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= 017009
(379 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 = 253 bits (646), Expect = 1e-67, Method: Compositional matrix adjust.
Identities = 131/315 (41%), Positives = 196/315 (62%), Gaps = 4/315 (1%)
Query: 47 WDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASIIK 106
W+ AQ + + ++ ++ L K ++D +++L E D D EA + +
Sbjct: 47 WNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEAD--DEETFNEAVAELD 104
Query: 107 ELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQRYKTR 166
L + L Q E ++ SG YD + I AG+GGT+AQDWA ML RMY+RW E + +KT
Sbjct: 105 ALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTE 164
Query: 167 VVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMP 226
++E+S GE AGIKS I++ G YAYG+L E G HR+VR+SPF++ G R TSFS A V P
Sbjct: 165 IIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYP 224
Query: 227 LLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLAN 286
+ ++ +D++I DL I RA G GGQ+VN+ E+AVRITHIPTG+ +C +RSQ N
Sbjct: 225 EV-DDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKN 283
Query: 287 KIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRTGHET 346
K +A+ ++KAKL + +++ +E + + + WG QIR+YV + +KD+RTG ET
Sbjct: 284 KDQAMKQMKAKLYEVEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSR-IKDLRTGVET 342
Query: 347 SDIVSVMDGELEPFI 361
+ +V+DG L+ FI
Sbjct: 343 RNTQAVLDGSLDQFI 357
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 251 bits (641), Expect = 5e-67, Method: Compositional matrix adjust.
Identities = 130/315 (41%), Positives = 195/315 (61%), Gaps = 4/315 (1%)
Query: 47 WDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASIIK 106
W+ AQ + + ++ ++ L K ++D +++L E D D EA + +
Sbjct: 47 WNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEAD--DEETFNEAVAELD 104
Query: 107 ELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQRYKTR 166
L + L Q E ++ SG YD + I AG+GGT+AQDWA ML RMY+RW E + +KT
Sbjct: 105 ALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTE 164
Query: 167 VVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMP 226
++E+S GE AGIKS I++ G YAYG+L E G HR+VR+SPF++ G R TSFS A V P
Sbjct: 165 IIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYP 224
Query: 227 LLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLAN 286
+ ++ +D++I DL I R G GGQ+VN+ E+AVRITHIPTG+ +C +RSQ N
Sbjct: 225 EV-DDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKN 283
Query: 287 KIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRTGHET 346
K +A+ ++KAKL + +++ +E + + + WG QIR+YV + +KD+RTG ET
Sbjct: 284 KDQAMKQMKAKLYELEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSR-IKDLRTGVET 342
Query: 347 SDIVSVMDGELEPFI 361
+ +V+DG L+ FI
Sbjct: 343 RNTQAVLDGSLDQFI 357
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 242 bits (618), Expect = 2e-64, Method: Compositional matrix adjust.
Identities = 129/315 (40%), Positives = 190/315 (60%), Gaps = 4/315 (1%)
Query: 47 WDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASIIK 106
W+ AQ + + ++ ++ L K ++D +++L E D D EA + +
Sbjct: 47 WNEPERAQALGKERSSLEAVVDTLDQXKQGLEDVSGLLELAVEAD--DEETFNEAVAELD 104
Query: 107 ELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQRYKTR 166
L + L Q E + SG YD + I AG+GGT+AQDWA L R Y+RW E + +KT
Sbjct: 105 ALEEKLAQLEFRRXFSGEYDSADCYLDIQAGSGGTEAQDWASXLERXYLRWAESRGFKTE 164
Query: 167 VVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMP 226
++E+S GE AGIKS I++ G YAYG+L E G HR+VR+SPF++ G R TSFS A V P
Sbjct: 165 IIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYP 224
Query: 227 LLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLAN 286
+ ++ +D++I DL I RA G GGQ+VN+ E+AVRITHIPTG+ +C +RSQ N
Sbjct: 225 EV-DDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKN 283
Query: 287 KIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRTGHET 346
K +A + KAKL + +++ +E + + WG QIR+YV + +KD+RTG ET
Sbjct: 284 KDQAXKQXKAKLYEVEXQKKNAEKQAXEDNKSDIGWGSQIRSYVLDDSR-IKDLRTGVET 342
Query: 347 SDIVSVMDGELEPFI 361
+ +V+DG L+ FI
Sbjct: 343 RNTQAVLDGSLDQFI 357
>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 = 216 bits (551), Expect = 1e-56, Method: Compositional matrix adjust.
