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= 012936
(453 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 301 bits (772), Expect = 3e-82, Method: Compositional matrix adjust.
Identities = 149/348 (42%), Positives = 220/348 (63%), Gaps = 2/348 (0%)
Query: 98 VIKKRLQWKNLNVRLNLLSAELNKPNLWDDPVHAGRISREHGSLMGKMKEVKAFEQELLE 157
V++ L + RL ++AEL +P++W++P A + +E SL + + +Q L +
Sbjct: 20 VLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLED 79
Query: 158 HIDMIKLAREENDTXXXXXXXXXXXTMRRKSKEKELDALLSGELDPCSCYIEVQAGAGGT 217
+++LA E +D + K + E + SGE D CY+++QAG+GGT
Sbjct: 80 VSGLLELAVEADDEETFNEAVAELDALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGT 139
Query: 218 ESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYAKAEVGVH 277
E+ DWASM+ +MY WA+ RG++ +++E GE+AGIK TIK+ G+YA+G+ + E GVH
Sbjct: 140 EAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVH 199
Query: 278 RLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRSGGAGGQHANTTD 337
RLVR SPFDSG RRHTSF++ V P D ++IN +DLRI+ +R+ GAGGQH N T+
Sbjct: 200 RLVRKSPFDSGGRRHTSFSSAFVYPEV-DDDIDIEINPADLRIDVYRTSGAGGQHVNRTE 258
Query: 338 SAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEIARQAQMNAEHTQSLTDIS 397
SAVRI HIPTGI CQN+RSQH+NK AM +++++ +LE+ ++ + +DI
Sbjct: 259 SAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYELEMQKKNAEKQAMEDNKSDIG 318
Query: 398 WGNQIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGFILSYLSASL 445
WG+QIR+YVL R +KDLRT E + +VL+G LD FI + L A L
Sbjct: 319 WGSQIRSYVLDDSR-IKDLRTGVETRNTQAVLDGSLDQFIEASLKAGL 365
>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 = 300 bits (769), Expect = 8e-82, Method: Compositional matrix adjust.
Identities = 148/348 (42%), Positives = 220/348 (63%), Gaps = 2/348 (0%)
Query: 98 VIKKRLQWKNLNVRLNLLSAELNKPNLWDDPVHAGRISREHGSLMGKMKEVKAFEQELLE 157
V++ L + RL ++AEL +P++W++P A + +E SL + + +Q L +
Sbjct: 20 VLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLED 79
Query: 158 HIDMIKLAREENDTXXXXXXXXXXXTMRRKSKEKELDALLSGELDPCSCYIEVQAGAGGT 217
+++LA E +D + K + E + SGE D CY+++QAG+GGT
Sbjct: 80 VSGLLELAVEADDEETFNEAVAELDALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGT 139
Query: 218 ESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYAKAEVGVH 277
E+ DWASM+ +MY WA+ RG++ +++E GE+AGIK TIK+ G+YA+G+ + E GVH
Sbjct: 140 EAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVH 199
Query: 278 RLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRSGGAGGQHANTTD 337
RLVR SPFDSG RRHTSF++ V P D ++IN +DLRI+ +R+ GAGGQH N T+
Sbjct: 200 RLVRKSPFDSGGRRHTSFSSAFVYPEV-DDDIDIEINPADLRIDVYRASGAGGQHVNRTE 258
Query: 338 SAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEIARQAQMNAEHTQSLTDIS 397
SAVRI HIPTGI CQN+RSQH+NK AM +++++ ++E+ ++ + +DI
Sbjct: 259 SAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYEVEMQKKNAEKQAMEDNKSDIG 318
Query: 398 WGNQIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGFILSYLSASL 445
WG+QIR+YVL R +KDLRT E + +VL+G LD FI + L A L
Sbjct: 319 WGSQIRSYVLDDSR-IKDLRTGVETRNTQAVLDGSLDQFIEASLKAGL 365
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 289 bits (739), Expect = 3e-78, Method: Compositional matrix adjust.
