factor Rf1 From A Crystal Structure Of The Whole
Ribosomal Complex". The Entire Crystal Structure
Contains One 70s Ribosome, Trnas, Mrna And Release
Factor Rf1 And Is Described In Remark 400.
pdb|3D5A|X Chain X, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of One 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes As Described In Remark 400.
pdb|3D5C|X Chain X, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400.
pdb|3MR8|V Chain V, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3mr8 Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 3ms1.
Molecule B In The Same Asymmetric Unit Is Deposited As
3mrz (50s) And 3ms0 (30s).
pdb|3MS0|V Chain V, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3ms0 Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 3mrz.
Molecule A In The Same Asymmetric Unit Is Deposited As
3mr8 (30s) And 3ms1 (50s)
Length = 354
Score = 274 bits (701), Expect = 5e-74, Method: Compositional matrix adjust.
Identities = 136/358 (37%), Positives = 221/358 (61%), Gaps = 5/358 (1%)
Query: 54 LITKLESAAKTWKDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEKQLEE 113
++ KL+ + +++L L+DPEV+ + YQ L++ AE+ EV+ R+++ + LE+
Sbjct: 1 MLDKLDRLEEEYRELEALLSDPEVLKDKGRYQSLSRRYAEMGEVIGLIREYRKVLEDLEQ 60
Query: 114 SRALAKENGNDEEMAEMIAXXXXXXXXXXXXXXXXXXXXXXPSDPLDARNIMLEVRAGAG 173
+ +L +D E+ EM P DP+D R+ ++E+RAG G
Sbjct: 61 AESLL----DDPELKEMAKAEREALLARKEALEKELERHLLPKDPMDERDAIVEIRAGTG 116
Query: 174 GDEAGIWAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYESG 233
G+EA ++A DL MY +++E+ ++ ++ S + GGF VV E++G Y KYESG
Sbjct: 117 GEEAALFARDLFNMYLRFAEEMGFETEVLDSHPTDLGGFSKVVFEVRGPGAYGTFKYESG 176
Query: 234 VHRVQRVPQTEAQGRVHTSTATVAIMPEADEVEVVIDPKDIELTTARSGGAGGQNVNKVE 293
VHRVQRVP TE QGR+HTSTATVA++P+A+E + ++ +I + R+ G GGQ VN +
Sbjct: 177 VHRVQRVPVTETQGRIHTSTATVAVLPKAEEEDFALNMDEIRIDVMRASGPGGQGVNTTD 236
Query: 294 TAIDLFHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQRLSQVGTG 353
+A+ + H PTGI + C + R+Q++N+ +AL +LR++L E+K E+ E++R RL+Q+GTG
Sbjct: 237 SAVRVVHLPTGIMVTCQDSRSQIKNREKALMILRSRLLEMKRAEEAERLRKTRLAQIGTG 296
Query: 354 ARAEKIRTYNYKDNRVTDHRLKM-NFELTSFLDGNIDNAVQSCAAMEQKELLEELAES 410
R+EKIRTYN+ +RVTDHR+ +L L G++ +++ +Q+ L LAE
Sbjct: 297 ERSEKIRTYNFPQSRVTDHRIGFTTHDLEGVLSGHLTPILEALKRADQERQLAALAEG 354
>pdb|1ZBT|A Chain A, Crystal Structure Of Peptide Chain Release Factor 1 (rf-1)
(smu.1085) From Streptococcus Mutans At 2.34 A
Resolution
Length = 371
Score = 269 bits (687), Expect = 2e-72, Method: Compositional matrix adjust.