Identities = 140/352 (39%), Positives = 202/352 (57%), Gaps = 8/352 (2%)
Query: 10 DVEAASDRVEEIRASXXXXXXXXXXXXXXXXXXDSSFWDNRAEAQETLQALTDVKDKINL 69
D+E + R+E +R D S W++ A++ Q ++ ++
Sbjct: 2 DLERLAQRLEGLRGYLDIPQKETRLKELERRLEDPSLWNDPEAARKVSQEAARLRRTVD- 60
Query: 70 LTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASIIKELNKALDQFELTQLLSGPYDKEG 129
F++ D +++L EE+ + + L+ ++E K LD+ LL+ P+ ++
Sbjct: 61 --TFRSLESDLQGLLELMEELPAEEREALKPE---LEEAAKKLDELYHQTLLNFPHAEKN 115
Query: 130 AVISITAGAGGTDAQDWADMLLRMYVRWGEKQRYKTRVVEKSLGEEAGIKSAVIEVEGRY 189
A+++I GAGGT+A DWA+MLLRMY R+ E+Q ++ VV+ + G EAGI A I V+G
Sbjct: 116 AILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGEN 175
Query: 190 AYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRA 249
AYG LS E G HR+VR SPF+A G R TSF+G EV+P + EE V PEE L I RA
Sbjct: 176 AYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEE-LRIDVMRA 234
Query: 250 GGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANKIKALSRLKAKLLVIAEEQRASE 309
G GGQ VN ++AVR+ H+PTG+TV C RSQ+ NK AL LKA+L + ++R E
Sbjct: 235 SGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKREEE 294
Query: 310 IKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRTGHETSDIVSVMDGELEPFI 361
+K +RG+ EWG QIR+YV VKD RTG D +V+DG+L I
Sbjct: 295 LKALRGEVRPIEWGSQIRSYVLD-KNYVKDHRTGLMRHDPENVLDGDLMDLI 345
>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 = 214 bits (546), Expect = 5e-56, Method: Compositional matrix adjust.
Identities = 135/319 (42%), Positives = 193/319 (60%), Gaps = 8/319 (2%)
Query: 43 DSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAA 102
D S W++ A++ Q ++ ++ F++ D +++L EE+ + + L+
Sbjct: 30 DPSLWNDPEAARKVSQEAARLRRTVD---TFRSLESDLQGLLELMEELPAEEREALKPE- 85
Query: 103 SIIKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQR 162
++E K LD+ LL+ P+ ++ A+++I GAGGT+A DWA+MLLRMY R+ E+Q
Sbjct: 86 --LEEAAKKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQG 143
Query: 163 YKTRVVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGA 222
++ VV+ + G EAGI A I V+G AYG LS E G HR+VR SPF+A G R TSF+G
Sbjct: 144 FQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGV 203
Query: 223 EVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERS 282
EV+P + EE V PEE L I RA G GGQ VN ++AVR+ H+PTG+TV C RS
Sbjct: 204 EVIPEVDEEVEVVLKPEE-LRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRS 262
Query: 283 QLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRT 342
Q+ NK AL LKA+L + ++R E+K +RG+ EWG QIR+YV VKD RT
Sbjct: 263 QIKNKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLD-KNYVKDHRT 321
Query: 343 GHETSDIVSVMDGELEPFI 361
G D +V+DG+L I
Sbjct: 322 GLMRHDPENVLDGDLMDLI 340
>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 = 214 bits (546), Expect = 5e-56, Method: Compositional matrix adjust.