Identities = 145/348 (41%), Positives = 214/348 (61%), Gaps = 2/348 (0%)
Query: 98 VIKKRLQWKNLNVRLNLLSAELNKPNLWDDPVHAGRISREHGSLMGKMKEVKAFEQELLE 157
V++ L + RL ++AEL +P++W++P A + +E SL + + +Q L +
Sbjct: 20 VLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQXKQGLED 79
Query: 158 HIDMIKLAREENDTXXXXXXXXXXXTMRRKSKEKELDALLSGELDPCSCYIEVQAGAGGT 217
+++LA E +D + K + E SGE D CY+++QAG+GGT
Sbjct: 80 VSGLLELAVEADDEETFNEAVAELDALEEKLAQLEFRRXFSGEYDSADCYLDIQAGSGGT 139
Query: 218 ESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYAKAEVGVH 277
E+ DWAS + + Y WA+ RG++ +++E GE+AGIK TIK+ G+YA+G+ + E GVH
Sbjct: 140 EAQDWASXLERXYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVH 199
Query: 278 RLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRSGGAGGQHANTTD 337
RLVR SPFDSG RRHTSF++ V P D ++IN +DLRI+ +R+ GAGGQH N T+
Sbjct: 200 RLVRKSPFDSGGRRHTSFSSAFVYPEV-DDDIDIEINPADLRIDVYRASGAGGQHVNRTE 258
Query: 338 SAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEIARQAQMNAEHTQSLTDIS 397
SAVRI HIPTGI CQN+RSQH+NK A ++++ ++E ++ + +DI
Sbjct: 259 SAVRITHIPTGIVTQCQNDRSQHKNKDQAXKQXKAKLYEVEXQKKNAEKQAXEDNKSDIG 318
Query: 398 WGNQIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGFILSYLSASL 445
WG+QIR+YVL R +KDLRT E + +VL+G LD FI + L A L
Sbjct: 319 WGSQIRSYVLDDSR-IKDLRTGVETRNTQAVLDGSLDQFIEASLKAGL 365
>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 = 219 bits (558), Expect = 2e-57, Method: Compositional matrix adjust.
Identities = 139/363 (38%), Positives = 204/363 (56%), Gaps = 8/363 (2%)
Query: 92 IAQSIQVIKKRLQWKNLNVRLNLLSAELNKPNLWDDPVHAGRISREHGSLMGKMKEVKAF 151
+AQ ++ ++ L RL L L P+LW+DP A ++S+E L + ++
Sbjct: 6 LAQRLEGLRGYLDIPQKETRLKELERRLEDPSLWNDPEAARKVSQEAARLRRTVDTFRSL 65
Query: 152 EQELLEHIDMIK-LAREENDTXXXXXXXXXXXTMRRKSKEKELDALLSGELDPCSCYIEV 210
E +L +++++ L EE + +K E LL+ + + +
Sbjct: 66 ESDLQGLLELMEELPAEEREALKPELEEAA-----KKLDELYHQTLLNFPHAEKNAILTI 120
Query: 211 QAGAGGTESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYA 270
Q GAGGTE+ DWA M+L+MY +A+R+G++V ++D PG AGI A I V GE A+G
Sbjct: 121 QPGAGGTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLL 180
Query: 271 KAEVGVHRLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRSGGAGG 330
E GVHRLVR SPFD+ RRHTSFA V VI D V + +LRI+ R+ G GG
Sbjct: 181 SPEAGVHRLVRPSPFDASGRRHTSFAGVEVI-PEVDEEVEVVLKPEELRIDVMRASGPGG 239
Query: 331 QHANTTDSAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEIARQAQMNAEHT 390
Q NTTDSAVR++H+PTGIT TCQ RSQ +NK A+ +L++R+ +LE ++ +
Sbjct: 240 QGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKREEELKALR 299
Query: 391 QSLTDISWGNQIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGFILSYLSASLDKDEG 450
+ I WG+QIR+YVL VKD RT DP++VL+GDL I + L + +G
Sbjct: 300 GEVRPIEWGSQIRSYVLD-KNYVKDHRTGLMRHDPENVLDGDLMDLIWAGLEWKAGRRQG 358
Query: 451 GQQ 453
++
Sbjct: 359 TEE 361
>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 = 218 bits (556), Expect = 4e-57, Method: Compositional matrix adjust.