Identities = 148/355 (41%), Positives = 216/355 (60%), Gaps = 1/355 (0%)
Query: 54 LITKLESAAKTWKDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEKQLEE 113
+ +L++ +++L L+DP+VVS+ + +L++ A E V+ YR++K + + +
Sbjct: 15 IYDQLQAVEDRYEELGELLSDPDVVSDTKRFXELSREEANSRETVAVYREYKQVVQNIAD 74
Query: 114 SRALAKENGNDEEMAEMIAXXXXXXXXXXXXXXXXXXXXXXPSDPLDARNIMLEVRAGAG 173
++ K+ D E+ E P DP D +NI+LE+R AG
Sbjct: 75 AQEXIKDASGDPELEEXAKEELKNSKVAKEEYEEKLRFLLLPKDPNDDKNIILEIRGAAG 134
Query: 174 GDEAGIWAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYESG 233
GDEA ++AGDL+ YQKY+E WK + +S GG K VV + G VYSKLKYESG
Sbjct: 135 GDEAALFAGDLLNXYQKYAENQGWKFEVXEASANGVGGLKEVVAXVSGQSVYSKLKYESG 194
Query: 234 VHRVQRVPQTEAQGRVHTSTATVAIMPEADEVEVVIDPKDIELTTARSGGAGGQNVNKVE 293
HRVQRVP TE+QGRVHTSTATV + PE +EVE IDPKD+ + + GAGGQNVNKV
Sbjct: 195 AHRVQRVPVTESQGRVHTSTATVLVXPEVEEVEYEIDPKDLRVDIYHASGAGGQNVNKVA 254
Query: 294 TAIDLFHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQRLSQVGTG 353
TA+ + H PT I++ EERTQ +N+ +A +++RA++ + + Q++ +R S VGTG
Sbjct: 255 TAVRIIHLPTNIKVEXQEERTQQKNRDKAXKIIRARVADHFAQIAQDEQDAERKSTVGTG 314
Query: 354 ARAEKIRTYNYKDNRVTDHRLKMNFE-LTSFLDGNIDNAVQSCAAMEQKELLEEL 407
R+E+IRTYN+ NRVTDHR+ + + L S L G +D + + +Q + LEEL
Sbjct: 315 DRSERIRTYNFPQNRVTDHRIGLTLQKLDSILSGKLDEVIDALILYDQTQKLEEL 369
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 360
Score = 268 bits (686), Expect = 3e-72, Method: Compositional matrix adjust.
Identities = 132/360 (36%), Positives = 220/360 (61%), Gaps = 6/360 (1%)
Query: 52 PYLITKLESAAKTWKDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEKQL 111
P ++ KLE+ + +++ L D + +++ ++ L++ A+L +V + ++ ++ +
Sbjct: 3 PSIVAKLEALHERHEEVQALLGDAQTIADQERFRALSREYAQLSDVSRCFTDWQQVQEDI 62
Query: 112 EESRALAKENGNDEEMAEMIAXXXXXXXXXXXXXXXXXXXXXXPSDPLDARNIMLEVRAG 171
E ++ + +D EM EM P DP D RN LEVRAG
Sbjct: 63 ETAQMML----DDPEMREMAQDELREAKEKSEQLEQQLQVLLLPKDPDDERNAFLEVRAG 118
Query: 172 AGGDEAGIWAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYE 231
GGDEA ++AGDL RMY +Y+E W+ ++S+SE E GG+K ++ +I G+ VY +LK+E
Sbjct: 119 TGGDEAALFAGDLFRMYSRYAEARRWRVEIMSASEGEHGGYKEIIAKISGDGVYGRLKFE 178
Query: 232 SGVHRVQRVPQTEAQGRVHTSTATVAIMPEADEVEVV-IDPKDIELTTARSGGAGGQNVN 290
SG HRVQRVP TE+QGR+HTS TVA+MPE + E+ ++P D+ + T RS GAGGQ+VN
Sbjct: 179 SGGHRVQRVPATESQGRIHTSACTVAVMPELPDAELPDVNPADLRIDTFRSSGAGGQHVN 238
Query: 291 KVETAIDLFHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQRLSQV 350
++AI + H PTGI + C +ER+Q +NK++AL +L A+++ ++ ++Q+ + R + +
Sbjct: 239 TTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLL 298
Query: 351 GTGARAEKIRTYNYKDNRVTDHRLKMN-FELTSFLDGNIDNAVQSCAAMEQKELLEELAE 409
G+G R+++ RTYN+ RVTDHR+ + + L ++G +D ++ Q + L L+E
Sbjct: 299 GSGDRSDRNRTYNFPQGRVTDHRINLTLYRLDEVMEGKLDMLIEPIIQEHQADQLAALSE 358
>pdb|1RQ0|A Chain A, Crystal Structure Of Peptide Releasing Factor 1
pdb|1RQ0|B Chain B, Crystal Structure Of Peptide Releasing Factor 1
pdb|1RQ0|C Chain C, Crystal Structure Of Peptide Releasing Factor 1
Length = 342
Score = 248 bits (633), Expect = 4e-66, Method: Compositional matrix adjust.
