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= 021839
(307 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 = 124 bits (311), Expect = 7e-29, Method: Compositional matrix adjust.
Identities = 64/150 (42%), Positives = 96/150 (64%), Gaps = 2/150 (1%)
Query: 140 GTDAQTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPT 199
G TSFS A V P + ++ +D++I DL I RA G GGQ+VN+ E+AVRITHIPT
Sbjct: 210 GGRRHTSFSSAFVYPEV-DDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPT 268
Query: 200 GVTVRCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVF 259
G+ +C +RSQ NK +A+ ++KAKL + +++ +E + + + WG QIR+YV
Sbjct: 269 GIVTQCQNDRSQHKNKDQAMKQMKAKLYEVEMQKKNAEKQAMEDNKSDIGWGSQIRSYVL 328
Query: 260 HPYKLVKDVRTGHETSDIVSVMDGELEPFI 289
+ +KD+RTG ET + +V+DG L+ FI
Sbjct: 329 DDSR-IKDLRTGVETRNTQAVLDGSLDQFI 357
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 34/114 (29%), Positives = 54/114 (47%), Gaps = 2/114 (1%)
Query: 47 WDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASIIK 106
W+ AQ + + ++ ++ L K ++D +++L E D D EA + +
Sbjct: 47 WNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEAD--DEETFNEAVAELD 104
Query: 107 ELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQTSFSGAEVMPLLPEES 160
L + L Q E ++ SG YD + I AG+GGT+AQ S E M L ES
Sbjct: 105 ALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAES 158
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 122 bits (305), Expect = 3e-28, Method: Compositional matrix adjust.
Identities = 63/150 (42%), Positives = 95/150 (63%), Gaps = 2/150 (1%)
Query: 140 GTDAQTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPT 199
G TSFS A V P + ++ +D++I DL I R G GGQ+VN+ E+AVRITHIPT
Sbjct: 210 GGRRHTSFSSAFVYPEV-DDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPT 268
Query: 200 GVTVRCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVF 259
G+ +C +RSQ NK +A+ ++KAKL + +++ +E + + + WG QIR+YV
Sbjct: 269 GIVTQCQNDRSQHKNKDQAMKQMKAKLYELEMQKKNAEKQAMEDNKSDIGWGSQIRSYVL 328
Query: 260 HPYKLVKDVRTGHETSDIVSVMDGELEPFI 289
+ +KD+RTG ET + +V+DG L+ FI
Sbjct: 329 DDSR-IKDLRTGVETRNTQAVLDGSLDQFI 357
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 34/114 (29%), Positives = 54/114 (47%), Gaps = 2/114 (1%)
Query: 47 WDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASIIK 106
W+ AQ + + ++ ++ L K ++D +++L E D D EA + +
Sbjct: 47 WNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEAD--DEETFNEAVAELD 104
Query: 107 ELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQTSFSGAEVMPLLPEES 160
L + L Q E ++ SG YD + I AG+GGT+AQ S E M L ES
Sbjct: 105 ALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAES 158
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 121 bits (303), Expect = 6e-28, Method: Compositional matrix adjust.