Identities = 137/347 (39%), Positives = 197/347 (56%), Gaps = 8/347 (2%)
Query: 92 IAQSIQVIKKRLQWKNLNVRLNLLSAELNKPNLWDDPVHAGRISREHGSLMGKMKEVKAF 151
+AQ ++ ++ L RL L L P+LW+DP A ++S+E L + ++
Sbjct: 1 LAQRLEGLRGYLDIPQKETRLKELERRLEDPSLWNDPEAARKVSQEAARLRRTVDTFRSL 60
Query: 152 EQELLEHIDMIK-LAREENDTXXXXXXXXXXXTMRRKSKEKELDALLSGELDPCSCYIEV 210
E +L +++++ L EE + +K E LL+ + + +
Sbjct: 61 ESDLQGLLELMEELPAEEREALKPELEEAA-----KKLDELYHQTLLNFPHAEKNAILTI 115
Query: 211 QAGAGGTESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYA 270
Q GAGGTE+ DWA M+L+MY +A+R+G++V ++D PG AGI A I V GE A+G
Sbjct: 116 QPGAGGTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLL 175
Query: 271 KAEVGVHRLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRSGGAGG 330
E GVHRLVR SPFD+ RRHTSFA V VI D V + +LRI+ R+ G GG
Sbjct: 176 SPEAGVHRLVRPSPFDASGRRHTSFAGVEVI-PEVDEEVEVVLKPEELRIDVMRASGPGG 234
Query: 331 QHANTTDSAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEIARQAQMNAEHT 390
Q NTTDSAVR++H+PTGIT TCQ RSQ +NK A+ +L++R+ +LE ++ +
Sbjct: 235 QGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKREEELKALR 294
Query: 391 QSLTDISWGNQIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGFI 437
+ I WG+QIR+YVL VKD RT DP++VL+GDL I
Sbjct: 295 GEVEPIEWGSQIRSYVLD-KNYVKDHRTGLMRHDPENVLDGDLMDLI 340
>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 = 218 bits (556), Expect = 5e-57, Method: Compositional matrix adjust.
Identities = 137/347 (39%), Positives = 197/347 (56%), Gaps = 8/347 (2%)
Query: 92 IAQSIQVIKKRLQWKNLNVRLNLLSAELNKPNLWDDPVHAGRISREHGSLMGKMKEVKAF 151
+AQ ++ ++ L RL L L P+LW+DP A ++S+E L + ++
Sbjct: 1 LAQRLEGLRGYLDIPQKETRLKELERRLEDPSLWNDPEAARKVSQEAARLRRTVDTFRSL 60
Query: 152 EQELLEHIDMIK-LAREENDTXXXXXXXXXXXTMRRKSKEKELDALLSGELDPCSCYIEV 210
E +L +++++ L EE + +K E LL+ + + +
Sbjct: 61 ESDLQGLLELMEELPAEEREALKPELEEAA-----KKLDELYHQTLLNFPHAEKNAILTI 115
Query: 211 QAGAGGTESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYA 270
Q GAGGTE+ DWA M+L+MY +A+R+G++V ++D PG AGI A I V GE A+G
Sbjct: 116 QPGAGGTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLL 175
Query: 271 KAEVGVHRLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRSGGAGG 330
E GVHRLVR SPFD+ RRHTSFA V VI D V + +LRI+ R+ G GG
Sbjct: 176 SPEAGVHRLVRPSPFDASGRRHTSFAGVEVI-PEVDEEVEVVLKPEELRIDVMRASGPGG 234
Query: 331 QHANTTDSAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEIARQAQMNAEHT 390
Q NTTDSAVR++H+PTGIT TCQ RSQ +NK A+ +L++R+ +LE ++ +
Sbjct: 235 QGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKREEELKALR 294
Query: 391 QSLTDISWGNQIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGFI 437
+ I WG+QIR+YVL VKD RT DP++VL+GDL I
Sbjct: 295 GEVRPIEWGSQIRSYVLD-KNYVKDHRTGLMRHDPENVLDGDLMDLI 340
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 216 bits (550), Expect = 2e-56, Method: Compositional matrix adjust.