Identities = 118/250 (47%), Positives = 172/250 (68%), Gaps = 2/250 (0%)
Query: 165 MLEVRAGAGGDEAGIWAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRV 224
++E+R G GG+EA ++A DL RMY +Y+E+ W + E + GG + VV +KG
Sbjct: 89 IVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKNA 148
Query: 225 YSKLKYESGVHRVQRVPQTEAQGRVHTSTATVAIMPEADEVEVVIDPKDIELTTARSGGA 284
Y LKYESGVHRVQRVP TE+ GR+HTSTATVA++PE +E ++ I P+D+++ T R+ G
Sbjct: 149 YGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGH 208
Query: 285 GGQNVNKVETAIDLFHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRT 344
GGQ VNK E+A+ + H PTGI + C ER+Q QNK AL++LRA+LY+++ +++ +I
Sbjct: 209 GGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREISQ 268
Query: 345 QRLSQVGTGARAEKIRTYNYKDNRVTDHRLKM-NFELTSFLDGNIDNAVQSCAAMEQKEL 403
+R SQ+GTG R+EKIRTYN+ NRVTDHR+ ++ L LDG++D + + +
Sbjct: 269 KRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDEIISKLIEHDIENN 328
Query: 404 LEELAESVGA 413
LEE+ +GA
Sbjct: 329 LEEVL-GIGA 337
>pdb|2FVO|A Chain A, Docking Of The Modified Rf1 X-ray Structure Into The Low
Resolution Cryo-em Map Of E.coli 70s Ribosome Bound With
Rf1
Length = 333
Score = 248 bits (632), Expect = 5e-66, Method: Compositional matrix adjust.
Identities = 116/244 (47%), Positives = 169/244 (69%), Gaps = 1/244 (0%)
Query: 165 MLEVRAGAGGDEAGIWAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRV 224
++E+R G GG+EA ++A DL RMY +Y+E+ W + E + GG + VV +KG
Sbjct: 89 IVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKNA 148
Query: 225 YSKLKYESGVHRVQRVPQTEAQGRVHTSTATVAIMPEADEVEVVIDPKDIELTTARSGGA 284
Y LKYESGVHRVQRVP TE+ GR+HTSTATVA++PE +E ++ I P+D+++ T R+ G
Sbjct: 149 YGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGH 208
Query: 285 GGQNVNKVETAIDLFHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRT 344
GGQ VNK E+A+ + H PTGI + C ER+Q QNK AL++LRA+LY+++ +++ +I
Sbjct: 209 GGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREISQ 268
Query: 345 QRLSQVGTGARAEKIRTYNYKDNRVTDHRLKM-NFELTSFLDGNIDNAVQSCAAMEQKEL 403
+R SQ+GTG R+EKIRTYN+ NRVTDHR+ ++ L LDG++D + + +
Sbjct: 269 KRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDEIISKLIEHDIENN 328
Query: 404 LEEL 407
LEE+
Sbjct: 329 LEEV 332
>pdb|1MI6|A Chain A, Docking Of The Modified Rf2 X-Ray Structure Into The Low
Resolution Cryo-Em Map Of Rf2 E.Coli 70s Ribosome
Length = 365
Score = 172 bits (436), Expect = 3e-43, Method: Compositional matrix adjust.
Identities = 103/334 (30%), Positives = 185/334 (55%), Gaps = 12/334 (3%)
Query: 66 KDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEKQLEESRALAKENGNDE 125
++++ +L P+V + P Q L + + L+ VV T + K + + LA E ++E
Sbjct: 35 EEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEADDEE 94
Query: 126 EMAEMIAXXXXXXXXXXXXXXXXXXXXXXPSDPLDARNIMLEVRAGAGGDEAGIWAGDLV 185
E +A S D+ + L+++AG+GG EA WA L
Sbjct: 95 TFNEAVAELDALEEKLAQLEFRRMF-----SGEYDSADCYLDIQAGSGGTEAQDWASMLE 149
Query: 186 RMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYESGVHRVQRVPQTEA 245
RMY +++E +K +I SE E G K+V ++I G+ Y L+ E+GVHR+ R ++
Sbjct: 150 RMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDS 209
Query: 246 QGRVHTSTATVAIMPEA-DEVEVVIDPKDIELTTARSGGAGGQNVNKVETAIDLFHKPTG 304
GR HTS ++ + PE D++++ I+P D+ + R+ GAGGQ+VN+ E+A+ + H PTG
Sbjct: 210 GGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTG 269
Query: 305 IRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQ--QEKIRTQRLSQVGTGARAEKIRTY 362
I C +R+Q +NK +A++ ++AKLYE++++++ +++ S +G G+ +IR+Y
Sbjct: 270 IVTQCQNDRSQHKNKDQAMKQMKAKLYEVEMQKKNAEKQAMEDNKSDIGWGS---QIRSY 326
Query: 363 NYKDNRVTDHRLKMNFELT-SFLDGNIDNAVQSC 395
D+R+ D R + T + LDG++D +++
Sbjct: 327 VLDDSRIKDLRTGVETRNTQAVLDGSLDQFIEAS 360
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 172 bits (435), Expect = 4e-43, Method: Compositional matrix adjust.