Identities = 64/150 (42%), Positives = 93/150 (62%), Gaps = 2/150 (1%)
Query: 140 GTDAQTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPT 199
G TSFS A V P + ++ +D++I DL I RA G GGQ+VN+ E+AVRITHIPT
Sbjct: 210 GGRRHTSFSSAFVYPEV-DDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPT 268
Query: 200 GVTVRCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVF 259
G+ +C +RSQ NK +A + KAKL + +++ +E + + WG QIR+YV
Sbjct: 269 GIVTQCQNDRSQHKNKDQAXKQXKAKLYEVEXQKKNAEKQAXEDNKSDIGWGSQIRSYVL 328
Query: 260 HPYKLVKDVRTGHETSDIVSVMDGELEPFI 289
+ +KD+RTG ET + +V+DG L+ FI
Sbjct: 329 DDSR-IKDLRTGVETRNTQAVLDGSLDQFI 357
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 33/114 (28%), Positives = 52/114 (45%), Gaps = 2/114 (1%)
Query: 47 WDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASIIK 106
W+ AQ + + ++ ++ L K ++D +++L E D D EA + +
Sbjct: 47 WNEPERAQALGKERSSLEAVVDTLDQXKQGLEDVSGLLELAVEAD--DEETFNEAVAELD 104
Query: 107 ELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQTSFSGAEVMPLLPEES 160
L + L Q E + SG YD + I AG+GGT+AQ S E L ES
Sbjct: 105 ALEEKLAQLEFRRXFSGEYDSADCYLDIQAGSGGTEAQDWASXLERXYLRWAES 158
>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 = 109 bits (273), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 73/202 (36%), Positives = 106/202 (52%), Gaps = 12/202 (5%)
Query: 89 EMDSTDAGLLEEAASIIKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQTSFS 148
E+ TD G + E +K N + + + SG + V + G TS +
Sbjct: 127 EIHETDLGGIREVVFFVKGKNA----YGILKYESGVH----RVQRVPVTESGGRIHTSTA 178
Query: 149 GAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEE 208
V+P + E+ D++I EDL+I RA G GGQ VNK E+AVRITH+PTG+ V C E
Sbjct: 179 TVAVLPEIEEK--DIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNE 236
Query: 209 RSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAV-KAEWGQQIRNYVFHPYKLVKD 267
RSQ NK AL L+A+L + +EQ+ EI Q R + E ++IR Y F P V D
Sbjct: 237 RSQYQNKQTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNF-PQNRVTD 295
Query: 268 VRTGHETSDIVSVMDGELEPFI 289
R + + + ++DG+L+ I
Sbjct: 296 HRINYTSYRLQEILDGDLDEII 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 = 109 bits (273), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 73/202 (36%), Positives = 106/202 (52%), Gaps = 12/202 (5%)
Query: 89 EMDSTDAGLLEEAASIIKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQTSFS 148
E+ TD G + E +K N + + + SG + V + G TS +
Sbjct: 127 EIHETDLGGIREVVFFVKGKNA----YGILKYESGVH----RVQRVPVTESGGRIHTSTA 178
Query: 149 GAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEE 208
V+P + E+ D++I EDL+I RA G GGQ VNK E+AVRITH+PTG+ V C E
Sbjct: 179 TVAVLPEIEEK--DIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNE 236
Query: 209 RSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAV-KAEWGQQIRNYVFHPYKLVKD 267
RSQ NK AL L+A+L + +EQ+ EI Q R + E ++IR Y F P V D
Sbjct: 237 RSQYQNKQTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNF-PQNRVTD 295
Query: 268 VRTGHETSDIVSVMDGELEPFI 289
R + + + ++DG+L+ I
Sbjct: 296 HRINYTSYRLQEILDGDLDEII 317
>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 = 99.8 bits (247), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 69/146 (47%), Positives = 89/146 (60%), Gaps = 2/146 (1%)
Query: 144 QTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTV 203
TSF+G EV+P + EE V PEE L I RA G GGQ VN ++AVR+ H+PTG+TV
Sbjct: 215 HTSFAGVEVIPEVDEEVEVVLKPEE-LRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITV 273
Query: 204 RCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYK 263
C RSQ+ NK AL LKA+L + ++R E+K +RG+ EWG QIR+YV
Sbjct: 274 TCQTTRSQIKNKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLD-KN 332
Query: 264 LVKDVRTGHETSDIVSVMDGELEPFI 289
VKD RTG D +V+DG+L I
Sbjct: 333 YVKDHRTGLMRHDPENVLDGDLMDLI 358
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 54/101 (53%), Gaps = 6/101 (5%)
Query: 43 DSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAA 102
