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= 021200
(316 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 360
Score = 281 bits (720), Expect = 2e-76, Method: Compositional matrix adjust.
Identities = 137/288 (47%), Positives = 197/288 (68%), Gaps = 2/288 (0%)
Query: 26 EDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDADERDCILEVRAGTGGEEASLFAV 85
+D +M +MA +EL A ++ ++ PKD DER+ LEVRAGTGG+EA+LFA
Sbjct: 70 DDPEMREMAQDELREAKEKSEQLEQQLQVLLLPKDPDDERNAFLEVRAGTGGDEAALFAG 129
Query: 86 DVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESGIHRVQRVPL 145
D+F+MY RY++ + W+ E++ +E + GYKE A ISG GVYG+LKFESG HRVQRVP
Sbjct: 130 DLFRMYSRYAEARRWRVEIMSASEGEHGGYKEIIAKISGDGVYGRLKFESGGHRVQRVPA 189
Query: 146 TEKSGRVHTSAVSVAILPQADEVDVRLRNE-DLRIDTYRSGGSGGQHANTTNSAVRVTHI 204
TE GR+HTSA +VA++P+ + ++ N DLRIDT+RS G+GGQH NTT+SA+R+TH+
Sbjct: 190 TESQGRIHTSACTVAVMPELPDAELPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHL 249
Query: 205 PTGMTISIQDERSQHMNXXXXXXXXXXXXYEMERSRIHLSRSKLRSEQIGSGDRSERIRT 264
PTG+ + QDERSQH N + E ++ + + R +GSGDRS+R RT
Sbjct: 250 PTGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLLGSGDRSDRNRT 309
Query: 265 YNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDALLLQQEMDAIASF 312
YNFPQGRVTDHR+ +T + + ++MEG+ LD+ I+ ++ + + D +A+
Sbjct: 310 YNFPQGRVTDHRINLTLYRLDEVMEGK-LDMLIEPIIQEHQADQLAAL 356
>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 = 259 bits (662), Expect = 1e-69, Method: Compositional matrix adjust.
Identities = 117/252 (46%), Positives = 175/252 (69%), Gaps = 4/252 (1%)
Query: 67 CILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVG 126
I+E+R GTGGEEA+LFA D+F+MY RY+++KGW EV + E+DL G +E + G
Sbjct: 88 AIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKN 147
Query: 127 VYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEVDVRLRNEDLRIDTYRSGG 186
YG LK+ESG+HRVQRVP+TE GR+HTS +VA+LP+ +E D+ +R EDL+I+T+R+ G
Sbjct: 148 AYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASG 207
Query: 187 SGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNXXXXXXXXXXXXYEMERSRIHLSRS 246
GGQ+ N T SAVR+TH+PTG+ +S Q+ERSQ+ N Y++++ + S
Sbjct: 208 HGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREIS 267
Query: 247 KLRSEQIGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDALL---LQ 303
+ R QIG+G+RSE+IRTYNFPQ RVTDHR+ T + + ++++G +LD I L+ ++
Sbjct: 268 QKRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSYRLQEILDG-DLDEIISKLIEHDIE 326
Query: 304 QEMDAIASFGST 315
++ + G++
Sbjct: 327 NNLEEVLGIGAS 338
>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 = 259 bits (661), Expect = 2e-69, Method: Compositional matrix adjust.
Identities = 116/235 (49%), Positives = 167/235 (71%), Gaps = 1/235 (0%)
Query: 67 CILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVG 126
I+E+R GTGGEEA+LFA D+F+MY RY+++KGW EV + E+DL G +E + G
Sbjct: 88 AIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKN 147
Query: 127 VYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEVDVRLRNEDLRIDTYRSGG 186
YG LK+ESG+HRVQRVP+TE GR+HTS +VA+LP+ +E D+ +R EDL+I+T+R+ G
Sbjct: 148 AYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASG 207
Query: 187 SGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNXXXXXXXXXXXXYEMERSRIHLSRS 246
GGQ+ N T SAVR+TH+PTG+ +S Q+ERSQ+ N Y++++ + S
Sbjct: 208 HGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREIS 267
Query: 247 KLRSEQIGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDALL 301
+ R QIG+G+RSE+IRTYNFPQ RVTDHR+ T + + ++++G +LD I L+
Sbjct: 268 QKRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSYRLQEILDG-DLDEIISKLI 321
>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 = 253 bits (646), Expect = 9e-68, Method: Compositional matrix adjust.