Identities = 135/319 (42%), Positives = 193/319 (60%), Gaps = 8/319 (2%)
Query: 43 DSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAA 102
D S W++ A++ Q ++ ++ F++ D +++L EE+ + + L+
Sbjct: 30 DPSLWNDPEAARKVSQEAARLRRTVD---TFRSLESDLQGLLELMEELPAEEREALKPE- 85
Query: 103 SIIKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQR 162
++E K LD+ LL+ P+ ++ A+++I GAGGT+A DWA+MLLRMY R+ E+Q
Sbjct: 86 --LEEAAKKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQG 143
Query: 163 YKTRVVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGA 222
++ VV+ + G EAGI A I V+G AYG LS E G HR+VR SPF+A G R TSF+G
Sbjct: 144 FQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGV 203
Query: 223 EVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERS 282
EV+P + EE V PEE L I RA G GGQ VN ++AVR+ H+PTG+TV C RS
Sbjct: 204 EVIPEVDEEVEVVLKPEE-LRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRS 262
Query: 283 QLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRT 342
Q+ NK AL LKA+L + ++R E+K +RG+ EWG QIR+YV VKD RT
Sbjct: 263 QIKNKELALKILKARLYELERKKREEELKALRGEVEPIEWGSQIRSYVLD-KNYVKDHRT 321
Query: 343 GHETSDIVSVMDGELEPFI 361
G D +V+DG+L I
Sbjct: 322 GLMRHDPENVLDGDLMDLI 340
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 214 bits (546), Expect = 6e-56, Method: Compositional matrix adjust.
Identities = 135/319 (42%), Positives = 193/319 (60%), Gaps = 8/319 (2%)
Query: 43 DSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAA 102
D S W++ A++ Q ++ ++ F++ D +++L EE+ + + L+
Sbjct: 35 DPSLWNDPEAARKVSQEAARLRRTVD---TFRSLESDLQGLLELMEELPAEEREALKPE- 90
Query: 103 SIIKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQR 162
++E K LD+ LL+ P+ ++ A+++I GAGGT+A DWA+MLLRMY R+ E+Q
Sbjct: 91 --LEEAAKKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQG 148
Query: 163 YKTRVVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGA 222
++ VV+ + G EAGI A I V+G AYG LS E G HR+VR SPF+A G R TSF+G
Sbjct: 149 FQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGV 208
Query: 223 EVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERS 282
EV+P + EE V PEE L I RA G GGQ VN ++AVR+ H+PTG+TV C RS
Sbjct: 209 EVIPEVDEEVEVVLKPEE-LRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRS 267
Query: 283 QLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRT 342
Q+ NK AL LKA+L + ++R E+K +RG+ EWG QIR+YV VKD RT
Sbjct: 268 QIKNKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLD-KNYVKDHRT 326
Query: 343 GHETSDIVSVMDGELEPFI 361
G D +V+DG+L I
Sbjct: 327 GLMRHDPENVLDGDLMDLI 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 = 214 bits (545), Expect = 6e-56, Method: Compositional matrix adjust.
Identities = 135/319 (42%), Positives = 193/319 (60%), Gaps = 8/319 (2%)
Query: 43 DSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAA 102
D S W++ A++ Q ++ ++ F++ D +++L EE+ + + L+
Sbjct: 48 DPSLWNDPEAARKVSQEAARLRRTVD---TFRSLESDLQGLLELMEELPAEEREALKPE- 103
Query: 103 SIIKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQR 162
++E K LD+ LL+ P+ ++ A+++I GAGGT+A DWA+MLLRMY R+ E+Q
Sbjct: 104 --LEEAAKKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQG 161
Query: 163 YKTRVVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGA 222
++ VV+ + G EAGI A I V+G AYG LS E G HR+VR SPF+A G R TSF+G
Sbjct: 162 FQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGV 221
Query: 223 EVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERS 282
EV+P + EE V PEE L I RA G GGQ VN ++AVR+ H+PTG+TV C RS
Sbjct: 222 EVIPEVDEEVEVVLKPEE-LRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRS 280
Query: 283 QLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRT 342
Q+ NK AL LKA+L + ++R E+K +RG+ EWG QIR+YV VKD RT
Sbjct: 281 QIKNKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLD-KNYVKDHRT 339
Query: 343 GHETSDIVSVMDGELEPFI 361
G D +V+DG+L I
Sbjct: 340 GLMRHDPENVLDGDLMDLI 358
>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 = 162 bits (409), Expect = 3e-40, Method: Compositional matrix adjust.