D S W++ A++ Q ++ ++ F++ D +++L EE+ + + L+
Sbjct: 48 DPSLWNDPEAARKVSQEAARLRRTVD---TFRSLESDLQGLLELMEELPAEEREALKPE- 103
Query: 103 SIIKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDA 143
++E K LD+ LL+ P+ ++ A+++I GAGGT+A
Sbjct: 104 --LEEAAKKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEA 142
>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 = 99.8 bits (247), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 69/146 (47%), Positives = 89/146 (60%), Gaps = 2/146 (1%)
Query: 144 QTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTV 203
TSF+G EV+P + EE V PEE L I RA G GGQ VN ++AVR+ H+PTG+TV
Sbjct: 202 HTSFAGVEVIPEVDEEVEVVLKPEE-LRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITV 260
Query: 204 RCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYK 263
C RSQ+ NK AL LKA+L + ++R E+K +RG+ EWG QIR+YV
Sbjct: 261 TCQTTRSQIKNKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLD-KN 319
Query: 264 LVKDVRTGHETSDIVSVMDGELEPFI 289
VKD RTG D +V+DG+L I
Sbjct: 320 YVKDHRTGLMRHDPENVLDGDLMDLI 345
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 31/134 (23%), Positives = 63/134 (47%), Gaps = 6/134 (4%)
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 AVISITAGAGGTDA 143
A+++I GAGGT+A
Sbjct: 116 AILTIQPGAGGTEA 129
>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 = 99.8 bits (247), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 69/146 (47%), Positives = 89/146 (60%), Gaps = 2/146 (1%)
Query: 144 QTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTV 203
TSF+G EV+P + EE V PEE L I RA G GGQ VN ++AVR+ H+PTG+TV
Sbjct: 197 HTSFAGVEVIPEVDEEVEVVLKPEE-LRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITV 255
Query: 204 RCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYK 263
C RSQ+ NK AL LKA+L + ++R E+K +RG+ EWG QIR+YV
Sbjct: 256 TCQTTRSQIKNKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLD-KN 314
Query: 264 LVKDVRTGHETSDIVSVMDGELEPFI 289
VKD RTG D +V+DG+L I
Sbjct: 315 YVKDHRTGLMRHDPENVLDGDLMDLI 340
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 54/101 (53%), Gaps = 6/101 (5%)
Query: 43 DSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAA 102
D S W++ A++ Q ++ ++ F++ D +++L EE+ + + L+
Sbjct: 30 DPSLWNDPEAARKVSQEAARLRRTVD---TFRSLESDLQGLLELMEELPAEEREALKPE- 85
Query: 103 SIIKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDA 143
++E K LD+ LL+ P+ ++ A+++I GAGGT+A
Sbjct: 86 --LEEAAKKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEA 124
>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 = 99.8 bits (247), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 69/146 (47%), Positives = 89/146 (60%), Gaps = 2/146 (1%)
Query: 144 QTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTV 203
TSF+G EV+P + EE V PEE L I RA G GGQ VN ++AVR+ H+PTG+TV
Sbjct: 197 HTSFAGVEVIPEVDEEVEVVLKPEE-LRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITV 255
Query: 204 RCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYK 263
C RSQ+ NK AL LKA+L + ++R E+K +RG+ EWG QIR+YV
Sbjct: 256 TCQTTRSQIKNKELALKILKARLYELERKKREEELKALRGEVEPIEWGSQIRSYVLD-KN 314
Query: 264 LVKDVRTGHETSDIVSVMDGELEPFI 289
VKD RTG D +V+DG+L I
Sbjct: 315 YVKDHRTGLMRHDPENVLDGDLMDLI 340
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 54/101 (53%), Gaps = 6/101 (5%)
Query: 43 DSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAA 102
D S W++ A++ Q ++ ++ F++ D +++L EE+ + + L+
Sbjct: 30 DPSLWNDPEAARKVSQEAARLRRTVD---TFRSLESDLQGLLELMEELPAEEREALKPE- 85
Query: 103 SIIKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDA 143
++E K LD+ LL+ P+ ++ A+++I GAGGT+A
Sbjct: 86 --LEEAAKKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEA 124
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 99.8 bits (247), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 69/146 (47%), Positives = 89/146 (60%), Gaps = 2/146 (1%)
