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= 020135
(330 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 = 222 bits (566), Expect = 2e-58, Method: Compositional matrix adjust.
Identities = 110/237 (46%), Positives = 161/237 (67%), Gaps = 5/237 (2%)
Query: 93 YSKANKELRKLRDSMHLISELRTKQKEIDGLKSLIYECSEDKDMLDMATEELCLAIDEEK 152
+ ++E +L D ++ + Q++I+ + ++ +D +M +MA +EL A ++ +
Sbjct: 35 FRALSREYAQLSDVSRCFTDWQQVQEDIETAQMML----DDPEMREMAQDELREAKEKSE 90
Query: 153 RXXXXXXXXXXPKDDADERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVG 212
+ PKD DER+ LEVRAGTGG+EA+LFA D+F+MY RY++ + W+ E++
Sbjct: 91 QLEQQLQVLLLPKDPDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMS 150
Query: 213 VTESDLRGYKEASAAISGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQAD 272
+E + GYKE A ISG GVYG+LKFESG HRVQRVP TE GR+HTSA +VA++P+
Sbjct: 151 ASEGEHGGYKEIIAKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSACTVAVMPELP 210
Query: 273 EVDVRLRNE-DLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMVK 328
+ ++ N DLRIDT+RS G+GGQH NTT+SA+R+TH+PTG+ + QDERSQH K
Sbjct: 211 DAELPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNK 267
>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 = 201 bits (511), Expect = 5e-52, Method: Compositional matrix adjust.
Identities = 86/158 (54%), Positives = 120/158 (75%)
Query: 173 CILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVG 232
I+E+R GTGGEEA+LFA D+F+MY RY+++KGW EV + E+DL G +E + G
Sbjct: 88 AIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKN 147
Query: 233 VYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEVDVRLRNEDLRIDTYRSGG 292
YG LK+ESG+HRVQRVP+TE GR+HTS +VA+LP+ +E D+ +R EDL+I+T+R+ G
Sbjct: 148 AYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASG 207
Query: 293 SGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMVKDS 330
GGQ+ N T SAVR+TH+PTG+ +S Q+ERSQ+ K +
Sbjct: 208 HGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQT 245
>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 = 201 bits (510), Expect = 6e-52, Method: Compositional matrix adjust.
Identities = 86/158 (54%), Positives = 120/158 (75%)
Query: 173 CILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVG 232
I+E+R GTGGEEA+LFA D+F+MY RY+++KGW EV + E+DL G +E + G
Sbjct: 88 AIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKN 147
Query: 233 VYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEVDVRLRNEDLRIDTYRSGG 292
YG LK+ESG+HRVQRVP+TE GR+HTS +VA+LP+ +E D+ +R EDL+I+T+R+ G
Sbjct: 148 AYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASG 207
Query: 293 SGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMVKDS 330
GGQ+ N T SAVR+TH+PTG+ +S Q+ERSQ+ K +
Sbjct: 208 HGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQT 245
>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 = 197 bits (501), Expect = 7e-51, Method: Compositional matrix adjust.
Identities = 98/232 (42%), Positives = 149/232 (64%), Gaps = 4/232 (1%)
Query: 93 YSKANKELRKLRDSMHLISELRTKQKEIDGLKSLIYECSEDKDMLDMATEELCLAIDEEK 152
Y ++ ++ + + LI E R ++++ +SL+ +D ++ +MA E + ++
Sbjct: 31 YQSLSRRYAEMGEVIGLIREYRKVLEDLEQAESLL----DDPELKEMAKAEREALLARKE 86
Query: 153 RXXXXXXXXXXPKDDADERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVG 212
PKD DERD I+E+RAGTGGEEA+LFA D+F MY R++++ G++ EV+
Sbjct: 87 ALEKELERHLLPKDPMDERDAIVEIRAGTGGEEAALFARDLFNMYLRFAEEMGFETEVLD 146
Query: 213 VTESDLRGYKEASAAISGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQAD 272
+DL G+ + + G G YG K+ESG+HRVQRVP+TE GR+HTS +VA+LP+A+
Sbjct: 147 SHPTDLGGFSKVVFEVRGPGAYGTFKYESGVHRVQRVPVTETQGRIHTSTATVAVLPKAE 206
Query: 273 EVDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQ 324
E D L +++RID R+ G GGQ NTT+SAVRV H+PTG+ ++ QD RSQ
Sbjct: 207 EEDFALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQ 258
>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 = 165 bits (418), Expect = 3e-41, Method: Compositional matrix adjust.