Identities = 131/298 (43%), Positives = 188/298 (63%), Gaps = 5/298 (1%)
Query: 3 LISELRTKQKEIDGLKSLIYECSEDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDA 62
LI E R ++++ +SL+ +D ++ +MA E + ++ PKD
Sbjct: 47 LIREYRKVLEDLEQAESLL----DDPELKEMAKAEREALLARKEALEKELERHLLPKDPM 102
Query: 63 DERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAI 122
DERD I+E+RAGTGGEEA+LFA D+F MY R++++ G++ EV+ +DL G+ + +
Sbjct: 103 DERDAIVEIRAGTGGEEAALFARDLFNMYLRFAEEMGFETEVLDSHPTDLGGFSKVVFEV 162
Query: 123 SGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEVDVRLRNEDLRIDTY 182
G G YG K+ESG+HRVQRVP+TE GR+HTS +VA+LP+A+E D L +++RID
Sbjct: 163 RGPGAYGTFKYESGVHRVQRVPVTETQGRIHTSTATVAVLPKAEEEDFALNMDEIRIDVM 222
Query: 183 RSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNXXXXXXXXXXXXYEMERSRIH 242
R+ G GGQ NTT+SAVRV H+PTG+ ++ QD RSQ N EM+R+
Sbjct: 223 RASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNREKALMILRSRLLEMKRAEEA 282
Query: 243 LSRSKLRSEQIGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDAL 300
K R QIG+G+RSE+IRTYNFPQ RVTDHR+G T H + ++ G +L ++AL
Sbjct: 283 ERLRKTRLAQIGTGERSEKIRTYNFPQSRVTDHRIGFTTHDLEGVLSG-HLTPILEAL 339
>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 = 220 bits (560), Expect = 1e-57, Method: Compositional matrix adjust.
Identities = 111/245 (45%), Positives = 158/245 (64%), Gaps = 1/245 (0%)
Query: 58 PKDDADERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKE 117
PKD D+++ ILE+R GG+EA+LFA D+ Y++Y++ +GWKFEV + + + G KE
Sbjct: 116 PKDPNDDKNIILEIRGAAGGDEAALFAGDLLNXYQKYAENQGWKFEVXEASANGVGGLKE 175
Query: 118 ASAAISGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEVDVRLRNEDL 177
A +SG VY KLK+ESG HRVQRVP+TE GRVHTS +V + P+ +EV+ + +DL
Sbjct: 176 VVAXVSGQSVYSKLKYESGAHRVQRVPVTESQGRVHTSTATVLVXPEVEEVEYEIDPKDL 235
Query: 178 RIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNXXXXXXXXXXXXYEME 237
R+D Y + G+GGQ+ N +AVR+ H+PT + + Q+ER+Q N +
Sbjct: 236 RVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEXQEERTQQKNRDKAXKIIRARVADHF 295
Query: 238 RSRIHLSRSKLRSEQIGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFI 297
+ R +G+GDRSERIRTYNFPQ RVTDHR+G+T + ++ G+ LD I
Sbjct: 296 AQIAQDEQDAERKSTVGTGDRSERIRTYNFPQNRVTDHRIGLTLQKLDSILSGK-LDEVI 354
Query: 298 DALLL 302
DAL+L
Sbjct: 355 DALIL 359
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 167 bits (424), Expect = 5e-42, Method: Compositional matrix adjust.
Identities = 90/242 (37%), Positives = 140/242 (57%), Gaps = 7/242 (2%)
Query: 63 DERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAI 122
D DC L+++AG+GG EA +A + +MY R+++ +G+K E++ +E ++ G K + I
Sbjct: 124 DSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKI 183
Query: 123 SGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQA-DEVDVRLRNEDLRIDT 181
SG YG L+ E+G+HR+ R + GR HTS S + P+ D++D+ + DLRID
Sbjct: 184 SGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDV 243
Query: 182 YRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNXXXXXXXXXXXXYEMERSRI 241
YR+ G+GGQH N T SAVR+THIPTG+ Q++RSQH N YE+E +
Sbjct: 244 YRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYELEMQKK 303
Query: 242 HLSRSKLRSEQ--IGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDA 299
+ + + + IG G +IR+Y R+ D R G+ +++G +LD FI+A
Sbjct: 304 NAEKQAMEDNKSDIGWG---SQIRSYVLDDSRIKDLRTGVETRNTQAVLDG-SLDQFIEA 359
Query: 300 LL 301
L
Sbjct: 360 SL 361
>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 = 167 bits (422), Expect = 9e-42, Method: Compositional matrix adjust.
