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= psy2490
(64 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 = 57.0 bits (136), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 22/42 (52%), Positives = 33/42 (78%)
Query: 21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
DY + ++E +++E+FV+G GPGGQA KT+NCVVL H+P+
Sbjct: 36 DYPALLPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPS 77
>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 = 39.7 bits (91), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
RRH S SS F ++D +I+ D++ R SG GGQ V +T + V +THIPT
Sbjct: 212 RRHTSF-SSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPT 268
>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 = 39.3 bits (90), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/45 (46%), Positives = 28/45 (62%), Gaps = 7/45 (15%)
Query: 25 VPKIDEKDIQER-------FVRGSGPGGQAVAKTNNCVVLTHIPT 62
+P+I+EKDI+ R R SG GGQ V KT + V +TH+PT
Sbjct: 183 LPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPT 227
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 39.3 bits (90), Expect = 5e-04, Method: Composition-based stats.
Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
RRH S SS F ++D +I+ D++ R SG GGQ V +T + V +THIPT
Sbjct: 212 RRHTSF-SSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPT 268
>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 = 39.3 bits (90), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/45 (46%), Positives = 28/45 (62%), Gaps = 7/45 (15%)
Query: 25 VPKIDEKDIQER-------FVRGSGPGGQAVAKTNNCVVLTHIPT 62
+P+I+EKDI+ R R SG GGQ V KT + V +TH+PT
Sbjct: 183 LPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPT 227
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 38.9 bits (89), Expect = 7e-04, Method: Composition-based stats.
Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
RRH S SS F ++D +I+ D++ R SG GGQ V +T + V +THIPT
Sbjct: 212 RRHTSF-SSAFVYPEVDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPT 268
>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 = 35.8 bits (81), Expect = 0.007, Method: Composition-based stats.
Identities = 18/45 (40%), Positives = 27/45 (60%), Gaps = 7/45 (15%)
Query: 25 VPKIDEKD-------IQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
+PK +E+D I+ +R SGPGGQ V T++ V + H+PT
Sbjct: 202 LPKAEEEDFALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPT 246
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 360
Score = 35.0 bits (79), Expect = 0.010, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 28/44 (63%)
Query: 19 DLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
+L +++P ++ D++ R SG GGQ V T++ + +TH+PT
Sbjct: 208 ELPDAELPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPT 251
>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 = 33.9 bits (76), Expect = 0.022, Method: Composition-based stats.
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 38 VRGSGPGGQAVAKTNNCVVLTHIPT 62
+R SGPGGQ V T++ V + H+PT
Sbjct: 245 MRASGPGGQGVNTTDSAVRVVHLPT 269
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 33.9 bits (76), Expect = 0.025, Method: Composition-based stats.
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 38 VRGSGPGGQAVAKTNNCVVLTHIPT 62
+R SGPGGQ V T++ V + H+PT
Sbjct: 232 MRASGPGGQGVNTTDSAVRVVHLPT 256
>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 = 33.9 bits (76), Expect = 0.025, Method: Composition-based stats.
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 38 VRGSGPGGQAVAKTNNCVVLTHIPT 62
+R SGPGGQ V T++ V + H+PT
Sbjct: 232 MRASGPGGQGVNTTDSAVRVVHLPT 256
>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 = 33.9 bits (76), Expect = 0.025, Method: Composition-based stats.
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 38 VRGSGPGGQAVAKTNNCVVLTHIPT 62
+R SGPGGQ V T++ V + H+PT
Sbjct: 227 MRASGPGGQGVNTTDSAVRVVHLPT 251
>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 = 33.5 bits (75), Expect = 0.027, Method: Composition-based stats.
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 38 VRGSGPGGQAVAKTNNCVVLTHIPT 62
+R SGPGGQ V T++ V + H+PT
Sbjct: 227 MRASGPGGQGVNTTDSAVRVVHLPT 251
>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 = 32.0 bits (71), Expect = 0.085, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 28 IDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTD 63
ID KD++ SG GGQ V K V + H+PT+
Sbjct: 230 IDPKDLRVDIYHASGAGGQNVNKVATAVRIIHLPTN 265
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
0.320 0.136 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,917,154
Number of Sequences: 62578
Number of extensions: 60074
Number of successful extensions: 95
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 78
Number of HSP's gapped (non-prelim): 17
length of query: 64
length of database: 14,973,337
effective HSP length: 35
effective length of query: 29
effective length of database: 12,783,107
effective search space: 370710103
effective search space used: 370710103
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)