Identities = 103/334 (30%), Positives = 185/334 (55%), Gaps = 12/334 (3%)
Query: 66 KDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEKQLEESRALAKENGNDE 125
++++ +L P+V + P Q L + + L+ VV T + K + + LA E ++E
Sbjct: 35 EEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEADDEE 94
Query: 126 EMAEMIAXXXXXXXXXXXXXXXXXXXXXXPSDPLDARNIMLEVRAGAGGDEAGIWAGDLV 185
E +A S D+ + L+++AG+GG EA WA L
Sbjct: 95 TFNEAVAELDALEEKLAQLEFRRMF-----SGEYDSADCYLDIQAGSGGTEAQDWASMLE 149
Query: 186 RMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYESGVHRVQRVPQTEA 245
RMY +++E +K +I SE E G K+V ++I G+ Y L+ E+GVHR+ R ++
Sbjct: 150 RMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDS 209
Query: 246 QGRVHTSTATVAIMPEA-DEVEVVIDPKDIELTTARSGGAGGQNVNKVETAIDLFHKPTG 304
GR HTS ++ + PE D++++ I+P D+ + R+ GAGGQ+VN+ E+A+ + H PTG
Sbjct: 210 GGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPTG 269
Query: 305 IRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQ--QEKIRTQRLSQVGTGARAEKIRTY 362
I C +R+Q +NK +A++ ++AKLYE++++++ +++ S +G G+ +IR+Y
Sbjct: 270 IVTQCQNDRSQHKNKDQAMKQMKAKLYELEMQKKNAEKQAMEDNKSDIGWGS---QIRSY 326
Query: 363 NYKDNRVTDHRLKMNFELT-SFLDGNIDNAVQSC 395
D+R+ D R + T + LDG++D +++
Sbjct: 327 VLDDSRIKDLRTGVETRNTQAVLDGSLDQFIEAS 360
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 166 bits (420), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 103/334 (30%), Positives = 182/334 (54%), Gaps = 12/334 (3%)
Query: 66 KDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEKQLEESRALAKENGNDE 125
++++ +L P+V + P Q L + + L+ VV T + K + + LA E ++E
Sbjct: 35 EEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQXKQGLEDVSGLLELAVEADDEE 94
Query: 126 EMAEMIAXXXXXXXXXXXXXXXXXXXXXXPSDPLDARNIMLEVRAGAGGDEAGIWAGDLV 185
E +A S D+ + L+++AG+GG EA WA L
Sbjct: 95 TFNEAVAELDALEEKLAQLEFRRXF-----SGEYDSADCYLDIQAGSGGTEAQDWASXLE 149
Query: 186 RMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYESGVHRVQRVPQTEA 245
R Y +++E +K +I SE E G K+V ++I G+ Y L+ E+GVHR+ R ++
Sbjct: 150 RXYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDS 209
Query: 246 QGRVHTSTATVAIMPEA-DEVEVVIDPKDIELTTARSGGAGGQNVNKVETAIDLFHKPTG 304
GR HTS ++ + PE D++++ I+P D+ + R+ GAGGQ+VN+ E+A+ + H PTG
Sbjct: 210 GGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTG 269
Query: 305 IRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQ--QEKIRTQRLSQVGTGARAEKIRTY 362
I C +R+Q +NK +A + +AKLYE++ +++ +++ S +G G+ +IR+Y
Sbjct: 270 IVTQCQNDRSQHKNKDQAXKQXKAKLYEVEXQKKNAEKQAXEDNKSDIGWGS---QIRSY 326
Query: 363 NYKDNRVTDHRLKMNFELT-SFLDGNIDNAVQSC 395
D+R+ D R + T + LDG++D +++
Sbjct: 327 VLDDSRIKDLRTGVETRNTQAVLDGSLDQFIEAS 360
>pdb|3F1E|X Chain X, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of One
70s Ribosome. The Entire Crystal Structure Contains Two
70s Ribosomes As Described In Remark 400.