Identities = 138/363 (38%), Positives = 202/363 (55%), Gaps = 8/363 (2%)
Query: 92 IAQSIQVIKKRLQWKNLNVRLNLLSAELNKPNLWDDPVHAGRISREHGSLMGKMKEVKAF 151
+AQ ++ + RL L L P+LW+DP A ++S+E L + ++
Sbjct: 6 LAQRLEGLGGIFDIPQKETRLKELERRLEDPSLWNDPEAARKVSQEAARLRRTVDTFRSL 65
Query: 152 EQELLEHIDMIK-LAREENDTXXXXXXXXXXXTMRRKSKEKELDALLSGELDPCSCYIEV 210
E +L +++++ L EE + +K E LL+ + + +
Sbjct: 66 ESDLQGLLELMEELPAEEREALKPELEEAA-----KKLDELYHQTLLNFPHAEKNAILTI 120
Query: 211 QAGAGGTESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYA 270
Q GAGGTE+ DWA M+L+MY +A+R+G++V ++D PG AGI A I V GE A+G
Sbjct: 121 QPGAGGTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLL 180
Query: 271 KAEVGVHRLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRSGGAGG 330
E GVHRLVR SPFD+ RRHTSFA V VI D V + +LRI+ R+ G GG
Sbjct: 181 SPEAGVHRLVRPSPFDASGRRHTSFAGVEVI-PEVDEEVEVVLKPEELRIDVMRASGPGG 239
Query: 331 QHANTTDSAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEIARQAQMNAEHT 390
Q NTTDSAVR++H+PTGIT TCQ RSQ +NK A+ +L++R+ +LE ++ +
Sbjct: 240 QGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKREEELKALR 299
Query: 391 QSLTDISWGNQIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGFILSYLSASLDKDEG 450
+ I WG+QIR+YVL VKD RT DP++VL+GDL I + L + +G
Sbjct: 300 GEVRPIEWGSQIRSYVLD-KNYVKDHRTGLMRHDPENVLDGDLMDLIWAGLEWKAGRRQG 358
Query: 451 GQQ 453
++
Sbjct: 359 TEE 361
>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 = 216 bits (549), Expect = 3e-56, Method: Compositional matrix adjust.
Identities = 136/345 (39%), Positives = 196/345 (56%), Gaps = 8/345 (2%)
Query: 110 VRLNLLSAELNKPNLWDDPVHAGRISREHGSLMGKMKEVKAFEQELLEHIDMIK-LAREE 168
RL L L P+LW+DP A ++S+E L + ++ E +L +++++ L EE
Sbjct: 37 TRLKELERRLEDPSLWNDPEAARKVSQEAARLRRTVDTFRSLESDLQGLLELMEELPAEE 96
Query: 169 NDTXXXXXXXXXXXTMRRKSKEKELDALLSGELDPCSCYIEVQAGAGGTESMDWASMVLQ 228
+ +K E LL+ + + +Q GAGGTE+ DWA M+L+
Sbjct: 97 REALKPELEEAA-----KKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLR 151
Query: 229 MYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYAKAEVGVHRLVRISPFDSG 288
MY +A+R+G++V ++D PG AGI A I V GE A+G E GVHRLVR SPFD+
Sbjct: 152 MYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDAS 211
Query: 289 KRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRSGGAGGQHANTTDSAVRIIHIPTG 348
RRHTSFA V VI D V + +LRI+ R+ G GGQ NTTDSAVR++H+PTG
Sbjct: 212 GRRHTSFAGVEVI-PEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTG 270
Query: 349 ITATCQNERSQHQNKASAMGVLQSRVNQLEIARQAQMNAEHTQSLTDISWGNQIRTYVLH 408
IT TCQ RSQ +NK A+ +L++R+ +LE ++ + + I WG+QIR+YVL
Sbjct: 271 ITVTCQTTRSQIKNKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLD 330
Query: 409 PYRMVKDLRTNYEVSDPDSVLEGDLDGFILSYLSASLDKDEGGQQ 453
VKD RT DP++VL+GDL I + L + +G ++
Sbjct: 331 -KNYVKDHRTGLMRHDPENVLDGDLMDLIWAGLEWKAGRRQGTEE 374
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 360
Score = 177 bits (449), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 103/239 (43%), Positives = 141/239 (58%), Gaps = 7/239 (2%)
Query: 202 DPCSCYIEVQAGAGGTESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKV 261
D + ++EV+AG GG E+ +A + +MY +A+ R +RV +M GE G K K+
Sbjct: 107 DERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMSASEGEHGGYKEIIAKI 166
Query: 262 DGEYAFGYAKAEVGVHRLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIE 321
G+ +G K E G HR+ R+ +S R HTS VAV+P D+ +N +DLRI+
Sbjct: 167 SGDGVYGRLKFESGGHRVQRVPATESQGRIHTSACTVAVMPELPDAEL-PDVNPADLRID 225
Query: 322 RFRSGGAGGQHANTTDSAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEIAR 381
FRS GAGGQH NTTDSA+RI H+PTGI CQ+ERSQH+NKA A+ VL +R++ E+A+
Sbjct: 226 TFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAAEMAK 285
Query: 382 QAQMNAEHTQSLT---DISWGNQIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGFI 437
+ Q A ++L D S N RTY P V D R N + D V+EG LD I
Sbjct: 286 RQQAEASTRRNLLGSGDRSDRN--RTYNF-PQGRVTDHRINLTLYRLDEVMEGKLDMLI 341
>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 = 171 bits (433), Expect = 7e-43, Method: Compositional matrix adjust.