Identities = 78/166 (46%), Positives = 115/166 (69%)
Query: 164 PKDDADERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKE 223
PKD D+++ ILE+R GG+EA+LFA D+ Y++Y++ +GWKFEV + + + G KE
Sbjct: 116 PKDPNDDKNIILEIRGAAGGDEAALFAGDLLNXYQKYAENQGWKFEVXEASANGVGGLKE 175
Query: 224 ASAAISGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEVDVRLRNEDL 283
A +SG VY KLK+ESG HRVQRVP+TE GRVHTS +V + P+ +EV+ + +DL
Sbjct: 176 VVAXVSGQSVYSKLKYESGAHRVQRVPVTESQGRVHTSTATVLVXPEVEEVEYEIDPKDL 235
Query: 284 RIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMVKD 329
R+D Y + G+GGQ+ N +AVR+ H+PT + + Q+ER+Q +D
Sbjct: 236 RVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEXQEERTQQKNRD 281
>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 = 151 bits (381), Expect = 5e-37, Method: Compositional matrix adjust.
Identities = 93/261 (35%), Positives = 150/261 (57%), Gaps = 12/261 (4%)
Query: 72 IERRSACLE--NLVNQPEASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGLKSLIYE 129
+E +A LE ++ N+PE + A KE L + + +++ +++ GL L E
Sbjct: 34 LEEVNAELEQPDVWNEPERAQA----LGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVE 89
Query: 130 CSEDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDADERDCILEVRAGTGGEEASLF 189
++D++ + A EL A++E+ D AD C L+++AG+GG EA +
Sbjct: 90 -ADDEETFNEAVAELD-ALEEKLAQLEFRRMFSGEYDSAD---CYLDIQAGSGGTEAQDW 144
Query: 190 AVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESGIHRVQRV 249
A + +MY R+++ +G+K E++ +E ++ G K + ISG YG L+ E+G+HR+ R
Sbjct: 145 ASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRK 204
Query: 250 PLTEKSGRVHTSAVSVAILPQA-DEVDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRVT 308
+ GR HTS S + P+ D++D+ + DLRID YR+ G+GGQH N T SAVR+T
Sbjct: 205 SPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRIT 264
Query: 309 HIPTGMTISIQDERSQHMVKD 329
HIPTG+ Q++RSQH KD
Sbjct: 265 HIPTGIVTQCQNDRSQHKNKD 285
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 151 bits (381), Expect = 5e-37, Method: Compositional matrix adjust.
Identities = 93/261 (35%), Positives = 150/261 (57%), Gaps = 12/261 (4%)
Query: 72 IERRSACLE--NLVNQPEASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGLKSLIYE 129
+E +A LE ++ N+PE + A KE L + + +++ +++ GL L E
Sbjct: 34 LEEVNAELEQPDVWNEPERAQA----LGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVE 89
Query: 130 CSEDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDADERDCILEVRAGTGGEEASLF 189
++D++ + A EL A++E+ D AD C L+++AG+GG EA +
Sbjct: 90 -ADDEETFNEAVAELD-ALEEKLAQLEFRRMFSGEYDSAD---CYLDIQAGSGGTEAQDW 144
Query: 190 AVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESGIHRVQRV 249
A + +MY R+++ +G+K E++ +E ++ G K + ISG YG L+ E+G+HR+ R
Sbjct: 145 ASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRK 204
Query: 250 PLTEKSGRVHTSAVSVAILPQA-DEVDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRVT 308
+ GR HTS S + P+ D++D+ + DLRID YR+ G+GGQH N T SAVR+T
Sbjct: 205 SPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRIT 264
Query: 309 HIPTGMTISIQDERSQHMVKD 329
HIPTG+ Q++RSQH KD
Sbjct: 265 HIPTGIVTQCQNDRSQHKNKD 285
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 147 bits (372), Expect = 6e-36, Method: Compositional matrix adjust.