Identities = 90/242 (37%), Positives = 140/242 (57%), Gaps = 7/242 (2%)
Query: 63 DERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAI 122
D DC L+++AG+GG EA +A + +MY R+++ +G+K E++ +E ++ G K + I
Sbjct: 124 DSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKI 183
Query: 123 SGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQA-DEVDVRLRNEDLRIDT 181
SG YG L+ E+G+HR+ R + GR HTS S + P+ D++D+ + DLRID
Sbjct: 184 SGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDV 243
Query: 182 YRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNXXXXXXXXXXXXYEMERSRI 241
YR+ G+GGQH N T SAVR+THIPTG+ Q++RSQH N YE+E +
Sbjct: 244 YRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYEVEMQKK 303
Query: 242 HLSRSKLRSEQ--IGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDA 299
+ + + + IG G +IR+Y R+ D R G+ +++G +LD FI+A
Sbjct: 304 NAEKQAMEDNKSDIGWG---SQIRSYVLDDSRIKDLRTGVETRNTQAVLDG-SLDQFIEA 359
Query: 300 LL 301
L
Sbjct: 360 SL 361
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 164 bits (415), Expect = 6e-41, Method: Compositional matrix adjust.
Identities = 91/242 (37%), Positives = 140/242 (57%), Gaps = 7/242 (2%)
Query: 63 DERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAI 122
D DC L+++AG+GG EA +A + + Y R+++ +G+K E++ +E ++ G K + I
Sbjct: 124 DSADCYLDIQAGSGGTEAQDWASXLERXYLRWAESRGFKTEIIEESEGEVAGIKSVTIKI 183
Query: 123 SGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQA-DEVDVRLRNEDLRIDT 181
SG YG L+ E+G+HR+ R + GR HTS S + P+ D++D+ + DLRID
Sbjct: 184 SGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDV 243
Query: 182 YRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNXXXXXXXXXXXXYEMERSRI 241
YR+ G+GGQH N T SAVR+THIPTG+ Q++RSQH N YE+E +
Sbjct: 244 YRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAXKQXKAKLYEVEXQKK 303
Query: 242 HLSRSKLRSEQ--IGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDA 299
+ + + IG G +IR+Y R+ D R G+ +++G +LD FI+A
Sbjct: 304 NAEKQAXEDNKSDIGWG---SQIRSYVLDDSRIKDLRTGVETRNTQAVLDG-SLDQFIEA 359
Query: 300 LL 301
L
Sbjct: 360 SL 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 = 139 bits (349), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 98/299 (32%), Positives = 154/299 (51%), Gaps = 10/299 (3%)
Query: 4 ISELRTKQKEIDGLKSLIYEC-SEDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDA 62
+ R+ + ++ GL L+ E +E+++ L EE +DE
Sbjct: 54 VDTFRSLESDLQGLLELMEELPAEEREALKPELEEAAKKLDELYHQTLLNFPHA------ 107
Query: 63 DERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAI 122
E++ IL ++ G GG EA +A + +MY R+++++G++ EVV +T G A +
Sbjct: 108 -EKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILV 166
Query: 123 SGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTS-AVSVAILPQADEVDVRLRNEDLRIDT 181
G YG L E+G+HR+ R + SGR HTS A I +EV+V L+ E+LRID
Sbjct: 167 KGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDV 226
Query: 182 YRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNXXXXXXXXXXXXYEMERSRI 241
R+ G GGQ NTT+SAVRV H+PTG+T++ Q RSQ N YE+ER +
Sbjct: 227 MRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKR 286
Query: 242 HLSRSKLRSEQIGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDAL 300
LR E + + +IR+Y + V DHR G+ H ++++G+ +D+ L
Sbjct: 287 EEELKALRGE-VEPIEWGSQIRSYVLDKNYVKDHRTGLMRHDPENVLDGDLMDLIWAGL 344
>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 = 138 bits (348), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 98/299 (32%), Positives = 154/299 (51%), Gaps = 10/299 (3%)
Query: 4 ISELRTKQKEIDGLKSLIYEC-SEDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDA 62
+ R+ + ++ GL L+ E +E+++ L EE +DE
Sbjct: 54 VDTFRSLESDLQGLLELMEELPAEEREALKPELEEAAKKLDELYHQTLLNFPHA------ 107