Identities = 102/255 (40%), Positives = 142/255 (55%), Gaps = 7/255 (2%)
Query: 110 KALDQF--ELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQRYKTRV 167
K LDQ EL LLS P + A++ I G GG +A +A L RMY R+ E++ + V
Sbjct: 67 KELDQLYQELLFLLS-PEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEV 125
Query: 168 VEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMPL 227
E + GI+ V V+G+ AYG L E G HR+ R + G TS + V+P
Sbjct: 126 AEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPE 185
Query: 228 LPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANK 287
+ E+ D++I EDL+I RA G GGQ VNK E+AVRITH+PTG+ V C ERSQ NK
Sbjct: 186 IEEK--DIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNK 243
Query: 288 IKALSRLKAKLLVIAEEQRASEIKQIRGDAV-KAEWGQQIRNYVFHPYKLVKDVRTGHET 346
AL L+A+L + +EQ+ EI Q R + E ++IR Y F P V D R + +
Sbjct: 244 QTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNF-PQNRVTDHRINYTS 302
Query: 347 SDIVSVMDGELEPFI 361
+ ++DG+L+ 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 = 161 bits (408), Expect = 4e-40, Method: Compositional matrix adjust.
Identities = 102/255 (40%), Positives = 142/255 (55%), Gaps = 7/255 (2%)
Query: 110 KALDQF--ELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQRYKTRV 167
K LDQ EL LLS P + A++ I G GG +A +A L RMY R+ E++ + V
Sbjct: 67 KELDQLYQELLFLLS-PEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEV 125
Query: 168 VEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMPL 227
E + GI+ V V+G+ AYG L E G HR+ R + G TS + V+P
Sbjct: 126 AEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPE 185
Query: 228 LPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANK 287
+ E+ D++I EDL+I RA G GGQ VNK E+AVRITH+PTG+ V C ERSQ NK
Sbjct: 186 IEEK--DIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNK 243
Query: 288 IKALSRLKAKLLVIAEEQRASEIKQIRGDAV-KAEWGQQIRNYVFHPYKLVKDVRTGHET 346
AL L+A+L + +EQ+ EI Q R + E ++IR Y F P V D R + +
Sbjct: 244 QTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNF-PQNRVTDHRINYTS 302
Query: 347 SDIVSVMDGELEPFI 361
+ ++DG+L+ 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 = 148 bits (373), Expect = 6e-36, Method: Compositional matrix adjust.
Identities = 99/326 (30%), Positives = 162/326 (49%), Gaps = 17/326 (5%)
Query: 43 DSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDD---AVTIV---KLTEEMDSTDAG 96
D ++ Q + ++ + I L+ +++ ++D A +++ +L E +
Sbjct: 21 DPEVLKDKGRYQSLSRRYAEMGEVIGLIREYRKVLEDLEQAESLLDDPELKEMAKAEREA 80
Query: 97 LLEEAASIIKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVR 156
LL ++ KEL + L L P D+ A++ I AG GG +A +A L MY+R
Sbjct: 81 LLARKEALEKELERHL-------LPKDPMDERDAIVEIRAGTGGEEAALFARDLFNMYLR 133
Query: 157 WGEKQRYKTRVVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQ 216
+ E+ ++T V++ + G V EV G AYG E G HR+ R +G
Sbjct: 134 FAEEMGFETEVLDSHPTDLGGFSKVVFEVRGPGAYGTFKYESGVHRVQRVPVTETQGRIH 193
Query: 217 TSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVR 276
TS + V+P EE D + +++ I RA G GGQ VN ++AVR+ H+PTG+ V
Sbjct: 194 TSTATVAVLPKAEEE--DFALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVT 251
Query: 277 CTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAV-KAEWGQQIRNYVFHPYK 335
C + RSQ+ N+ KAL L+++LL + + A +++ R + E ++IR Y F P
Sbjct: 252 CQDSRSQIKNREKALMILRSRLLEMKRAEEAERLRKTRLAQIGTGERSEKIRTYNF-PQS 310
Query: 336 LVKDVRTGHETSDIVSVMDGELEPFI 361
V D R G T D+ V+ G L P +
Sbjct: 311 RVTDHRIGFTTHDLEGVLSGHLTPIL 336
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 360
Score = 141 bits (355), Expect = 7e-34, Method: Compositional matrix adjust.