pdb|3F1G|X Chain X, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400
Length = 378
Score = 134 bits (336), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 105/344 (30%), Positives = 176/344 (51%), Gaps = 26/344 (7%)
Query: 66 KDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFK-DCEKQLEESRALAKENGND 124
K+L +L DP + ++P +K++Q A L V T+R + D + LE L E
Sbjct: 40 KELERRLEDPSLWNDPEAARKVSQEAARLRRTVDTFRSLESDLQGLLELMEELPAEEREA 99
Query: 125 -----EEMAEMIAXXXXXXXXXXXXXXXXXXXXXXPSDPLDARNIMLEVRAGAGGDEAGI 179
EE A+ + P +N +L ++ GAGG EA
Sbjct: 100 LKPELEEAAKKLDELYHQTLLNF---------------PHAEKNAILTIQPGAGGTEACD 144
Query: 180 WAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYESGVHRVQR 239
WA L+RMY +++E+ ++ ++ + + G + +KG Y L E+GVHR+ R
Sbjct: 145 WAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVR 204
Query: 240 VPQTEAQGRVHTSTA-TVAIMPEADEVEVVIDPKDIELTTARSGGAGGQNVNKVETAIDL 298
+A GR HTS A I +EVEVV+ P+++ + R+ G GGQ VN ++A+ +
Sbjct: 205 PSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRV 264
Query: 299 FHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQRLSQVGTGARAEK 358
H PTGI + C R+Q++NK AL++L+A+LYE++ ++++E+++ R +V +
Sbjct: 265 VHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKREEELKALR-GEVRPIEWGSQ 323
Query: 359 IRTYNYKDNRVTDHRLK-MNFELTSFLDGNIDNAVQSCAAMEQK 401
IR+Y N V DHR M + + LDG++ + + A +E K
Sbjct: 324 IRSYVLDKNYVKDHRTGLMRHDPENVLDGDLMDLI--WAGLEWK 365
>pdb|2WH1|Y Chain Y, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|2WH3|Y Chain Y, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome). This File Contains The
30s Subunit
Length = 351
Score = 134 bits (336), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 105/344 (30%), Positives = 176/344 (51%), Gaps = 26/344 (7%)
Query: 66 KDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFK-DCEKQLEESRALAKENGND 124
K+L +L DP + ++P +K++Q A L V T+R + D + LE L E
Sbjct: 22 KELERRLEDPSLWNDPEAARKVSQEAARLRRTVDTFRSLESDLQGLLELMEELPAEEREA 81
Query: 125 -----EEMAEMIAXXXXXXXXXXXXXXXXXXXXXXPSDPLDARNIMLEVRAGAGGDEAGI 179
EE A+ + P +N +L ++ GAGG EA
Sbjct: 82 LKPELEEAAKKLDELYHQTLLNF---------------PHAEKNAILTIQPGAGGTEACD 126
Query: 180 WAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYESGVHRVQR 239
WA L+RMY +++E+ ++ ++ + + G + +KG Y L E+GVHR+ R
Sbjct: 127 WAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVR 186
Query: 240 VPQTEAQGRVHTSTA-TVAIMPEADEVEVVIDPKDIELTTARSGGAGGQNVNKVETAIDL 298
+A GR HTS A I +EVEVV+ P+++ + R+ G GGQ VN ++A+ +
Sbjct: 187 PSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRV 246
Query: 299 FHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQRLSQVGTGARAEK 358
H PTGI + C R+Q++NK AL++L+A+LYE++ ++++E+++ R +V +
Sbjct: 247 VHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKREEELKALR-GEVEPIEWGSQ 305
Query: 359 IRTYNYKDNRVTDHRLK-MNFELTSFLDGNIDNAVQSCAAMEQK 401
IR+Y N V DHR M + + LDG++ + + A +E K
Sbjct: 306 IRSYVLDKNYVKDHRTGLMRHDPENVLDGDLMDLI--WAGLEWK 347
>pdb|2X9R|Y Chain Y, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9T|Y Chain Y, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
Length = 351
Score = 134 bits (336), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 105/344 (30%), Positives = 176/344 (51%), Gaps = 26/344 (7%)
Query: 66 KDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFK-DCEKQLEESRALAKENGND 124
K+L +L DP + ++P +K++Q A L V T+R + D + LE L E
Sbjct: 22 KELERRLEDPSLWNDPEAARKVSQEAARLRRTVDTFRSLESDLQGLLELMEELPAEEREA 81
Query: 125 -----EEMAEMIAXXXXXXXXXXXXXXXXXXXXXXPSDPLDARNIMLEVRAGAGGDEAGI 179
EE A+ + P +N +L ++ GAGG EA
Sbjct: 82 LKPELEEAAKKLDELYHQTLLNF---------------PHAEKNAILTIQPGAGGTEACD 126
Query: 180 WAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYESGVHRVQR 239
