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= psy15210
(278 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 320 bits (820), Expect = 6e-88, Method: Compositional matrix adjust.
Identities = 150/262 (57%), Positives = 182/262 (69%)
Query: 10 NKLNNKIKEIEFHQFFNDPLDFNNCFIDIQSGAGGIEAQDWASMLLRQYLRYCERKGFIV 69
+ L K+ ++EF + F+ D +C++DIQ+G+GG EAQDWASML R YLR+ E +GF
Sbjct: 104 DALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKT 163
Query: 70 EILEKSNGEITGIKTVTLKIKGKYAYGFLKSESGIHRLVRKSPFDSSNNRHTSFSSLFVY 129
EI+E+S GE+ GIK+VT+KI G YAYG+L++E+G+HRLVRKSPFDS RHTSFSS FVY
Sbjct: 164 EIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVY 223
Query: 130 PEXXXXXXXXXXPADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHRN 189
PE PADLRID YRASGAGGQH+N+T+SAVRITHIPTGIV QCQNDRSQH+N
Sbjct: 224 PEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKN 283
Query: 190 KSEAWDMXXXXXXXXXXXXXXXXXXXXXXXXXXXXWGYQIRSYVLDKSRIKDLRTNLETK 249
K +A WG QIRSYVLD SRIKDLRT +ET+
Sbjct: 284 KDQAMKQMKAKLYEVEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSRIKDLRTGVETR 343
Query: 250 NIKDILDGDLDNFIIASLKQHL 271
N + +LDG LD FI ASLK L
Sbjct: 344 NTQAVLDGSLDQFIEASLKAGL 365
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 318 bits (814), Expect = 3e-87, Method: Compositional matrix adjust.
Identities = 149/262 (56%), Positives = 181/262 (69%)
Query: 10 NKLNNKIKEIEFHQFFNDPLDFNNCFIDIQSGAGGIEAQDWASMLLRQYLRYCERKGFIV 69
+ L K+ ++EF + F+ D +C++DIQ+G+GG EAQDWASML R YLR+ E +GF
Sbjct: 104 DALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKT 163
Query: 70 EILEKSNGEITGIKTVTLKIKGKYAYGFLKSESGIHRLVRKSPFDSSNNRHTSFSSLFVY 129
EI+E+S GE+ GIK+VT+KI G YAYG+L++E+G+HRLVRKSPFDS RHTSFSS FVY
Sbjct: 164 EIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVY 223
Query: 130 PEXXXXXXXXXXPADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHRN 189
PE PADLRID YR SGAGGQH+N+T+SAVRITHIPTGIV QCQNDRSQH+N
Sbjct: 224 PEVDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKN 283
Query: 190 KSEAWDMXXXXXXXXXXXXXXXXXXXXXXXXXXXXWGYQIRSYVLDKSRIKDLRTNLETK 249
K +A WG QIRSYVLD SRIKDLRT +ET+
Sbjct: 284 KDQAMKQMKAKLYELEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSRIKDLRTGVETR 343
Query: 250 NIKDILDGDLDNFIIASLKQHL 271
N + +LDG LD FI ASLK L
Sbjct: 344 NTQAVLDGSLDQFIEASLKAGL 365
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 315 bits (808), Expect = 1e-86, Method: Compositional matrix adjust.