Identities = 97/255 (38%), Positives = 147/255 (57%), Gaps = 10/255 (3%)
Query: 190 EKELDALLSGELDPCS------CYIEVQAGAGGTESMDWASMVLQMYKSWAQRRGYRVTL 243
EKELD L L S +E++ G GG E+ +A + +MY +A+R+G+ + +
Sbjct: 66 EKELDQLYQELLFLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEV 125
Query: 244 MDEMPGEIAGIKRATIKVDGEYAFGYAKAEVGVHRLVRISPFDSGKRRHTSFAAVAVIPN 303
+ ++ GI+ V G+ A+G K E GVHR+ R+ +SG R HTS A VAV+P
Sbjct: 126 AEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPE 185
Query: 304 SGDSSTHVQINESDLRIERFRSGGAGGQHANTTDSAVRIIHIPTGITATCQNERSQHQNK 363
+ ++I DL+IE FR+ G GGQ+ N T+SAVRI H+PTGI +CQNERSQ+QNK
Sbjct: 186 IEEKD--IEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNK 243
Query: 364 ASAMGVLQSRVNQLEIA-RQAQMNAEHTQSLTDISWGNQIRTYVLHPYRMVKDLRTNYEV 422
+A+ +L++R+ QL+ ++ +++ + + +IRTY P V D R NY
Sbjct: 244 QTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNF-PQNRVTDHRINYTS 302
Query: 423 SDPDSVLEGDLDGFI 437
+L+GDLD I
Sbjct: 303 YRLQEILDGDLDEII 317
>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 = 171 bits (433), Expect = 7e-43, Method: Compositional matrix adjust.
Identities = 97/255 (38%), Positives = 147/255 (57%), Gaps = 10/255 (3%)
Query: 190 EKELDALLSGELDPCS------CYIEVQAGAGGTESMDWASMVLQMYKSWAQRRGYRVTL 243
EKELD L L S +E++ G GG E+ +A + +MY +A+R+G+ + +
Sbjct: 66 EKELDQLYQELLFLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEV 125
Query: 244 MDEMPGEIAGIKRATIKVDGEYAFGYAKAEVGVHRLVRISPFDSGKRRHTSFAAVAVIPN 303
+ ++ GI+ V G+ A+G K E GVHR+ R+ +SG R HTS A VAV+P
Sbjct: 126 AEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPE 185
Query: 304 SGDSSTHVQINESDLRIERFRSGGAGGQHANTTDSAVRIIHIPTGITATCQNERSQHQNK 363
+ ++I DL+IE FR+ G GGQ+ N T+SAVRI H+PTGI +CQNERSQ+QNK
Sbjct: 186 IEEKD--IEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNK 243
Query: 364 ASAMGVLQSRVNQLEIA-RQAQMNAEHTQSLTDISWGNQIRTYVLHPYRMVKDLRTNYEV 422
+A+ +L++R+ QL+ ++ +++ + + +IRTY P V D R NY
Sbjct: 244 QTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNF-PQNRVTDHRINYTS 302
Query: 423 SDPDSVLEGDLDGFI 437
+L+GDLD I
Sbjct: 303 YRLQEILDGDLDEII 317
>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 = 158 bits (399), Expect = 8e-39, Method: Compositional matrix adjust.