Identities = 93/261 (35%), Positives = 149/261 (57%), Gaps = 12/261 (4%)
Query: 72 IERRSACLE--NLVNQPEASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGLKSLIYE 129
+E +A LE ++ N+PE + A KE L + + + + +++ GL L E
Sbjct: 34 LEEVNAELEQPDVWNEPERAQA----LGKERSSLEAVVDTLDQXKQGLEDVSGLLELAVE 89
Query: 130 CSEDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDADERDCILEVRAGTGGEEASLF 189
++D++ + A EL A++E+ D AD C L+++AG+GG EA +
Sbjct: 90 -ADDEETFNEAVAELD-ALEEKLAQLEFRRXFSGEYDSAD---CYLDIQAGSGGTEAQDW 144
Query: 190 AVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESGIHRVQRV 249
A + + Y R+++ +G+K E++ +E ++ G K + ISG YG L+ E+G+HR+ R
Sbjct: 145 ASXLERXYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRK 204
Query: 250 PLTEKSGRVHTSAVSVAILPQA-DEVDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRVT 308
+ GR HTS S + P+ D++D+ + DLRID YR+ G+GGQH N T SAVR+T
Sbjct: 205 SPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRIT 264
Query: 309 HIPTGMTISIQDERSQHMVKD 329
HIPTG+ Q++RSQH KD
Sbjct: 265 HIPTGIVTQCQNDRSQHKNKD 285
>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 = 127 bits (319), Expect = 9e-30, Method: Compositional matrix adjust.
Identities = 94/263 (35%), Positives = 143/263 (54%), Gaps = 21/263 (7%)
Query: 66 EQRVLAIERRSACLEN--LVNQPEASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGL 123
E R+ +ERR LE+ L N PEA+ K ++E +LR + + R+ + ++ GL
Sbjct: 36 ETRLKELERR---LEDPSLWNDPEAA----RKVSQEAARLRRT---VDTFRSLESDLQGL 85
Query: 124 KSLIYEC-SEDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDADERDCILEVRAGTG 182
L+ E +E+++ L EE +DE E++ IL ++ G G
Sbjct: 86 LELMEELPAEEREALKPELEEAAKKLDELYHQTLLNFPHA-------EKNAILTIQPGAG 138
Query: 183 GEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESG 242
G EA +A + +MY R+++++G++ EVV +T G A + G YG L E+G
Sbjct: 139 GTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAG 198
Query: 243 IHRVQRVPLTEKSGRVHTS-AVSVAILPQADEVDVRLRNEDLRIDTYRSGGSGGQHANTT 301
+HR+ R + SGR HTS A I +EV+V L+ E+LRID R+ G GGQ NTT
Sbjct: 199 VHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTT 258
Query: 302 NSAVRVTHIPTGMTISIQDERSQ 324
+SAVRV H+PTG+T++ Q RSQ
Sbjct: 259 DSAVRVVHLPTGITVTCQTTRSQ 281
>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 = 126 bits (317), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 94/263 (35%), Positives = 143/263 (54%), Gaps = 21/263 (7%)
Query: 66 EQRVLAIERRSACLEN--LVNQPEASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGL 123
E R+ +ERR LE+ L N PEA+ K ++E +LR + + R+ + ++ GL
Sbjct: 18 ETRLKELERR---LEDPSLWNDPEAA----RKVSQEAARLRRT---VDTFRSLESDLQGL 67
Query: 124 KSLIYEC-SEDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDADERDCILEVRAGTG 182
L+ E +E+++ L EE +DE E++ IL ++ G G
Sbjct: 68 LELMEELPAEEREALKPELEEAAKKLDELYHQTLLNFPHA-------EKNAILTIQPGAG 120
Query: 183 GEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESG 242
G EA +A + +MY R+++++G++ EVV +T G A + G YG L E+G
Sbjct: 121 GTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAG 180
Query: 243 IHRVQRVPLTEKSGRVHTS-AVSVAILPQADEVDVRLRNEDLRIDTYRSGGSGGQHANTT 301
+HR+ R + SGR HTS A I +EV+V L+ E+LRID R+ G GGQ NTT
Sbjct: 181 VHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTT 240
Query: 302 NSAVRVTHIPTGMTISIQDERSQ 324
+SAVRV H+PTG+T++ Q RSQ
Sbjct: 241 DSAVRVVHLPTGITVTCQTTRSQ 263
>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 = 126 bits (317), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 94/263 (35%), Positives = 143/263 (54%), Gaps = 21/263 (7%)