WA L+RMY +++E+ ++ ++ + + G + +KG Y L E+GVHR+ R
Sbjct: 127 WAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVR 186
Query: 240 VPQTEAQGRVHTSTA-TVAIMPEADEVEVVIDPKDIELTTARSGGAGGQNVNKVETAIDL 298
+A GR HTS A I +EVEVV+ P+++ + R+ G GGQ VN ++A+ +
Sbjct: 187 PSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRV 246
Query: 299 FHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQRLSQVGTGARAEK 358
H PTGI + C R+Q++NK AL++L+A+LYE++ ++++E+++ R +V +
Sbjct: 247 VHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKREEELKALR-GEVRPIEWGSQ 305
Query: 359 IRTYNYKDNRVTDHRLK-MNFELTSFLDGNIDNAVQSCAAMEQK 401
IR+Y N V DHR M + + LDG++ + + A +E K
Sbjct: 306 IRSYVLDKNYVKDHRTGLMRHDPENVLDGDLMDLI--WAGLEWK 347
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 133 bits (335), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 105/344 (30%), Positives = 176/344 (51%), Gaps = 26/344 (7%)
Query: 66 KDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFK-DCEKQLEESRALAKENGND 124
K+L +L DP + ++P +K++Q A L V T+R + D + LE L E
Sbjct: 27 KELERRLEDPSLWNDPEAARKVSQEAARLRRTVDTFRSLESDLQGLLELMEELPAEEREA 86
Query: 125 -----EEMAEMIAXXXXXXXXXXXXXXXXXXXXXXPSDPLDARNIMLEVRAGAGGDEAGI 179
EE A+ + P +N +L ++ GAGG EA
Sbjct: 87 LKPELEEAAKKLDELYHQTLLNF---------------PHAEKNAILTIQPGAGGTEACD 131
Query: 180 WAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYESGVHRVQR 239
WA L+RMY +++E+ ++ ++ + + G + +KG Y L E+GVHR+ R
Sbjct: 132 WAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVR 191
Query: 240 VPQTEAQGRVHTSTA-TVAIMPEADEVEVVIDPKDIELTTARSGGAGGQNVNKVETAIDL 298
+A GR HTS A I +EVEVV+ P+++ + R+ G GGQ VN ++A+ +
Sbjct: 192 PSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRV 251
Query: 299 FHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQRLSQVGTGARAEK 358
H PTGI + C R+Q++NK AL++L+A+LYE++ ++++E+++ R +V +
Sbjct: 252 VHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKREEELKALR-GEVRPIEWGSQ 310
Query: 359 IRTYNYKDNRVTDHRLK-MNFELTSFLDGNIDNAVQSCAAMEQK 401
IR+Y N V DHR M + + LDG++ + + A +E K
Sbjct: 311 IRSYVLDKNYVKDHRTGLMRHDPENVLDGDLMDLI--WAGLEWK 352
>pdb|2B9M|Y Chain Y, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf2
From A Crystal Structure Of The Whole Ribosomal Complex.
This File Contains The 30s Ribosomal Subunit, Trnas,
Mrna And Release Factor Rf2 From A Crystal Structure Of
The Whole Ribosomal Complex". The Entire Crystal
Structure Contains One 70s Ribosome, Trnas, Mrna And
Release Factor Rf2 And Is Described In Remark 400
Length = 365
Score = 133 bits (335), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 105/344 (30%), Positives = 176/344 (51%), Gaps = 26/344 (7%)
Query: 66 KDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFK-DCEKQLEESRALAKENGND 124
K+L +L DP + ++P +K++Q A L V T+R + D + LE L E
Sbjct: 27 KELERRLEDPSLWNDPEAARKVSQEAARLRRTVDTFRSLESDLQGLLELMEELPAEEREA 86
Query: 125 -----EEMAEMIAXXXXXXXXXXXXXXXXXXXXXXPSDPLDARNIMLEVRAGAGGDEAGI 179
EE A+ + P +N +L ++ GAGG EA
Sbjct: 87 LKPELEEAAKKLDELYHQTLLNF---------------PHAEKNAILTIQPGAGGTEACD 131
Query: 180 WAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYESGVHRVQR 239
WA L+RMY +++E+ ++ ++ + + G + +KG Y L E+GVHR+ R
Sbjct: 132 WAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVR 191
Query: 240 VPQTEAQGRVHTSTA-TVAIMPEADEVEVVIDPKDIELTTARSGGAGGQNVNKVETAIDL 298
+A GR HTS A I +EVEVV+ P+++ + R+ G GGQ VN ++A+ +
Sbjct: 192 PSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRV 251
Query: 299 FHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQRLSQVGTGARAEK 358
H PTGI + C R+Q++NK AL++L+A+LYE++ ++++E+++ R +V +
Sbjct: 252 VHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKREEELKALR-GEVRPIEWGSQ 310
Query: 359 IRTYNYKDNRVTDHRLK-MNFELTSFLDGNIDNAVQSCAAMEQK 401