Query: 144 QTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTV 203
TSF+G EV+P + EE V PEE L I RA G GGQ VN ++AVR+ H+PTG+TV
Sbjct: 202 HTSFAGVEVIPEVDEEVEVVLKPEE-LRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITV 260
Query: 204 RCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYK 263
C RSQ+ NK AL LKA+L + ++R E+K +RG+ EWG QIR+YV
Sbjct: 261 TCQTTRSQIKNKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLD-KN 319
Query: 264 LVKDVRTGHETSDIVSVMDGELEPFI 289
VKD RTG D +V+DG+L I
Sbjct: 320 YVKDHRTGLMRHDPENVLDGDLMDLI 345
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 54/101 (53%), Gaps = 6/101 (5%)
Query: 43 DSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAA 102
D S W++ A++ Q ++ ++ F++ D +++L EE+ + + L+
Sbjct: 35 DPSLWNDPEAARKVSQEAARLRRTVD---TFRSLESDLQGLLELMEELPAEEREALKPE- 90
Query: 103 SIIKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDA 143
++E K LD+ LL+ P+ ++ A+++I GAGGT+A
Sbjct: 91 --LEEAAKKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEA 129
>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 = 92.8 bits (229), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 53/147 (36%), Positives = 81/147 (55%), Gaps = 4/147 (2%)
Query: 144 QTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTV 203
TS + V+P EE D + +++ I RA G GGQ VN ++AVR+ H+PTG+ V
Sbjct: 193 HTSTATVAVLPKAEEE--DFALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMV 250
Query: 204 RCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAV-KAEWGQQIRNYVFHPY 262
C + RSQ+ N+ KAL L+++LL + + A +++ R + E ++IR Y F P
Sbjct: 251 TCQDSRSQIKNREKALMILRSRLLEMKRAEEAERLRKTRLAQIGTGERSEKIRTYNF-PQ 309
Query: 263 KLVKDVRTGHETSDIVSVMDGELEPFI 289
V D R G T D+ V+ G L P +
Sbjct: 310 SRVTDHRIGFTTHDLEGVLSGHLTPIL 336
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 360
Score = 84.0 bits (206), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 56/153 (36%), Positives = 82/153 (53%), Gaps = 15/153 (9%)
Query: 144 QTSFSGAEVMPLLPEESMDVQIPE---EDLEISFSRAGGKGGQNVNKVETAVRITHIPTG 200
TS VMP LP D ++P+ DL I R+ G GGQ+VN ++A+RITH+PTG
Sbjct: 197 HTSACTVAVMPELP----DAELPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTG 252
Query: 201 VTVRCTEERSQLANKIKALSRLKAKL----LVIAEEQRASEIKQIRGDAVKAEWGQQIRN 256
+ V C +ERSQ NK KALS L A++ + ++ AS + + G +++ + R
Sbjct: 253 IVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLLGSGDRSD---RNRT 309
Query: 257 YVFHPYKLVKDVRTGHETSDIVSVMDGELEPFI 289
Y F P V D R + VM+G+L+ I
Sbjct: 310 YNF-PQGRVTDHRINLTLYRLDEVMEGKLDMLI 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 = 76.6 bits (187), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 49/129 (37%), Positives = 71/129 (55%), Gaps = 8/129 (6%)
Query: 165 IPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANKIKALSRLKA 224
I +DL + A G GGQNVNKV TAVRI H+PT + V EER+Q N+ KA ++A
Sbjct: 230 IDPKDLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEXQEERTQQKNRDKAXKIIRA 289
Query: 225 K----LLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRTGHETSDIVSV 280
+ IA++++ +E K G ++E +IR Y F P V D R G + S+
Sbjct: 290 RVADHFAQIAQDEQDAERKSTVGTGDRSE---RIRTYNF-PQNRVTDHRIGLTLQKLDSI 345
Query: 281 MDGELEPFI 289
+ G+L+ I
Sbjct: 346 LSGKLDEVI 354
>pdb|2RSM|A Chain A, Solution Structure And Sirna-Mediated Knockdown Analysis
Of The Mitochondrial Disease-Related Protein C12orf65
(Ict2)
Length = 115
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 26/44 (59%)
Query: 167 EEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERS 210
E +LE F + G GGQ NK V + H+P+G+ V+C + RS
Sbjct: 45 ESELEEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRS 88
>pdb|4DH9|Y Chain Y, Crystal Structure Of Yaej Bound To The 70s Ribosome
Length = 140
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 35/100 (35%), Positives = 49/100 (49%), Gaps = 24/100 (24%)
Query: 160 SMDVQIPEEDLEISFSRAGGKGGQNVNKVETA------VRITHIPT-------------- 199