Query: 66 EQRVLAIERRSACLEN--LVNQPEASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGL 123
E R+ +ERR LE+ L N PEA+ K ++E +LR + + R+ + ++ GL
Sbjct: 18 ETRLKELERR---LEDPSLWNDPEAA----RKVSQEAARLRRT---VDTFRSLESDLQGL 67
Query: 124 KSLIYEC-SEDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDADERDCILEVRAGTG 182
L+ E +E+++ L EE +DE E++ IL ++ G G
Sbjct: 68 LELMEELPAEEREALKPELEEAAKKLDELYHQTLLNFPHA-------EKNAILTIQPGAG 120
Query: 183 GEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESG 242
G EA +A + +MY R+++++G++ EVV +T G A + G YG L E+G
Sbjct: 121 GTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAG 180
Query: 243 IHRVQRVPLTEKSGRVHTS-AVSVAILPQADEVDVRLRNEDLRIDTYRSGGSGGQHANTT 301
+HR+ R + SGR HTS A I +EV+V L+ E+LRID R+ G GGQ NTT
Sbjct: 181 VHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTT 240
Query: 302 NSAVRVTHIPTGMTISIQDERSQ 324
+SAVRV H+PTG+T++ Q RSQ
Sbjct: 241 DSAVRVVHLPTGITVTCQTTRSQ 263
>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 = 126 bits (317), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 94/263 (35%), Positives = 143/263 (54%), Gaps = 21/263 (7%)
Query: 66 EQRVLAIERRSACLEN--LVNQPEASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGL 123
E R+ +ERR LE+ L N PEA+ K ++E +LR + + R+ + ++ GL
Sbjct: 23 ETRLKELERR---LEDPSLWNDPEAA----RKVSQEAARLRRT---VDTFRSLESDLQGL 72
Query: 124 KSLIYEC-SEDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDADERDCILEVRAGTG 182
L+ E +E+++ L EE +DE E++ IL ++ G G
Sbjct: 73 LELMEELPAEEREALKPELEEAAKKLDELYHQTLLNFPHA-------EKNAILTIQPGAG 125
Query: 183 GEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESG 242
G EA +A + +MY R+++++G++ EVV +T G A + G YG L E+G
Sbjct: 126 GTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAG 185
Query: 243 IHRVQRVPLTEKSGRVHTS-AVSVAILPQADEVDVRLRNEDLRIDTYRSGGSGGQHANTT 301
+HR+ R + SGR HTS A I +EV+V L+ E+LRID R+ G GGQ NTT
Sbjct: 186 VHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTT 245
Query: 302 NSAVRVTHIPTGMTISIQDERSQ 324
+SAVRV H+PTG+T++ Q RSQ
Sbjct: 246 DSAVRVVHLPTGITVTCQTTRSQ 268
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 126 bits (316), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 94/263 (35%), Positives = 143/263 (54%), Gaps = 21/263 (7%)
Query: 66 EQRVLAIERRSACLEN--LVNQPEASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGL 123
E R+ +ERR LE+ L N PEA+ K ++E +LR + + R+ + ++ GL
Sbjct: 23 ETRLKELERR---LEDPSLWNDPEAA----RKVSQEAARLRRT---VDTFRSLESDLQGL 72
Query: 124 KSLIYEC-SEDKDMLDMATEELCLAIDEEKRXXXXXXXXXXPKDDADERDCILEVRAGTG 182
L+ E +E+++ L EE +DE E++ IL ++ G G
Sbjct: 73 LELMEELPAEEREALKPELEEAAKKLDELYHQTLLNFPHA-------EKNAILTIQPGAG 125
Query: 183 GEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESG 242
G EA +A + +MY R+++++G++ EVV +T G A + G YG L E+G
Sbjct: 126 GTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAG 185
Query: 243 IHRVQRVPLTEKSGRVHTS-AVSVAILPQADEVDVRLRNEDLRIDTYRSGGSGGQHANTT 301
+HR+ R + SGR HTS A I +EV+V L+ E+LRID R+ G GGQ NTT
Sbjct: 186 VHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTT 245
Query: 302 NSAVRVTHIPTGMTISIQDERSQ 324
+SAVRV H+PTG+T++ Q RSQ
Sbjct: 246 DSAVRVVHLPTGITVTCQTTRSQ 268
>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 = 0.24, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 23/46 (50%)
Query: 278 LRNEDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERS 323
L +L + G GGQ N T++ V + H+P+G+ + RS
Sbjct: 43 LNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRS 88
>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 = 0.29, Method: Composition-based stats.