Identities = 152/262 (58%), Positives = 184/262 (70%)
Query: 10 NKLNNKIKEIEFHQFFNDPLDFNNCFIDIQSGAGGIEAQDWASMLLRQYLRYCERKGFIV 69
+ L K+ ++EF + F+ D +C++DIQ+G+GG EAQDWAS L R YLR+ E +GF
Sbjct: 104 DALEEKLAQLEFRRXFSGEYDSADCYLDIQAGSGGTEAQDWASXLERXYLRWAESRGFKT 163
Query: 70 EILEKSNGEITGIKTVTLKIKGKYAYGFLKSESGIHRLVRKSPFDSSNNRHTSFSSLFVY 129
EI+E+S GE+ GIK+VT+KI G YAYG+L++E+G+HRLVRKSPFDS RHTSFSS FVY
Sbjct: 164 EIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVY 223
Query: 130 PEXXXXXXXXXXPADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHRN 189
PE PADLRID YRASGAGGQH+N+T+SAVRITHIPTGIV QCQNDRSQH+N
Sbjct: 224 PEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKN 283
Query: 190 KSEAWDMXXXXXXXXXXXXXXXXXXXXXXXXXXXXWGYQIRSYVLDKSRIKDLRTNLETK 249
K +A WG QIRSYVLD SRIKDLRT +ET+
Sbjct: 284 KDQAXKQXKAKLYEVEXQKKNAEKQAXEDNKSDIGWGSQIRSYVLDDSRIKDLRTGVETR 343
Query: 250 NIKDILDGDLDNFIIASLKQHL 271
N + +LDG LD FI ASLK L
Sbjct: 344 NTQAVLDGSLDQFIEASLKAGL 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 = 218 bits (554), Expect = 4e-57, Method: Compositional matrix adjust.
Identities = 117/265 (44%), Positives = 150/265 (56%), Gaps = 4/265 (1%)
Query: 4 EIEDNTNKLNNKIKEIEFHQFFNDPLDFNNCFIDIQSGAGGIEAQDWASMLLRQYLRYCE 63
E+E+ KL+ E+ N P N + IQ GAGG EA DWA MLLR Y R+ E
Sbjct: 85 ELEEAAKKLD----ELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAE 140
Query: 64 RKGFIVEILEKSNGEITGIKTVTLKIKGKYAYGFLKSESGIHRLVRKSPFDSSNNRHTSF 123
R+GF VE+++ + G GI + +KG+ AYG L E+G+HRLVR SPFD+S RHTSF
Sbjct: 141 RQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSF 200
Query: 124 SSLFVYPEXXXXXXXXXXPADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQND 183
+ + V PE P +LRID RASG GGQ +N TDSAVR+ H+PTGI V CQ
Sbjct: 201 AGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTT 260
Query: 184 RSQHRNKSEAWDMXXXXXXXXXXXXXXXXXXXXXXXXXXXXWGYQIRSYVLDKSRIKDLR 243
RSQ +NK A + WG QIRSYVLDK+ +KD R
Sbjct: 261 RSQIKNKELALKILKARLYELERKKREEELKALRGEVEPIEWGSQIRSYVLDKNYVKDHR 320
Query: 244 TNLETKNIKDILDGDLDNFIIASLK 268
T L + +++LDGDL + I A L+
Sbjct: 321 TGLMRHDPENVLDGDLMDLIWAGLE 345
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 218 bits (554), Expect = 4e-57, Method: Compositional matrix adjust.
Identities = 117/265 (44%), Positives = 150/265 (56%), Gaps = 4/265 (1%)
Query: 4 EIEDNTNKLNNKIKEIEFHQFFNDPLDFNNCFIDIQSGAGGIEAQDWASMLLRQYLRYCE 63
E+E+ KL+ E+ N P N + IQ GAGG EA DWA MLLR Y R+ E
Sbjct: 90 ELEEAAKKLD----ELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAE 145
Query: 64 RKGFIVEILEKSNGEITGIKTVTLKIKGKYAYGFLKSESGIHRLVRKSPFDSSNNRHTSF 123
R+GF VE+++ + G GI + +KG+ AYG L E+G+HRLVR SPFD+S RHTSF
Sbjct: 146 RQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSF 205
Query: 124 SSLFVYPEXXXXXXXXXXPADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQND 183
+ + V PE P +LRID RASG GGQ +N TDSAVR+ H+PTGI V CQ
Sbjct: 206 AGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTT 265
Query: 184 RSQHRNKSEAWDMXXXXXXXXXXXXXXXXXXXXXXXXXXXXWGYQIRSYVLDKSRIKDLR 243
RSQ +NK A + WG QIRSYVLDK+ +KD R
Sbjct: 266 RSQIKNKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLDKNYVKDHR 325
Query: 244 TNLETKNIKDILDGDLDNFIIASLK 268
T L + +++LDGDL + I A L+
Sbjct: 326 TGLMRHDPENVLDGDLMDLIWAGLE 350
>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 = 217 bits (553), Expect = 4e-57, Method: Compositional matrix adjust.