Identities = 87/245 (35%), Positives = 129/245 (52%), Gaps = 15/245 (6%)
Query: 124 PYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQRYKTRVVEKSLGEEAGIKSAVI 183
P D+ A + + AG GG +A +A L RMY R+ E +R++ ++ S GE G K +
Sbjct: 105 PDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMSASEGEHGGYKEIIA 164
Query: 184 EVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMPLLPEESMDVQIPE---E 240
++ G YG L E G HR+ R ++G TS VMP LP D ++P+
Sbjct: 165 KISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSACTVAVMPELP----DAELPDVNPA 220
Query: 241 DLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANKIKALSRLKAKL-- 298
DL I R+ G GGQ+VN ++A+RITH+PTG+ V C +ERSQ NK KALS L A++
Sbjct: 221 DLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHA 280
Query: 299 --LVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRTGHETSDIVSVMDGE 356
+ ++ AS + + G +++ R Y F P V D R + VM+G+
Sbjct: 281 AEMAKRQQAEASTRRNLLGSGDRSDRN---RTYNF-PQGRVTDHRINLTLYRLDEVMEGK 336
Query: 357 LEPFI 361
L+ I
Sbjct: 337 LDMLI 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 = 116 bits (290), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 85/246 (34%), Positives = 125/246 (50%), Gaps = 10/246 (4%)
Query: 120 LLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQRYKTRVVEKSLGEEAGIK 179
L P D + ++ I AGG +A +A LL Y ++ E Q +K V E S G+K
Sbjct: 115 LPKDPNDDKNIILEIRGAAGGDEAALFAGDLLNXYQKYAENQGWKFEVXEASANGVGGLK 174
Query: 180 SAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMPLLPEESMDVQIPE 239
V V G+ Y L E G HR+ R ++G TS A V+ E ++ +I
Sbjct: 175 EVVAXVSGQSVYSKLKYESGAHRVQRVPVTESQGRVHTST--ATVLVXPEVEEVEYEIDP 232
Query: 240 EDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANKIKALSRLKAKL- 298
+DL + A G GGQNVNKV TAVRI H+PT + V EER+Q N+ KA ++A++
Sbjct: 233 KDLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEXQEERTQQKNRDKAXKIIRARVA 292
Query: 299 ---LVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRTGHETSDIVSVMDG 355
IA++++ +E K G ++E +IR Y F P V D R G + S++ G
Sbjct: 293 DHFAQIAQDEQDAERKSTVGTGDRSE---RIRTYNF-PQNRVTDHRIGLTLQKLDSILSG 348
Query: 356 ELEPFI 361
+L+ I
Sbjct: 349 KLDEVI 354
>pdb|2RSM|A Chain A, Solution Structure And Sirna-Mediated Knockdown Analysis
Of The Mitochondrial Disease-Related Protein C12orf65
(Ict2)
Length = 115
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 34/62 (54%)
Query: 239 EEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANKIKALSRLKAKL 298
E +LE F + G GGQ NK V + H+P+G+ V+C + RS N+ A L+ K+
Sbjct: 45 ESELEEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRKIARKVLQEKV 104
Query: 299 LV 300
V
Sbjct: 105 DV 106
>pdb|4DH9|Y Chain Y, Crystal Structure Of Yaej Bound To The 70s Ribosome
Length = 140
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 35/100 (35%), Positives = 49/100 (49%), Gaps = 24/100 (24%)
Query: 232 SMDVQIPEEDLEISFSRAGGKGGQNVNKVETA------VRITHIPT-------------- 271
S V IP+ +LEI+ RA G GGQ+VNK TA +R + +P
Sbjct: 5 SRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLI 64
Query: 272 ---GVTV-RCTEERSQLANKIKALSRLKAKLLVIAEEQRA 307
GV V + E RSQ N+ AL+RL A + + E++A