Query: 63 DERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAI 122
E++ IL ++ G GG EA +A + +MY R+++++G++ EVV +T G A +
Sbjct: 108 -EKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILV 166
Query: 123 SGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTS-AVSVAILPQADEVDVRLRNEDLRIDT 181
G YG L E+G+HR+ R + SGR HTS A I +EV+V L+ E+LRID
Sbjct: 167 KGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDV 226
Query: 182 YRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNXXXXXXXXXXXXYEMERSRI 241
R+ G GGQ NTT+SAVRV H+PTG+T++ Q RSQ N YE+ER +
Sbjct: 227 MRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKR 286
Query: 242 HLSRSKLRSEQIGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDAL 300
LR E + + +IR+Y + V DHR G+ H ++++G+ +D+ L
Sbjct: 287 EEELKALRGE-VRPIEWGSQIRSYVLDKNYVKDHRTGLMRHDPENVLDGDLMDLIWAGL 344
>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 = 138 bits (348), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 98/299 (32%), Positives = 154/299 (51%), Gaps = 10/299 (3%)
Query: 4 ISELRTKQKEIDGLKSLIYEC-SEDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDA 62
+ R+ + ++ GL L+ E +E+++ L EE +DE
Sbjct: 59 VDTFRSLESDLQGLLELMEELPAEEREALKPELEEAAKKLDELYHQTLLNFPHA------ 112
Query: 63 DERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAI 122
E++ IL ++ G GG EA +A + +MY R+++++G++ EVV +T G A +
Sbjct: 113 -EKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILV 171
Query: 123 SGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTS-AVSVAILPQADEVDVRLRNEDLRIDT 181
G YG L E+G+HR+ R + SGR HTS A I +EV+V L+ E+LRID
Sbjct: 172 KGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDV 231
Query: 182 YRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNXXXXXXXXXXXXYEMERSRI 241
R+ G GGQ NTT+SAVRV H+PTG+T++ Q RSQ N YE+ER +
Sbjct: 232 MRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKR 291
Query: 242 HLSRSKLRSEQIGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDAL 300
LR E + + +IR+Y + V DHR G+ H ++++G+ +D+ L
Sbjct: 292 EEELKALRGE-VRPIEWGSQIRSYVLDKNYVKDHRTGLMRHDPENVLDGDLMDLIWAGL 349
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 138 bits (348), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 98/299 (32%), Positives = 154/299 (51%), Gaps = 10/299 (3%)
Query: 4 ISELRTKQKEIDGLKSLIYEC-SEDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDA 62
+ R+ + ++ GL L+ E +E+++ L EE +DE
Sbjct: 59 VDTFRSLESDLQGLLELMEELPAEEREALKPELEEAAKKLDELYHQTLLNFPHA------ 112
Query: 63 DERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAI 122
E++ IL ++ G GG EA +A + +MY R+++++G++ EVV +T G A +
Sbjct: 113 -EKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILV 171
Query: 123 SGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTS-AVSVAILPQADEVDVRLRNEDLRIDT 181
G YG L E+G+HR+ R + SGR HTS A I +EV+V L+ E+LRID
Sbjct: 172 KGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDV 231
Query: 182 YRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNXXXXXXXXXXXXYEMERSRI 241
R+ G GGQ NTT+SAVRV H+PTG+T++ Q RSQ N YE+ER +
Sbjct: 232 MRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKR 291
Query: 242 HLSRSKLRSEQIGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDAL 300
LR E + + +IR+Y + V DHR G+ H ++++G+ +D+ L
Sbjct: 292 EEELKALRGE-VRPIEWGSQIRSYVLDKNYVKDHRTGLMRHDPENVLDGDLMDLIWAGL 349
>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 = 138 bits (347), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 98/299 (32%), Positives = 154/299 (51%), Gaps = 10/299 (3%)
Query: 4 ISELRTKQKEIDGLKSLIYEC-SEDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDA 62
+ R+ + ++ GL L+ E +E+++ L EE +DE