Identities = 117/265 (44%), Positives = 150/265 (56%), Gaps = 4/265 (1%)
Query: 4 EIEDNTNKLNNKIKEIEFHQFFNDPLDFNNCFIDIQSGAGGIEAQDWASMLLRQYLRYCE 63
E+E+ KL+ E+ N P N + IQ GAGG EA DWA MLLR Y R+ E
Sbjct: 90 ELEEAAKKLD----ELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAE 145
Query: 64 RKGFIVEILEKSNGEITGIKTVTLKIKGKYAYGFLKSESGIHRLVRKSPFDSSNNRHTSF 123
R+GF VE+++ + G GI + +KG+ AYG L E+G+HRLVR SPFD+S RHTSF
Sbjct: 146 RQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSF 205
Query: 124 SSLFVYPEXXXXXXXXXXPADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQND 183
+ + V PE P +LRID RASG GGQ +N TDSAVR+ H+PTGI V CQ
Sbjct: 206 AGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTT 265
Query: 184 RSQHRNKSEAWDMXXXXXXXXXXXXXXXXXXXXXXXXXXXXWGYQIRSYVLDKSRIKDLR 243
RSQ +NK A + WG QIRSYVLDK+ +KD R
Sbjct: 266 RSQIKNKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLDKNYVKDHR 325
Query: 244 TNLETKNIKDILDGDLDNFIIASLK 268
T L + +++LDGDL + I A L+
Sbjct: 326 TGLMRHDPENVLDGDLMDLIWAGLE 350
>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 = 217 bits (553), Expect = 4e-57, Method: Compositional matrix adjust.
Identities = 117/265 (44%), Positives = 150/265 (56%), Gaps = 4/265 (1%)
Query: 4 EIEDNTNKLNNKIKEIEFHQFFNDPLDFNNCFIDIQSGAGGIEAQDWASMLLRQYLRYCE 63
E+E+ KL+ E+ N P N + IQ GAGG EA DWA MLLR Y R+ E
Sbjct: 85 ELEEAAKKLD----ELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAE 140
Query: 64 RKGFIVEILEKSNGEITGIKTVTLKIKGKYAYGFLKSESGIHRLVRKSPFDSSNNRHTSF 123
R+GF VE+++ + G GI + +KG+ AYG L E+G+HRLVR SPFD+S RHTSF
Sbjct: 141 RQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSF 200
Query: 124 SSLFVYPEXXXXXXXXXXPADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQND 183
+ + V PE P +LRID RASG GGQ +N TDSAVR+ H+PTGI V CQ
Sbjct: 201 AGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTT 260
Query: 184 RSQHRNKSEAWDMXXXXXXXXXXXXXXXXXXXXXXXXXXXXWGYQIRSYVLDKSRIKDLR 243
RSQ +NK A + WG QIRSYVLDK+ +KD R
Sbjct: 261 RSQIKNKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLDKNYVKDHR 320
Query: 244 TNLETKNIKDILDGDLDNFIIASLK 268
T L + +++LDGDL + I A L+
Sbjct: 321 TGLMRHDPENVLDGDLMDLIWAGLE 345
>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 = 217 bits (553), Expect = 5e-57, Method: Compositional matrix adjust.