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 113 LRTKQKEIDGLKSLIYECSEDKDMLDMATEELCLAIDEE 151
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 = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 276 VRLRNEDLRIDTYRSGGSGGQHANTTNSAV 305
V + + +L I R+ G+GGQH N T+SA+
Sbjct: 8 VSIADNELEITAIRAQGAGGQHVNKTSSAI 37
>pdb|2UVA|G Chain G, Crystal Structure Of Fatty Acid Synthase From Thermomyces
Lanuginosus At 3.1 Angstrom Resolution. This File
Contains The Beta Subunits Of The Fatty Acid Synthase.
The Entire Crystal Structure Consists Of One
Heterododecameric Fatty Acid Synthase And Is Described In
Remark 400
pdb|2UVA|H Chain H, Crystal Structure Of Fatty Acid Synthase From Thermomyces
Lanuginosus At 3.1 Angstrom Resolution. This File
Contains The Beta Subunits Of The Fatty Acid Synthase.
The Entire Crystal Structure Consists Of One
Heterododecameric Fatty Acid Synthase And Is Described In
Remark 400
pdb|2UVA|I Chain I, Crystal Structure Of Fatty Acid Synthase From Thermomyces
Lanuginosus At 3.1 Angstrom Resolution. This File
Contains The Beta Subunits Of The Fatty Acid Synthase.
The Entire Crystal Structure Consists Of One
Heterododecameric Fatty Acid Synthase And Is Described In
Remark 400
pdb|2UVA|J Chain J, Crystal Structure Of Fatty Acid Synthase From Thermomyces
Lanuginosus At 3.1 Angstrom Resolution. This File
Contains The Beta Subunits Of The Fatty Acid Synthase.
The Entire Crystal Structure Consists Of One
Heterododecameric Fatty Acid Synthase And Is Described In
Remark 400
pdb|2UVA|K Chain K, Crystal Structure Of Fatty Acid Synthase From Thermomyces
Lanuginosus At 3.1 Angstrom Resolution. This File
Contains The Beta Subunits Of The Fatty Acid Synthase.
The Entire Crystal Structure Consists Of One
Heterododecameric Fatty Acid Synthase And Is Described In
Remark 400
pdb|2UVA|L Chain L, Crystal Structure Of Fatty Acid Synthase From Thermomyces
Lanuginosus At 3.1 Angstrom Resolution. This File
Contains The Beta Subunits Of The Fatty Acid Synthase.