Identities = 102/320 (31%), Positives = 165/320 (51%), Gaps = 17/320 (5%)
Query: 122 PNLWDDPVHAGRISR---EHGSLMGKMKEVKAFEQELLEHIDMIKLAREENDTXXXXXXX 178
P + D +SR E G ++G ++E + ++LE ++ + ++ +
Sbjct: 22 PEVLKDKGRYQSLSRRYAEMGEVIGLIREYR----KVLEDLEQAESLLDDPELKEMAKAE 77
Query: 179 XXXXTMRRKSKEKELD--ALLSGELDPCSCYIEVQAGAGGTESMDWASMVLQMYKSWAQR 236
R+++ EKEL+ L +D +E++AG GG E+ +A + MY +A+
Sbjct: 78 REALLARKEALEKELERHLLPKDPMDERDAIVEIRAGTGGEEAALFARDLFNMYLRFAEE 137
Query: 237 RGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYAKAEVGVHRLVRISPFDSGKRRHTSFA 296
G+ ++D P ++ G + +V G A+G K E GVHR+ R+ ++ R HTS A
Sbjct: 138 MGFETEVLDSHPTDLGGFSKVVFEVRGPGAYGTFKYESGVHRVQRVPVTETQGRIHTSTA 197
Query: 297 AVAVIPNSGDSSTHVQINESDLRIERFRSGGAGGQHANTTDSAVRIIHIPTGITATCQNE 356
VAV+P + + +N ++RI+ R+ G GGQ NTTDSAVR++H+PTGI TCQ+
Sbjct: 198 TVAVLPKAEEED--FALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDS 255
Query: 357 RSQHQNKASAMGVLQSRVNQLEIARQAQMNAEHTQSLTDISWG---NQIRTYVLHPYRMV 413
RSQ +N+ A+ +L+SR+ LE+ R + L I G +IRTY P V
Sbjct: 256 RSQIKNREKALMILRSRL--LEMKRAEEAERLRKTRLAQIGTGERSEKIRTYNF-PQSRV 312
Query: 414 KDLRTNYEVSDPDSVLEGDL 433
D R + D + VL G L
Sbjct: 313 TDHRIGFTTHDLEGVLSGHL 332
>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 = 119 bits (297), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 95/340 (27%), Positives = 160/340 (47%), Gaps = 9/340 (2%)
Query: 104 QWKNLNVRLNLLSAELNKPNLWDDPVHAGRISREHGS---LMGKMKEVKAFEQELLEHID 160
Q + + R L L+ P++ D +SRE + + +E K Q + + +
Sbjct: 18 QLQAVEDRYEELGELLSDPDVVSDTKRFXELSREEANSRETVAVYREYKQVVQNIADAQE 77
Query: 161 MIKLAREENDTXXXXXXXXXXXTMRRKSKEKELDALL--SGELDPCSCYIEVQAGAGGTE 218
IK A + + + ++ E++L LL D + +E++ AGG E
Sbjct: 78 XIKDASGDPELEEXAKEELKNSKVAKEEYEEKLRFLLLPKDPNDDKNIILEIRGAAGGDE 137
Query: 219 SMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYAKAEVGVHR 278
+ +A +L Y+ +A+ +G++ + + + G+K V G+ + K E G HR
Sbjct: 138 AALFAGDLLNXYQKYAENQGWKFEVXEASANGVGGLKEVVAXVSGQSVYSKLKYESGAHR 197
Query: 279 LVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRSGGAGGQHANTTDS 338
+ R+ +S R HTS A V V P +I+ DLR++ + + GAGGQ+ N +
Sbjct: 198 VQRVPVTESQGRVHTSTATVLVXPEV--EEVEYEIDPKDLRVDIYHASGAGGQNVNKVAT 255
Query: 339 AVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRV-NQLEIARQAQMNAEHTQSLTDIS 397
AVRIIH+PT I Q ER+Q +N+ A ++++RV + Q + +AE ++
Sbjct: 256 AVRIIHLPTNIKVEXQEERTQQKNRDKAXKIIRARVADHFAQIAQDEQDAERKSTVGTGD 315
Query: 398 WGNQIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGFI 437
+IRTY P V D R + DS+L G LD I
Sbjct: 316 RSERIRTYNF-PQNRVTDHRIGLTLQKLDSILSGKLDEVI 354
>pdb|2RSM|A Chain A, Solution Structure And Sirna-Mediated Knockdown Analysis
Of The Mitochondrial Disease-Related Protein C12orf65
(Ict2)
Length = 115
Score = 53.5 bits (127), Expect = 3e-07, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 41/80 (51%)
Query: 296 AAVAVIPNSGDSSTHVQINESDLRIERFRSGGAGGQHANTTDSAVRIIHIPTGITATCQN 355
A+ + D + +NES+L + + G GGQ N T + V + H+P+GI C
Sbjct: 26 ASTVQVAGRKDYPALLPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQ 85
Query: 356 ERSQHQNKASAMGVLQSRVN 375
RS QN+ A VLQ +V+
Sbjct: 86 TRSVDQNRKIARKVLQEKVD 105