Identities = 117/265 (44%), Positives = 150/265 (56%), Gaps = 4/265 (1%)
Query: 4 EIEDNTNKLNNKIKEIEFHQFFNDPLDFNNCFIDIQSGAGGIEAQDWASMLLRQYLRYCE 63
E+E+ KL+ E+ N P N + IQ GAGG EA DWA MLLR Y R+ E
Sbjct: 103 ELEEAAKKLD----ELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAE 158
Query: 64 RKGFIVEILEKSNGEITGIKTVTLKIKGKYAYGFLKSESGIHRLVRKSPFDSSNNRHTSF 123
R+GF VE+++ + G GI + +KG+ AYG L E+G+HRLVR SPFD+S RHTSF
Sbjct: 159 RQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSF 218
Query: 124 SSLFVYPEXXXXXXXXXXPADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQND 183
+ + V PE P +LRID RASG GGQ +N TDSAVR+ H+PTGI V CQ
Sbjct: 219 AGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTT 278
Query: 184 RSQHRNKSEAWDMXXXXXXXXXXXXXXXXXXXXXXXXXXXXWGYQIRSYVLDKSRIKDLR 243
RSQ +NK A + WG QIRSYVLDK+ +KD R
Sbjct: 279 RSQIKNKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLDKNYVKDHR 338
Query: 244 TNLETKNIKDILDGDLDNFIIASLK 268
T L + +++LDGDL + I A L+
Sbjct: 339 TGLMRHDPENVLDGDLMDLIWAGLE 363
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 360
Score = 181 bits (459), Expect = 4e-46, Method: Compositional matrix adjust.
Identities = 97/251 (38%), Positives = 138/251 (54%), Gaps = 1/251 (0%)
Query: 27 DPLDFNNCFIDIQSGAGGIEAQDWASMLLRQYLRYCERKGFIVEILEKSNGEITGIKTVT 86
DP D N F+++++G GG EA +A L R Y RY E + + VEI+ S GE G K +
Sbjct: 104 DPDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMSASEGEHGGYKEII 163
Query: 87 LKIKGKYAYGFLKSESGIHRLVRKSPFDSSNNRHTSFSSLFVYPEXXXXXXXXXXPADLR 146
KI G YG LK ESG HR+ R +S HTS ++ V PE PADLR
Sbjct: 164 AKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSACTVAVMPELPDAELPDVNPADLR 223
Query: 147 IDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHRNKSEAWD-MXXXXXXXXX 205
IDT+R+SGAGGQH+N TDSA+RITH+PTGIVV+CQ++RSQH+NK++A +
Sbjct: 224 IDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAAEM 283
Query: 206 XXXXXXXXXXXXXXXXXXXWGYQIRSYVLDKSRIKDLRTNLETKNIKDILDGDLDNFIIA 265
+ R+Y + R+ D R NL + ++++G LD I
Sbjct: 284 AKRQQAEASTRRNLLGSGDRSDRNRTYNFPQGRVTDHRINLTLYRLDEVMEGKLDMLIEP 343
Query: 266 SLKQHLLNKIT 276
+++H +++
Sbjct: 344 IIQEHQADQLA 354
>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 = 177 bits (450), Expect = 4e-45, Method: Compositional matrix adjust.
Identities = 99/248 (39%), Positives = 139/248 (56%), Gaps = 3/248 (1%)
Query: 24 FFNDPLDFNNCFIDIQSGAGGIEAQDWASMLLRQYLRYCERKGFIVEILEKSNGEITGIK 83
F P + ++I+ G GG EA +A L R Y RY ERKG+ +E+ E ++ GI+
Sbjct: 78 FLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIR 137
Query: 84 TVTLKIKGKYAYGFLKSESGIHRLVRKSPFDSSNNRHTSFSSLFVYPEXXXXXXXXXXPA 143
V +KGK AYG LK ESG+HR+ R +S HTS +++ V PE P
Sbjct: 138 EVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIR-PE 196
Query: 144 DLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHRNKSEAWD-MXXXXXX 202
DL+I+T+RASG GGQ++NKT+SAVRITH+PTGIVV CQN+RSQ++NK A +
Sbjct: 197 DLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQ 256
Query: 203 XXXXXXXXXXXXXXXXXXXXXXWGYQIRSYVLDKSRIKDLRTNLETKNIKDILDGDLDNF 262
+IR+Y ++R+ D R N + +++ILDGDLD
Sbjct: 257 LQKEQKEREISQKRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDE- 315
Query: 263 IIASLKQH 270
II+ L +H
Sbjct: 316 IISKLIEH 323
>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 = 177 bits (450), Expect = 4e-45, Method: Compositional matrix adjust.
