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= psy2492
(162 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2RSM|A Chain A, Solution Structure And Sirna-Mediated Knockdown Analysis
Of The Mitochondrial Disease-Related Protein C12orf65
(Ict2)
Length = 115
Score = 93.6 bits (231), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 40/77 (51%), Positives = 58/77 (75%)
Query: 47 YSTIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTA 106
Y + ++E +++E+FV+G GPGGQA KT+NCVVL H+P+GIV+KCHQ+RS+ +NRK A
Sbjct: 37 YPALLPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRKIA 96
Query: 107 RELLVAQWDVQVNGEDS 123
R++L + DV N S
Sbjct: 97 RKVLQEKVDVFYNSGPS 113
>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 = 64.3 bits (155), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 40/117 (34%), Positives = 64/117 (54%), Gaps = 7/117 (5%)
Query: 3 IKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNLVSNIDIYSTIPKIDEKDIQER- 61
I+ V++ ++ +N GI ES V + + + ++ + +P+I+EKDI+ R
Sbjct: 136 IREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRP 195
Query: 62 ------FVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVA 112
R SG GGQ V KT + V +TH+PTGIV+ C RS +N++TA +L A
Sbjct: 196 EDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRA 252
>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 = 64.3 bits (155), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 40/117 (34%), Positives = 64/117 (54%), Gaps = 7/117 (5%)
Query: 3 IKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNLVSNIDIYSTIPKIDEKDIQER- 61
I+ V++ ++ +N GI ES V + + + ++ + +P+I+EKDI+ R
Sbjct: 136 IREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRP 195
Query: 62 ------FVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVA 112
R SG GGQ V KT + V +TH+PTGIV+ C RS +N++TA +L A
Sbjct: 196 EDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRA 252
>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 = 56.6 bits (135), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 43/70 (61%), Gaps = 7/70 (10%)
Query: 48 STIPKIDEKD-------IQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLS 100
+ +PK +E+D I+ +R SGPGGQ V T++ V + H+PTGI++ C SRS
Sbjct: 200 AVLPKAEEEDFALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQI 259
Query: 101 ENRKTARELL 110
+NR+ A +L
Sbjct: 260 KNREKALMIL 269
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 360
Score = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 40/65 (61%)
Query: 48 STIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTAR 107
+ +P ++ D++ R SG GGQ V T++ + +TH+PTGIV++C RS +N+ A
Sbjct: 212 AELPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKAL 271
Query: 108 ELLVA 112
+L A
Sbjct: 272 SVLGA 276
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 34/50 (68%)
Query: 63 VRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVA 112
+R SGPGGQ V T++ V + H+PTGI + C +RS +N++ A ++L A
Sbjct: 232 MRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKA 281
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 34/50 (68%)
Query: 63 VRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVA 112
+R SGPGGQ V T++ V + H+PTGI + C +RS +N++ A ++L A
Sbjct: 232 MRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKA 281
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 34/50 (68%)
Query: 63 VRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVA 112
+R SGPGGQ V T++ V + H+PTGI + C +RS +N++ A ++L A
Sbjct: 245 MRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKA 294
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 34/50 (68%)
Query: 63 VRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVA 112
+R SGPGGQ V T++ V + H+PTGI + C +RS +N++ A ++L A
Sbjct: 227 MRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKA 276
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 34/50 (68%)
Query: 63 VRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVA 112
+R SGPGGQ V T++ V + H+PTGI + C +RS +N++ A ++L A
Sbjct: 227 MRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKA 276
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 5/71 (7%)
Query: 43 NIDIYSTIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSEN 102
+IDI +I+ D++ R SG GGQ V +T + V +THIPTGIV +C RS +N
Sbjct: 229 DIDI-----EINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKN 283