Sbjct: 72 VDTFRSLESDLQGLLELMEELPAEEREALKPELEEAAKKLDELYHQTLLNFPHA------ 125
Query: 63 DERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAI 122
E++ IL ++ G GG EA +A + +MY R+++++G++ EVV +T G A +
Sbjct: 126 -EKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILV 184
Query: 123 SGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTS-AVSVAILPQADEVDVRLRNEDLRIDT 181
G YG L E+G+HR+ R + SGR HTS A I +EV+V L+ E+LRID
Sbjct: 185 KGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDV 244
Query: 182 YRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNXXXXXXXXXXXXYEMERSRI 241
R+ G GGQ NTT+SAVRV H+PTG+T++ Q RSQ N YE+ER +
Sbjct: 245 MRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKR 304
Query: 242 HLSRSKLRSEQIGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDAL 300
LR E + + +IR+Y + V DHR G+ H ++++G+ +D+ L
Sbjct: 305 EEELKALRGE-VRPIEWGSQIRSYVLDKNYVKDHRTGLMRHDPENVLDGDLMDLIWAGL 362
>pdb|2RSM|A Chain A, Solution Structure And Sirna-Mediated Knockdown Analysis
Of The Mitochondrial Disease-Related Protein C12orf65
(Ict2)
Length = 115
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 24/50 (48%)
Query: 172 LRNEDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMN 221
L +L + G GGQ N T++ V + H+P+G+ + RS N
Sbjct: 43 LNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQN 92
>pdb|1Y4M|A Chain A, Crystal Structure Of Human Endogenous Retrovirus
Herv-Frd Envelope Protein (Syncitin-2)
pdb|1Y4M|B Chain B, Crystal Structure Of Human Endogenous Retrovirus
Herv-Frd Envelope Protein (Syncitin-2)
pdb|1Y4M|C Chain C, Crystal Structure Of Human Endogenous Retrovirus
Herv-Frd Envelope Protein (Syncitin-2)
Length = 53
Score = 32.7 bits (73), Expect = 0.24, Method: Composition-based stats.
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 7 LRTKQKEIDGLKSLIYECSEDKDMLDMATEELCLAIDEE 45
L T Q++ID L +++ + DML A +CLA+DE+
Sbjct: 9 LTTMQEQIDSLAAVVLQNRRGLDMLTAAQGGICLALDEK 47
>pdb|2JY9|A Chain A, Nmr Structure Of Putative Trna Hydrolase Domain From
Salmonella Typhimurium. Northeast Structural Genomics
Consortium Target Str220
Length = 148
Score = 31.6 bits (70), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 170 VRLRNEDLRIDTYRSGGSGGQHANTTNSAV 199
V + + +L I R+ G+GGQH N T+SA+
Sbjct: 8 VSIADNELEITAIRAQGAGGQHVNKTSSAI 37
>pdb|2WFC|A Chain A, Crystal Structure Of Peroxiredoxin 5 From Arenicola Marina
pdb|2WFC|B Chain B, Crystal Structure Of Peroxiredoxin 5 From Arenicola Marina
pdb|2WFC|C Chain C, Crystal Structure Of Peroxiredoxin 5 From Arenicola Marina
pdb|2WFC|D Chain D, Crystal Structure Of Peroxiredoxin 5 From Arenicola Marina
Length = 167
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 86 DVFKMYERYSQKKGWKFEVVGV-----TESDLRGYKEASAAISGVGV 127
D M E ++ KKG F V G +++ L GY E +AAI G GV
Sbjct: 21 DKVNMAELFAGKKGVLFAVPGAFTPGSSKTHLPGYVEQAAAIHGKGV 67
>pdb|4DH9|Y Chain Y, Crystal Structure Of Yaej Bound To The 70s Ribosome
Length = 140
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 176 DLRIDTYRSGGSGGQHANTTNSAV 199
+L I R+ G+GGQH N T++A+
Sbjct: 14 ELEITAIRAQGAGGQHVNKTSTAI 37
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 0.132 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,292,729
Number of Sequences: 62578
Number of extensions: 314500
Number of successful extensions: 622
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: 587
Number of HSP's gapped (non-prelim): 18
length of query: 316
length of database: 14,973,337
effective HSP length: 99
effective length of query: 217
effective length of database: 8,778,115
effective search space: 1904850955
effective search space used: 1904850955
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: 51 (24.3 bits)