Identities = 99/248 (39%), Positives = 139/248 (56%), Gaps = 3/248 (1%)
Query: 24 FFNDPLDFNNCFIDIQSGAGGIEAQDWASMLLRQYLRYCERKGFIVEILEKSNGEITGIK 83
F P + ++I+ G GG EA +A L R Y RY ERKG+ +E+ E ++ GI+
Sbjct: 78 FLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIR 137
Query: 84 TVTLKIKGKYAYGFLKSESGIHRLVRKSPFDSSNNRHTSFSSLFVYPEXXXXXXXXXXPA 143
V +KGK AYG LK ESG+HR+ R +S HTS +++ V PE P
Sbjct: 138 EVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIR-PE 196
Query: 144 DLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHRNKSEAWD-MXXXXXX 202
DL+I+T+RASG GGQ++NKT+SAVRITH+PTGIVV CQN+RSQ++NK A +
Sbjct: 197 DLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQ 256
Query: 203 XXXXXXXXXXXXXXXXXXXXXXWGYQIRSYVLDKSRIKDLRTNLETKNIKDILDGDLDNF 262
+IR+Y ++R+ D R N + +++ILDGDLD
Sbjct: 257 LQKEQKEREISQKRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDE- 315
Query: 263 IIASLKQH 270
II+ L +H
Sbjct: 316 IISKLIEH 323
>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 = 152 bits (383), Expect = 3e-37, Method: Compositional matrix adjust.
Identities = 87/255 (34%), Positives = 133/255 (52%), Gaps = 5/255 (1%)
Query: 17 KEIEFHQFFNDPLDFNNCFIDIQSGAGGIEAQDWASMLLRQYLRYCERKGFIVEILEKSN 76
KE+E H DP+D + ++I++G GG EA +A L YLR+ E GF E+L+
Sbjct: 90 KELERHLLPKDPMDERDAIVEIRAGTGGEEAALFARDLFNMYLRFAEEMGFETEVLDSHP 149
Query: 77 GEITGIKTVTLKIKGKYAYGFLKSESGIHRLVRKSPFDSSNNR-HTSFSSLFVYPEXXXX 135
++ G V +++G AYG K ESG+HR V++ P + R HTS +++ V P+
Sbjct: 150 TDLGGFSKVVFEVRGPGAYGTFKYESGVHR-VQRVPVTETQGRIHTSTATVAVLPKAEEE 208
Query: 136 XXXXXXPADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHRNKSEAWD 195
++RID RASG GGQ +N TDSAVR+ H+PTGI+V CQ+ RSQ +N+ +A
Sbjct: 209 DFALNMD-EIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNREKALM 267
Query: 196 -MXXXXXXXXXXXXXXXXXXXXXXXXXXXXWGYQIRSYVLDKSRIKDLRTNLETKNIKDI 254
+ +IR+Y +SR+ D R T +++ +
Sbjct: 268 ILRSRLLEMKRAEEAERLRKTRLAQIGTGERSEKIRTYNFPQSRVTDHRIGFTTHDLEGV 327
Query: 255 LDGDLDNFIIASLKQ 269
L G L I+ +LK+
Sbjct: 328 LSGHL-TPILEALKR 341
>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 = 130 bits (326), Expect = 9e-31, Method: Compositional matrix adjust.