IR+Y N V DHR M + + LDG++ + + A +E K
Sbjct: 311 IRSYVLDKNYVKDHRTGLMRHDPENVLDGDLMDLI--WAGLEWK 352
>pdb|2RSM|A Chain A, Solution Structure And Sirna-Mediated Knockdown Analysis
Of The Mitochondrial Disease-Related Protein C12orf65
(Ict2)
Length = 115
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%)
Query: 269 IDPKDIELTTARSGGAGGQNVNKVETAIDLFHKPTGIRIFCTEERTQLQNKSRALQLLRA 328
++ ++E + G GGQ NK + L H P+GI + C + R+ QN+ A ++L+
Sbjct: 43 LNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRKIARKVLQE 102
Query: 329 KL 330
K+
Sbjct: 103 KV 104
>pdb|2JVA|A Chain A, Nmr Solution Structure Of Peptidyl-Trna Hydrolase Domain
Protein From Pseudomonas Syringae Pv. Tomato. Northeast
Structural Genomics Consortium Target Psr211
Length = 108
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/26 (65%), Positives = 21/26 (80%)
Query: 273 DIELTTARSGGAGGQNVNKVETAIDL 298
+IELT R+ GAGGQNVNKV +A+ L
Sbjct: 14 EIELTAIRAQGAGGQNVNKVSSAMHL 39
>pdb|4DH9|Y Chain Y, Crystal Structure Of Yaej Bound To The 70s Ribosome
Length = 140
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 22/33 (66%)
Query: 266 EVVIDPKDIELTTARSGGAGGQNVNKVETAIDL 298
V I ++E+T R+ GAGGQ+VNK TAI L
Sbjct: 7 HVAIPDGELEITAIRAQGAGGQHVNKTSTAIHL 39
>pdb|2JY9|A Chain A, Nmr Structure Of Putative Trna Hydrolase Domain From
Salmonella Typhimurium. Northeast Structural Genomics
Consortium Target Str220
Length = 148
Score = 35.8 bits (81), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 22/32 (68%)
Query: 267 VVIDPKDIELTTARSGGAGGQNVNKVETAIDL 298
V I ++E+T R+ GAGGQ+VNK +AI L
Sbjct: 8 VSIADNELEITAIRAQGAGGQHVNKTSSAIHL 39
>pdb|1U3B|A Chain A, Auto-Inhibition Mechanism Of X11sMINTS FAMILY SCAFFOLD
Proteins Revealed By The Closed Conformation Of The
Tandem Pdz Domains
Length = 185
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 9/74 (12%)
Query: 188 YQ-KYSEQNSWKCTLISSSEAEKGGFKTV--VMEIKGNRVYSKLKYESGVHRVQRVPQTE 244
YQ +S QN C+L+ AE+GG + ++EI G V + +E VH + +
Sbjct: 105 YQLGFSVQNGIICSLMRGGIAERGGVRVGHRIIEINGQSVVAT-PHEKIVHIL-----SN 158
Query: 245 AQGRVHTSTATVAI 258
A G +H T A+
Sbjct: 159 AVGEIHMKTMPAAM 172
>pdb|1Z47|A Chain A, Structure Of The Atpase Subunit Cysa Of The Putative
Sulfate Atp-Binding Cassette (Abc) Transporter From
Alicyclobacillus Acidocaldarius
pdb|1Z47|B Chain B, Structure Of The Atpase Subunit Cysa Of The Putative
Sulfate Atp-Binding Cassette (Abc) Transporter From
Alicyclobacillus Acidocaldarius
Length = 355
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 247 GRVHTSTATVAIMP---EADEVEVVIDPKDIELTTA 279
GR+ + A + + P E EV VV+ PKD+EL A
Sbjct: 259 GRIEVAGAALPVDPAVSEGSEVAVVVRPKDVELQPA 294
>pdb|1J26|A Chain A, Solution Structure Of A Putative Peptidyl-Trna Hydrolase
Domain In A Mouse Hypothetical Protein
Length = 112
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 274 IELTTARSGGAGGQNVNKVETAIDL-FH 300
+ ++ RS G GGQNVNKV + ++ FH
Sbjct: 22 LSISYCRSSGPGGQNVNKVNSKAEVRFH 49
>pdb|3Q46|A Chain A, Magnesium Activated Inorganic Pyrophosphatase From
Thermococcus Thioreducens Bound To Hydrolyzed Product At
0.99 Angstrom Resolution
Length = 178
Score = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 6/67 (8%)
Query: 44 PKLICMAEPYLITKLE-SAAKTWKDLSVKLADPEVVSNPSEYQKLAQ-SMAELDEVVSTY 101
P I A P I K+E S K WK L+V + DP ++++ ++ A LDE+ +
Sbjct: 82 PLTIIEARPIGIMKMEDSGDKDWKVLAVPVEDPYF----NDWKDISDVPKAFLDEIAHFF 137
Query: 102 RKFKDCE 108
+++K+ +
Sbjct: 138 QRYKELQ 144
>pdb|3I98|A Chain A, X-Ray Crystallographic Structure Of Inorganic
Pyrophosphatase At 298k From Archaeon Thermococcus
Thioreducens
pdb|3I98|B Chain B, X-Ray Crystallographic Structure Of Inorganic
Pyrophosphatase At 298k From Archaeon Thermococcus
Thioreducens