Query: 103 RKTARELLVAQ 113
+ A + + A+
Sbjct: 284 KDQAMKQMKAK 294
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/64 (42%), Positives = 38/64 (59%), Gaps = 5/64 (7%)
Query: 43 NIDIYSTIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSEN 102
+IDI +I+ D++ R SG GGQ V +T + V +THIPTGIV +C RS +N
Sbjct: 229 DIDI-----EINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKN 283
Query: 103 RKTA 106
+ A
Sbjct: 284 KDQA 287
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 50.8 bits (120), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 5/71 (7%)
Query: 43 NIDIYSTIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSEN 102
+IDI +I+ D++ R SG GGQ V +T + V +THIPTGIV +C RS +N
Sbjct: 229 DIDI-----EINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKN 283
Query: 103 RKTARELLVAQ 113
+ A + + A+
Sbjct: 284 KDQAMKQMKAK 294
>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 = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 33/60 (55%)
Query: 53 IDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVA 112
ID KD++ SG GGQ V K V + H+PT I ++ + R+ +NR A +++ A
Sbjct: 230 IDPKDLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEXQEERTQQKNRDKAXKIIRA 289
>pdb|3ILV|A Chain A, Crystal Structure Of A Glutamine-Dependent Nad(+)
Synthetase From Cytophaga Hutchinsonii
Length = 634
Score = 29.3 bits (64), Expect = 1.0, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 8 WPMRDRNLAGIRLLESQVTITRELRNDGYHRNLVSNIDIYSTIPKIDEKDIQERF 62
W ++RN G+ ++ +++ T ELR Y + ++ Y + +I+ K I+ER
Sbjct: 497 WAEKNRNQHGLHIV-NKLAPTAELRPSEYTQTDERDLXPYDVLARIERKAIKERL 550
>pdb|1CCW|B Chain B, Structure Of The Coenzyme B12 Dependent Enzyme Glutamate
Mutase From Clostridium Cochlearium
pdb|1CCW|D Chain D, Structure Of The Coenzyme B12 Dependent Enzyme Glutamate
Mutase From Clostridium Cochlearium
pdb|1CB7|B Chain B, Glutamate Mutase From Clostridium Cochlearium
Reconstituted With Methyl-Cobalamin
pdb|1CB7|D Chain D, Glutamate Mutase From Clostridium Cochlearium
Reconstituted With Methyl-Cobalamin
pdb|1I9C|B Chain B, Glutamate Mutase From Clostridium Cochlearium: Complex
With Adenosylcobalamin And Substrate
pdb|1I9C|D Chain D, Glutamate Mutase From Clostridium Cochlearium: Complex
With Adenosylcobalamin And Substrate
Length = 483
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 16 AGIRLLESQVTITRELRNDGYHRNLVSNIDIYSTIPKIDE 55
AG+ LL+ + + R L+++G L S ID Y+ + DE
Sbjct: 67 AGVALLDEHIELLRYLQDEGGADFLPSTIDAYTRQNRYDE 106
>pdb|1P8J|A Chain A, Crystal Structure Of The Proprotein Convertase Furin
pdb|1P8J|B Chain B, Crystal Structure Of The Proprotein Convertase Furin
pdb|1P8J|C Chain C, Crystal Structure Of The Proprotein Convertase Furin
pdb|1P8J|D Chain D, Crystal Structure Of The Proprotein Convertase Furin
pdb|1P8J|E Chain E, Crystal Structure Of The Proprotein Convertase Furin
pdb|1P8J|F Chain F, Crystal Structure Of The Proprotein Convertase Furin
pdb|1P8J|G Chain G, Crystal Structure Of The Proprotein Convertase Furin
pdb|1P8J|H Chain H, Crystal Structure Of The Proprotein Convertase Furin
Length = 471
Score = 27.7 bits (60), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 12/60 (20%)
Query: 15 LAGIRLLESQVTITRELRNDGYHRNLVSNIDIYSTI--PKIDEKDI-------QERFVRG 65
+ G+R+L+ +VT E R+ G + N +I IYS P+ D K + +E F RG
Sbjct: 114 IGGVRMLDGEVTDAVEARSLGLNPN---HIHIYSASWGPEDDGKTVDGPARLAEEAFFRG 170
>pdb|2INP|L Chain L, Structure Of The Phenol Hydroxylase-Regulatory Protein
Complex
Length = 89
Score = 26.2 bits (56), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 2/48 (4%)
Query: 70 GQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQ 117
+AV + N + H P +I+ + L NR+T E L WDVQ
Sbjct: 19 AEAVMEDNPDAEMQHQPA--MIRIQAEKRLVINRETMEEKLGRDWDVQ 64
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.133 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,474,710
Number of Sequences: 62578
Number of extensions: 167447
Number of successful extensions: 448
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 424
Number of HSP's gapped (non-prelim): 29
length of query: 162
length of database: 14,973,337
effective HSP length: 91
effective length of query: 71
effective length of database: 9,278,739
effective search space: 658790469
effective search space used: 658790469
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)