>pdb|4DH9|Y Chain Y, Crystal Structure Of Yaej Bound To The 70s Ribosome
Length = 140
Score = 37.0 bits (84), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 44/104 (42%), Gaps = 30/104 (28%)
Query: 308 STHVQINESDLRIERFRSGGAGGQHANTTDSAVRIIHIPTGITAT--------------- 352
S HV I + +L I R+ GAGGQH N T +A IH+ I A+
Sbjct: 5 SRHVAIPDGELEITAIRAQGAGGQHVNKTSTA---IHLRFDIRASSLPEYYKERLLAASH 61
Query: 353 ------------CQNERSQHQNKASAMGVLQSRVNQLEIARQAQ 384
Q RSQ N+ +A+ L + + +L ++A+
Sbjct: 62 HLISSDGVIVIKAQEYRSQELNREAALARLVAMIKELTTEKKAR 105
>pdb|2JY9|A Chain A, Nmr Structure Of Putative Trna Hydrolase Domain From
Salmonella Typhimurium. Northeast Structural Genomics
Consortium Target Str220
Length = 148
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/45 (44%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 308 STHVQINESDLRIERFRSGGAGGQHANTTDSAVRIIHIPTGITAT 352
S V I +++L I R+ GAGGQH N T SA IH+ I A+
Sbjct: 5 SRTVSIADNELEITAIRAQGAGGQHVNKTSSA---IHLRFDIRAS 46
>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 = 28.5 bits (62), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 36/87 (41%), Gaps = 30/87 (34%)
Query: 308 STHVQINESDLRIERFRSGGAGGQHANTTDSAVRIIHIPTGITAT--------------- 352
S +V + ++++ + R+ GAGGQ+ N SA +H+ I A+
Sbjct: 5 SNNVHLPDAEIELTAIRAQGAGGQNVNKVSSA---MHLRFDINASSLPPFYKERLLALND 61
Query: 353 ------------CQNERSQHQNKASAM 367
Q R+Q QN+A A+
Sbjct: 62 SRITSDGVIVLKAQQYRTQEQNRADAL 88
>pdb|2XAA|A Chain A, Alcohol Dehydrogenase Adh-'a' From Rhodococcus Ruber Dsm
44541 At Ph 8.5 In Complex With Nad And Butane-1,4-Diol
pdb|2XAA|B Chain B, Alcohol Dehydrogenase Adh-'a' From Rhodococcus Ruber Dsm
44541 At Ph 8.5 In Complex With Nad And Butane-1,4-Diol
pdb|2XAA|C Chain C, Alcohol Dehydrogenase Adh-'a' From Rhodococcus Ruber Dsm
44541 At Ph 8.5 In Complex With Nad And Butane-1,4-Diol
pdb|2XAA|D Chain D, Alcohol Dehydrogenase Adh-'a' From Rhodococcus Ruber Dsm
44541 At Ph 8.5 In Complex With Nad And Butane-1,4-Diol
pdb|3JV7|A Chain A, Structure Of Adh-A From Rhodococcus Ruber
pdb|3JV7|B Chain B, Structure Of Adh-A From Rhodococcus Ruber
pdb|3JV7|C Chain C, Structure Of Adh-A From Rhodococcus Ruber
pdb|3JV7|D Chain D, Structure Of Adh-A From Rhodococcus Ruber
Length = 345
Score = 28.5 bits (62), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 6/80 (7%)
Query: 17 LGENISGFGSNGLLRLKNPCGSTEVLLFPRGCRWFSTQAAVEPSTSDGLTVDGIVASQWT 76
LGE ++GFG + + P G RG + T+AA T GL G +A ++
Sbjct: 71 LGEGVTGFGVGDAVAVYGPWGCGACHACARGRENYCTRAADLGITPPGLGSPGSMA-EYM 129
Query: 77 ILDESE-----GDWKSHAAA 91
I+D + GD AAA
Sbjct: 130 IVDSARHLVPIGDLDPVAAA 149
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 0.131 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,107,993
Number of Sequences: 62578
Number of extensions: 501078
Number of successful extensions: 1267
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1222
Number of HSP's gapped (non-prelim): 18
length of query: 453
length of database: 14,973,337
effective HSP length: 102
effective length of query: 351
effective length of database: 8,590,381
effective search space: 3015223731
effective search space used: 3015223731
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)