pdb|3I98|C Chain C, X-Ray Crystallographic Structure Of Inorganic
Pyrophosphatase At 298k From Archaeon Thermococcus
Thioreducens
pdb|3I98|D Chain D, X-Ray Crystallographic Structure Of Inorganic
Pyrophosphatase At 298k From Archaeon Thermococcus
Thioreducens
pdb|3I98|E Chain E, X-Ray Crystallographic Structure Of Inorganic
Pyrophosphatase At 298k From Archaeon Thermococcus
Thioreducens
pdb|3I98|F Chain F, X-Ray Crystallographic Structure Of Inorganic
Pyrophosphatase At 298k From Archaeon Thermococcus
Thioreducens
pdb|3Q4W|A Chain A, The Structure Of Archaeal Inorganic Pyrophosphatase In
Complex With Substrate
pdb|3Q5V|A Chain A, The Structure Of Inorganic Pyrophosphatase From
Thermococcus Thioreducens In Complex With Magnesium And
Sulfate
pdb|3Q5V|B Chain B, The Structure Of Inorganic Pyrophosphatase From
Thermococcus Thioreducens In Complex With Magnesium And
Sulfate
pdb|3Q9M|A Chain A, The Structure Archaeal Inorganic Pyrophosphatase In
Complex With Pyrophosphate
pdb|3Q9M|B Chain B, The Structure Archaeal Inorganic Pyrophosphatase In
Complex With Pyrophosphate
pdb|3Q9M|C Chain C, The Structure Archaeal Inorganic Pyrophosphatase In
Complex With Pyrophosphate
pdb|3Q3L|A Chain A, The Neutron Crystallographic Structure Of Inorganic
Pyrophosphatase From Thermococcus Thioreducens
pdb|3Q3L|B Chain B, The Neutron Crystallographic Structure Of Inorganic
Pyrophosphatase From Thermococcus Thioreducens
pdb|3Q3L|C Chain C, The Neutron Crystallographic Structure Of Inorganic
Pyrophosphatase From Thermococcus Thioreducens
pdb|3Q3L|D Chain D, The Neutron Crystallographic Structure Of Inorganic
Pyrophosphatase From Thermococcus Thioreducens
pdb|3Q3L|E Chain E, The Neutron Crystallographic Structure Of Inorganic
Pyrophosphatase From Thermococcus Thioreducens
pdb|3Q3L|F Chain F, The Neutron Crystallographic Structure Of Inorganic
Pyrophosphatase From Thermococcus Thioreducens
pdb|3R5U|A Chain A, The Structure Of Manganese Bound Thermococcus Thioreducens
Inorganic Pyrophosphatase
pdb|3R5U|B Chain B, The Structure Of Manganese Bound Thermococcus Thioreducens
Inorganic Pyrophosphatase
pdb|3R5V|A Chain A, The Structure Of Calcium Bound Thermococcus Thioreducens
Inorganic Pyrophosphatase At 298k
pdb|3R5V|B Chain B, The Structure Of Calcium Bound Thermococcus Thioreducens
Inorganic Pyrophosphatase At 298k
pdb|3R5V|C Chain C, The Structure Of Calcium Bound Thermococcus Thioreducens
Inorganic Pyrophosphatase At 298k
pdb|3R5V|D Chain D, The Structure Of Calcium Bound Thermococcus Thioreducens
Inorganic Pyrophosphatase At 298k
pdb|3R5V|E Chain E, The Structure Of Calcium Bound Thermococcus Thioreducens
Inorganic Pyrophosphatase At 298k
pdb|3R5V|F Chain F, The Structure Of Calcium Bound Thermococcus Thioreducens
Inorganic Pyrophosphatase At 298k
Length = 178
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 6/67 (8%)
Query: 44 PKLICMAEPYLITKLE-SAAKTWKDLSVKLADPEVVSNPSEYQKLAQ-SMAELDEVVSTY 101
P I A P I K+E S K WK L+V + DP ++++ ++ A LDE+ +
Sbjct: 82 PLTIIEARPIGIMKMEDSGDKDWKVLAVPVEDPYF----NDWKDISDVPKAFLDEIAHFF 137
Query: 102 RKFKDCE 108
+++K+ +
Sbjct: 138 QRYKELQ 144
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
0.313 0.128 0.355
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,875,867
Number of Sequences: 62578
Number of extensions: 400768
Number of successful extensions: 867
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 831
Number of HSP's gapped (non-prelim): 32
length of query: 416
length of database: 14,973,337
effective HSP length: 101
effective length of query: 315
effective length of database: 8,652,959
effective search space: 2725682085
effective search space used: 2725682085
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)