S V IP+ +LEI+ RA G GGQ+VNK TA +R + +P
Sbjct: 5 SRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLI 64
Query: 200 ---GVTV-RCTEERSQLANKIKALSRLKAKLLVIAEEQRA 235
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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 26/35 (74%)
Query: 160 SMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRI 194
S +V +P+ ++E++ RA G GGQNVNKV +A+ +
Sbjct: 5 SNNVHLPDAEIELTAIRAQGAGGQNVNKVSSAMHL 39
>pdb|1J26|A Chain A, Solution Structure Of A Putative Peptidyl-Trna Hydrolase
Domain In A Mouse Hypothetical Protein
Length = 112
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 165 IPEEDLEISFSRAGGKGGQNVNKVETAVRI 194
IP + L IS+ R+ G GGQNVNKV + +
Sbjct: 17 IPLDRLSISYCRSSGPGGQNVNKVNSKAEV 46
>pdb|2JY9|A Chain A, Nmr Structure Of Putative Trna Hydrolase Domain From
Salmonella Typhimurium. Northeast Structural Genomics
Consortium Target Str220
Length = 148
Score = 35.0 bits (79), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 29/100 (29%), Positives = 47/100 (47%), Gaps = 24/100 (24%)
Query: 160 SMDVQIPEEDLEISFSRAGGKGGQNVNKVETA------VRITHIPTG------------- 200
S V I + +LEI+ RA G GGQ+VNK +A +R + +P
Sbjct: 5 SRTVSIADNELEITAIRAQGAGGQHVNKTSSAIHLRFDIRASGLPEYYKQRLLTASHHLI 64
Query: 201 -----VTVRCTEERSQLANKIKALSRLKAKLLVIAEEQRA 235
+ ++ E RSQ N+ A++RL A + + EQ++
Sbjct: 65 SDDGVIIIKAQEFRSQELNREAAIARLVAVIKELTAEQKS 104
>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 = 1.1, 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|1VL1|A Chain A, Crystal Structure Of 6-Phosphogluconolactonase (Tm1154)
From Thermotoga Maritima At 1.70a Resolution
Length = 232
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 28/111 (25%), Positives = 48/111 (43%), Gaps = 8/111 (7%)
Query: 106 KELNKALDQFELTQLLSGPYDKEGAVISIT-AGAGGTDAQTSFSGAEVMPLLPEESMDVQ 164
+E+ A DQF+L L GP +G V SI G D +F+ P +P ++ +
Sbjct: 129 REIRSATDQFDLAILGMGP---DGHVASIFDLETGNKDNLVTFTDPSGDPKVPRVTLTFR 185
Query: 165 IPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANK 215
L + F +G + +N++ ++ T +P VR E+ K
Sbjct: 186 ALNTSLYVLFLI---RGKEKINRLTEILKDTPLP-AYFVRGKEKTVWFVGK 232
>pdb|1PBT|A Chain A, The Crystal Structure Of Tm1154, Oxidoreductase, SolDEVB
Family From Thermotoga Maritima
Length = 244
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 28/111 (25%), Positives = 48/111 (43%), Gaps = 8/111 (7%)
Query: 106 KELNKALDQFELTQLLSGPYDKEGAVISIT-AGAGGTDAQTSFSGAEVMPLLPEESMDVQ 164
+E+ A DQF+L L GP +G V SI G D +F+ P +P ++ +
Sbjct: 139 REIRSATDQFDLAILGXGP---DGHVASIFDLETGNKDNLVTFTDPSGDPKVPRVTLTFR 195
Query: 165 IPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANK 215
L + F +G + +N++ ++ T +P VR E+ K
Sbjct: 196 ALNTSLYVLFLI---RGKEKINRLTEILKDTPLP-AYFVRGKEKTVWFVGK 242
>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 = 27.7 bits (60), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 40/92 (43%), Gaps = 8/92 (8%)
Query: 161 MDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANKIKALS 220
+ + + LE++ S++ K N+ E + T P+ VTV+ SQ + + S
Sbjct: 787 CEFSVTQNRLEVNISQSTYKDPNNLAFNEIKILGTEEPSNVTVKHNGVPSQTSPTVTYDS 846
Query: 221 RLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQ 252
LK ++ ++I + G+A EW
Sbjct: 847 NLKVAII--------TDIDLLLGEAYTVEWAH 870
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
0.312 0.129 0.349
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,370,555
Number of Sequences: 62578
Number of extensions: 266493
Number of successful extensions: 782
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 741
Number of HSP's gapped (non-prelim): 41
length of query: 307
length of database: 14,973,337
effective HSP length: 99
effective length of query: 208
effective length of database: 8,778,115
effective search space: 1825847920
effective search space used: 1825847920
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: 51 (24.3 bits)