Sbjct: 65 SSDGVIVIKAQEYRSQELNREAALARLVAMIKELTTEKKA 104
>pdb|2JVA|A Chain A, Nmr Solution Structure Of Peptidyl-Trna Hydrolase Domain
Protein From Pseudomonas Syringae Pv. Tomato. Northeast
Structural Genomics Consortium Target Psr211
Length = 108
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 26/35 (74%)
Query: 232 SMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRI 266
S +V +P+ ++E++ RA G GGQNVNKV +A+ +
Sbjct: 5 SNNVHLPDAEIELTAIRAQGAGGQNVNKVSSAMHL 39
>pdb|2JY9|A Chain A, Nmr Structure Of Putative Trna Hydrolase Domain From
Salmonella Typhimurium. Northeast Structural Genomics
Consortium Target Str220
Length = 148
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 29/100 (29%), Positives = 47/100 (47%), Gaps = 24/100 (24%)
Query: 232 SMDVQIPEEDLEISFSRAGGKGGQNVNKVETA------VRITHIPTG------------- 272
S V I + +LEI+ RA G GGQ+VNK +A +R + +P
Sbjct: 5 SRTVSIADNELEITAIRAQGAGGQHVNKTSSAIHLRFDIRASGLPEYYKQRLLTASHHLI 64
Query: 273 -----VTVRCTEERSQLANKIKALSRLKAKLLVIAEEQRA 307
+ ++ E RSQ N+ A++RL A + + EQ++
Sbjct: 65 SDDGVIIIKAQEFRSQELNREAAIARLVAVIKELTAEQKS 104
>pdb|1J26|A Chain A, Solution Structure Of A Putative Peptidyl-Trna Hydrolase
Domain In A Mouse Hypothetical Protein
Length = 112
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 237 IPEEDLEISFSRAGGKGGQNVNKVETAVRI 266
IP + L IS+ R+ G GGQNVNKV + +
Sbjct: 17 IPLDRLSISYCRSSGPGGQNVNKVNSKAEV 46
>pdb|3UAQ|A Chain A, Crystal Structure Of The N-Lobe Domain Of Lactoferrin
Binding Protein B (Lbpb) Of Moraxella Bovis
pdb|3UAQ|B Chain B, Crystal Structure Of The N-Lobe Domain Of Lactoferrin
Binding Protein B (Lbpb) Of Moraxella Bovis
Length = 341
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 168 VEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMPL 227
++ G+E G S +V G+YA +G HR V ++ F+AK L T + + +
Sbjct: 208 MDSGFGDEVGATSFAEQVFGQYA-----PRQGNHRAVFKADFDAKKLTGTLSTKQKAIAS 262
Query: 228 LPEESMD 234
PE +D
Sbjct: 263 SPETYVD 269
>pdb|4I37|A Chain A, Crystal Structure Of Rabbit Ryanodine Receptor 1 (residues
1-536) Disease Mutant R402g
Length = 536
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 76 KMDDAVTIVKLTEEMDSTDAGLLEEAASIIKELNKALDQFELTQLLSGP 124
MDDA+ + + +E +S AG++ A + + K LD F SGP
Sbjct: 383 HMDDALFLTRCQQE-ESQAAGMIHSTAGLYNQFIKGLDSFSGKPRGSGP 430
>pdb|1EKU|A Chain A, Crystal Structure Of A Biologically Active Single Chain
Mutant Of Human Ifn-Gamma
pdb|1EKU|B Chain B, Crystal Structure Of A Biologically Active Single Chain
Mutant Of Human Ifn-Gamma
Length = 265
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 30/115 (26%), Positives = 48/115 (41%), Gaps = 9/115 (7%)
Query: 47 WDNRAEAQETLQALTDVKDKIN--LLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASI 104
+ N + Q +++ +K+ +N K K DD KLT TD + +A
Sbjct: 58 FKNFKDDQSIQKSVETIKEDMNVKFFNSNKKKRDD---FEKLTN-YSVTDLNVQRKA--- 110
Query: 105 IKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGE 159
I EL + + +F + GPY KE + AG +D D + L + W E
Sbjct: 111 IDELIQVMAEFSTEEQQEGPYVKEAENLKKYFNAGHSDVADNGTLFLGILKNWKE 165
>pdb|2QLY|A Chain A, Crystral Structure Of The N-Terminal Subunit Of Human