The Entire Crystal Structure Consists Of One
Heterododecameric Fatty Acid Synthase And Is Described In
Remark 400
pdb|2UVC|G Chain G, Crystal Structure Of Fatty Acid Synthase Complexed With
Nadp+ From Thermomyces Lanuginosus At 3.1 Angstrom
Resolution. This File Contains The Beta Subunits Of The
Fatty Acid Synthase. The Entire Crystal Structure
Consists Of One Heterododecameric Fatty Acid Synthase And
Is Described In Remark 400
pdb|2UVC|H Chain H, Crystal Structure Of Fatty Acid Synthase Complexed With
Nadp+ From Thermomyces Lanuginosus At 3.1 Angstrom
Resolution. This File Contains The Beta Subunits Of The
Fatty Acid Synthase. The Entire Crystal Structure
Consists Of One Heterododecameric Fatty Acid Synthase And
Is Described In Remark 400
pdb|2UVC|I Chain I, Crystal Structure Of Fatty Acid Synthase Complexed With
Nadp+ From Thermomyces Lanuginosus At 3.1 Angstrom
Resolution. This File Contains The Beta Subunits Of The
Fatty Acid Synthase. The Entire Crystal Structure
Consists Of One Heterododecameric Fatty Acid Synthase And
Is Described In Remark 400
pdb|2UVC|J Chain J, Crystal Structure Of Fatty Acid Synthase Complexed With
Nadp+ From Thermomyces Lanuginosus At 3.1 Angstrom
Resolution. This File Contains The Beta Subunits Of The
Fatty Acid Synthase. The Entire Crystal Structure
Consists Of One Heterododecameric Fatty Acid Synthase And
Is Described In Remark 400
pdb|2UVC|K Chain K, Crystal Structure Of Fatty Acid Synthase Complexed With
Nadp+ From Thermomyces Lanuginosus At 3.1 Angstrom
Resolution. This File Contains The Beta Subunits Of The
Fatty Acid Synthase. The Entire Crystal Structure
Consists Of One Heterododecameric Fatty Acid Synthase And
Is Described In Remark 400
pdb|2UVC|L Chain L, Crystal Structure Of Fatty Acid Synthase Complexed With
Nadp+ From Thermomyces Lanuginosus At 3.1 Angstrom
Resolution. This File Contains The Beta Subunits Of The
Fatty Acid Synthase. The Entire Crystal Structure
Consists Of One Heterododecameric Fatty Acid Synthase And
Is Described In Remark 400
Length = 2060
Score = 31.2 bits (69), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 53 STEMLSNDLIKIMEQRVLAIERRSACLENLVNQPEASP------AEYSKANKELRKLRDS 106
S + L+ D I+ +E+R ++E + + L+N + E P A Y +A+ +L +D
Sbjct: 936 SLKKLTGDFIRRVEERFTSVEGQPSLLQNYSDLDEPYPAVDRILAAYPEASTQLINAQDV 995
Query: 107 MH-LISELRTKQKEIDGLKSL 126
H L+ R QK + + +L
Sbjct: 996 QHFLLLCQRRGQKPVPFVPAL 1016
>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: 192 DVFKMYERYSQKKGWKFEVVGV-----TESDLRGYKEASAAISGVGV 233
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 = 1.6, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 282 DLRIDTYRSGGSGGQHANTTNSAV 305
+L I R+ G+GGQH N T++A+
Sbjct: 14 ELEITAIRAQGAGGQHVNKTSTAI 37
>pdb|1XGY|L Chain L, Crystal Structure Of Anti-Meta I Rhodopsin Fab Fragment
K42- 41l
pdb|1XGY|M Chain M, Crystal Structure Of Anti-Meta I Rhodopsin Fab Fragment
K42- 41l
Length = 216
Score = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 21/43 (48%)
Query: 8 IALHLGALRQLESSSSISHRNPLLHQRWFVQRAAATPSLSNFR 50
+ L A SS S+ H N + + W++QR +P L +R
Sbjct: 13 VTLGTSASISCRSSKSLLHSNGITYLYWYLQRPGQSPQLLIYR 55
>pdb|1Q72|L Chain L, Anti-Cocaine Antibody M82g2 Complexed With Cocaine
pdb|1QYG|L Chain L, Anti-Cocaine Antibody M82g2 Complexed With
Benzoylecgonine
pdb|1RFD|L Chain L, Anti-Cocaine Antibody M82g2
pdb|1RIU|L Chain L, Anti-Cocaine Antibody M82g2 Complexed With
Norbenzoylecgonine
pdb|1RIV|L Chain L, Anti-Cocaine Antibody M82g2 Complexed With Meta-
Oxybenzoylecgonine
Length = 218
Score = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 20 SSSSISHRNPLLHQRWFVQRAAATPSLSNFR 50
SS S+ H N + WF+QR +P L +R
Sbjct: 25 SSKSLLHSNGYTYLHWFLQRPGQSPQLLIYR 55
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
0.315 0.130 0.362
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,890,902
Number of Sequences: 62578
Number of extensions: 338404
Number of successful extensions: 890
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 857
Number of HSP's gapped (non-prelim): 32
length of query: 330
length of database: 14,973,337
effective HSP length: 99
effective length of query: 231
effective length of database: 8,778,115
effective search space: 2027744565
effective search space used: 2027744565
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: 52 (24.6 bits)