Identities = 84/260 (32%), Positives = 125/260 (48%), Gaps = 8/260 (3%)
Query: 13 NNKIKEIEFHQ------FFNDPLDFNNCFIDIQSGAGGIEAQDWASMLLRQYLRYCERKG 66
N+K+ + E+ + DP D N ++I+ AGG EA +A LL Y +Y E +G
Sbjct: 98 NSKVAKEEYEEKLRFLLLPKDPNDDKNIILEIRGAAGGDEAALFAGDLLNXYQKYAENQG 157
Query: 67 FIVEILEKSNGEITGIKTVTLKIKGKYAYGFLKSESGIHRLVRKSPFDSSNNRHTSFSSL 126
+ E+ E S + G+K V + G+ Y LK ESG HR+ R +S HTS +++
Sbjct: 158 WKFEVXEASANGVGGLKEVVAXVSGQSVYSKLKYESGAHRVQRVPVTESQGRVHTSTATV 217
Query: 127 FVYPEXXXXXXXXXXPADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQ 186
V P DLR+D Y ASGAGGQ++NK +AVRI H+PT I V+ Q +R+Q
Sbjct: 218 LVX-PEVEEVEYEIDPKDLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEXQEERTQ 276
Query: 187 HRNKSEAWDMXXXXXXXX-XXXXXXXXXXXXXXXXXXXXWGYQIRSYVLDKSRIKDLRTN 245
+N+ +A + +IR+Y ++R+ D R
Sbjct: 277 QKNRDKAXKIIRARVADHFAQIAQDEQDAERKSTVGTGDRSERIRTYNFPQNRVTDHRIG 336
Query: 246 LETKNIKDILDGDLDNFIIA 265
L + + IL G LD I A
Sbjct: 337 LTLQKLDSILSGKLDEVIDA 356
>pdb|2RSM|A Chain A, Solution Structure And Sirna-Mediated Knockdown Analysis
Of The Mitochondrial Disease-Related Protein C12orf65
(Ict2)
Length = 115
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 143 ADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHRNKSEA 193
++L + G GGQ NKT + V + H+P+GIVV+C RS +N+ A
Sbjct: 46 SELEEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRKIA 96
>pdb|2JY9|A Chain A, Nmr Structure Of Putative Trna Hydrolase Domain From
Salmonella Typhimurium. Northeast Structural Genomics
Consortium Target Str220
Length = 148
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 15/24 (62%), Positives = 18/24 (75%)
Query: 144 DLRIDTYRASGAGGQHINKTDSAV 167
+L I RA GAGGQH+NKT SA+
Sbjct: 14 ELEITAIRAQGAGGQHVNKTSSAI 37
>pdb|4DH9|Y Chain Y, Crystal Structure Of Yaej Bound To The 70s Ribosome
Length = 140
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 33/75 (44%), Gaps = 24/75 (32%)
Query: 144 DLRIDTYRASGAGGQHINKTDSA------VRITHIPT------------------GIVVQ 179
+L I RA GAGGQH+NKT +A +R + +P IV++
Sbjct: 14 ELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIK 73
Query: 180 CQNDRSQHRNKSEAW 194
Q RSQ N+ A
Sbjct: 74 AQEYRSQELNREAAL 88
>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 = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 24/76 (31%)
Query: 143 ADLRIDTYRASGAGGQHINKTDSAVRI------THIPT------------------GIVV 178
A++ + RA GAGGQ++NK SA+ + + +P IV+
Sbjct: 13 AEIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITSDGVIVL 72
Query: 179 QCQNDRSQHRNKSEAW 194
+ Q R+Q +N+++A
Sbjct: 73 KAQQYRTQEQNRADAL 88
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
0.318 0.136 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,166,507
Number of Sequences: 62578
Number of extensions: 258772
Number of successful extensions: 554
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 521
Number of HSP's gapped (non-prelim): 24
length of query: 278
length of database: 14,973,337
effective HSP length: 98
effective length of query: 180
effective length of database: 8,840,693
effective search space: 1591324740
effective search space used: 1591324740
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)