Maltase- Glucoamylase
pdb|2QMJ|A Chain A, Crystral Structure Of The N-Terminal Subunit Of Human
Maltase- Glucoamylase In Complex With Acarbose
pdb|3CTT|A Chain A, Crystal Complex Of N-Terminal Human Maltase-Glucoamylase
With Casuarine
Length = 870
Score = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 40/92 (43%), Gaps = 8/92 (8%)
Query: 233 MDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANKIKALS 292
+ + + LE++ S++ K N+ E + T P+ VTV+ SQ + + S
Sbjct: 787 CEFSVTQNRLEVNISQSTYKDPNNLAFNEIKILGTEEPSNVTVKHNGVPSQTSPTVTYDS 846
Query: 293 RLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQ 324
LK ++ ++I + G+A EW
Sbjct: 847 NLKVAII--------TDIDLLLGEAYTVEWAH 870
>pdb|3L4T|A Chain A, Crystal Complex Of N-Terminal Human Maltase-Glucoamylase
With Bj2661
pdb|3L4U|A Chain A, Crystal Complex Of N-Terminal Human Maltase-Glucoamylase
With De-O-Sulfonated Kotalanol
pdb|3L4V|A Chain A, Crystal Complex Of N-Terminal Human Maltase-Glucoamylase
With Kotalanol
pdb|3L4W|A Chain A, Crystal Complex Of N-Terminal Human Maltase-Glucoamylase
With Miglitol
pdb|3L4X|A Chain A, Crystal Complex Of N-Terminal Human Maltase-Glucoamylase
With Nr4-8
pdb|3L4Y|A Chain A, Crystal Complex Of N-Terminal Human Maltase-Glucoamylase
With Nr4-8ii
pdb|3L4Z|A Chain A, Crystal Complex Of N-Terminal Human Maltase-Glucoamylase
With Salacinol
Length = 875
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 40/90 (44%), Gaps = 8/90 (8%)
Query: 233 MDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANKIKALS 292
+ + + LE++ S++ K N+ E + T P+ VTV+ SQ + + S
Sbjct: 787 CEFSVTQNRLEVNISQSTYKDPNNLAFNEIKILGTEEPSNVTVKHNGVPSQTSPTVTYDS 846
Query: 293 RLKAKLLVIAEEQRASEIKQIRGDAVKAEW 322
LK ++ ++I + G+A EW
Sbjct: 847 NLKVAII--------TDIDLLLGEAYTVEW 868
>pdb|2V6B|A Chain A, Crystal Structure Of Lactate Dehydrogenase From
Deinococcus Radiodurans (Apo Form)
pdb|2V6B|B Chain B, Crystal Structure Of Lactate Dehydrogenase From
Deinococcus Radiodurans (Apo Form)
pdb|2V6B|C Chain C, Crystal Structure Of Lactate Dehydrogenase From
Deinococcus Radiodurans (Apo Form)
pdb|2V6B|D Chain D, Crystal Structure Of Lactate Dehydrogenase From
Deinococcus Radiodurans (Apo Form)
Length = 304
Score = 28.1 bits (61), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 185 VEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMP 226
V+G +A+GY+ GE G ++ S G+ F A+ +P
Sbjct: 157 VDGTHAHGYVLGEHGDSEVLAWSSAMVAGMPVADFMQAQNLP 198
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.313 0.131 0.360
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,613,486
Number of Sequences: 62578
Number of extensions: 367069
Number of successful extensions: 1004
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 961
Number of HSP's gapped (non-prelim): 31
length of query: 379
length of database: 14,973,337
effective HSP length: 100
effective length of query: 279
effective length of database: 8,715,537
effective search space: 2431634823
effective search space used: 2431634823
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)