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= 032906
(130 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 67.0 bits (162), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 26/50 (52%), Positives = 36/50 (72%)
Query: 69 MDAYKSSGPGGQHRNKRESAVRLKHVPTGVIALAAEDRSQHKNRASALSH 118
+D Y++SG GGQH N+ ESAVR+ H+PTG++ DRSQHKN+ A+
Sbjct: 241 IDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQ 290
>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 = 66.6 bits (161), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 26/50 (52%), Positives = 36/50 (72%)
Query: 69 MDAYKSSGPGGQHRNKRESAVRLKHVPTGVIALAAEDRSQHKNRASALSH 118
+D Y++SG GGQH N+ ESAVR+ H+PTG++ DRSQHKN+ A+
Sbjct: 241 IDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQ 290
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 65.5 bits (158), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 26/47 (55%), Positives = 35/47 (74%)
Query: 69 MDAYKSSGPGGQHRNKRESAVRLKHVPTGVIALAAEDRSQHKNRASA 115
+D Y++SG GGQH N+ ESAVR+ H+PTG++ DRSQHKN+ A
Sbjct: 241 IDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQA 287
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 360
Score = 64.7 bits (156), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 26/49 (53%), Positives = 38/49 (77%)
Query: 69 MDAYKSSGPGGQHRNKRESAVRLKHVPTGVIALAAEDRSQHKNRASALS 117
+D ++SSG GGQH N +SA+R+ H+PTG++ ++RSQHKN+A ALS
Sbjct: 224 IDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALS 272
>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 = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 39/51 (76%)
Query: 66 ECEMDAYKSSGPGGQHRNKRESAVRLKHVPTGVIALAAEDRSQHKNRASAL 116
+ +++ +++SG GGQ+ NK ESAVR+ H+PTG++ +RSQ++N+ +AL
Sbjct: 197 DLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTAL 247
>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 = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 39/51 (76%)
Query: 66 ECEMDAYKSSGPGGQHRNKRESAVRLKHVPTGVIALAAEDRSQHKNRASAL 116
+ +++ +++SG GGQ+ NK ESAVR+ H+PTG++ +RSQ++N+ +AL
Sbjct: 197 DLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTAL 247
>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 = 56.2 bits (134), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 25/51 (49%), Positives = 34/51 (66%)
Query: 66 ECEMDAYKSSGPGGQHRNKRESAVRLKHVPTGVIALAAEDRSQHKNRASAL 116
E +D ++SGPGGQ N +SAVR+ H+PTG++ + RSQ KNR AL
Sbjct: 216 EIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNREKAL 266
>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 = 52.4 bits (124), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 24/51 (47%), Positives = 32/51 (62%)
Query: 66 ECEMDAYKSSGPGGQHRNKRESAVRLKHVPTGVIALAAEDRSQHKNRASAL 116
E +D ++SGPGGQ N +SAVR+ H+PTG+ RSQ KN+ AL
Sbjct: 239 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELAL 289
>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 = 52.4 bits (124), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 24/51 (47%), Positives = 32/51 (62%)
Query: 66 ECEMDAYKSSGPGGQHRNKRESAVRLKHVPTGVIALAAEDRSQHKNRASAL 116
E +D ++SGPGGQ N +SAVR+ H+PTG+ RSQ KN+ AL
Sbjct: 221 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELAL 271
>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 = 52.4 bits (124), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 24/51 (47%), Positives = 32/51 (62%)
Query: 66 ECEMDAYKSSGPGGQHRNKRESAVRLKHVPTGVIALAAEDRSQHKNRASAL 116
E +D ++SGPGGQ N +SAVR+ H+PTG+ RSQ KN+ AL
Sbjct: 221 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELAL 271
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 24/51 (47%), Positives = 32/51 (62%)
Query: 66 ECEMDAYKSSGPGGQHRNKRESAVRLKHVPTGVIALAAEDRSQHKNRASAL 116
E +D ++SGPGGQ N +SAVR+ H+PTG+ RSQ KN+ AL
Sbjct: 226 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELAL 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 = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 24/51 (47%), Positives = 32/51 (62%)
Query: 66 ECEMDAYKSSGPGGQHRNKRESAVRLKHVPTGVIALAAEDRSQHKNRASAL 116
E +D ++SGPGGQ N +SAVR+ H+PTG+ RSQ KN+ AL
Sbjct: 226 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELAL 276
>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 = 49.7 bits (117), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 33/51 (64%)
Query: 65 RECEMDAYKSSGPGGQHRNKRESAVRLKHVPTGVIALAAEDRSQHKNRASA 115
++ +D Y +SG GGQ+ NK +AVR+ H+PT + E+R+Q KNR A
Sbjct: 233 KDLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEXQEERTQQKNRDKA 283
>pdb|2RSM|A Chain A, Solution Structure And Sirna-Mediated Knockdown Analysis
Of The Mitochondrial Disease-Related Protein C12orf65
(Ict2)
Length = 115
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 28/50 (56%)
Query: 66 ECEMDAYKSSGPGGQHRNKRESAVRLKHVPTGVIALAAEDRSQHKNRASA 115
E E K GPGGQ NK + V LKHVP+G++ + RS +NR A
Sbjct: 47 ELEEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRKIA 96
>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 = 33.5 bits (75), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 33/75 (44%), Gaps = 24/75 (32%)
Query: 66 ECEMDAYKSSGPGGQHRNKRESAVRLKH-----------------------VPTGVIALA 102
E E+ A ++ G GGQ+ NK SA+ L+ GVI L
Sbjct: 14 EIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITSDGVIVLK 73
Query: 103 AED-RSQHKNRASAL 116
A+ R+Q +NRA AL
Sbjct: 74 AQQYRTQEQNRADAL 88
>pdb|2JY9|A Chain A, Nmr Structure Of Putative Trna Hydrolase Domain From
Salmonella Typhimurium. Northeast Structural Genomics
Consortium Target Str220
Length = 148
Score = 33.1 bits (74), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 28/98 (28%), Positives = 44/98 (44%), Gaps = 28/98 (28%)
Query: 56 LELTDDELFRECEMDAYKSSGPGGQHRNKRESAVRLK---------------------HV 94
+ + D+EL E+ A ++ G GGQH NK SA+ L+ H+
Sbjct: 8 VSIADNEL----EITAIRAQGAGGQHVNKTSSAIHLRFDIRASGLPEYYKQRLLTASHHL 63
Query: 95 PT--GVIALAAED-RSQHKNRASALSHSFGPQSEEQCE 129
+ GVI + A++ RSQ NR +A++ E E
Sbjct: 64 ISDDGVIIIKAQEFRSQELNREAAIARLVAVIKELTAE 101
>pdb|4DH9|Y Chain Y, Crystal Structure Of Yaej Bound To The 70s Ribosome
Length = 140
Score = 32.7 bits (73), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 24/76 (31%)
Query: 66 ECEMDAYKSSGPGGQHRNKRESAVRLK---------------------HVPT--GVIALA 102
E E+ A ++ G GGQH NK +A+ L+ H+ + GVI +
Sbjct: 14 ELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIK 73
Query: 103 AED-RSQHKNRASALS 117
A++ RSQ NR +AL+
Sbjct: 74 AQEYRSQELNREAALA 89
>pdb|1N3L|A Chain A, Crystal Structure Of A Human Aminoacyl-Trna Synthetase
Cytokine
pdb|1Q11|A Chain A, Crystal Structure Of An Active Fragment Of Human
Tyrosyl-Trna Synthetase With Tyrosinol
Length = 372
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 59 TDDELFRECEMDAYKSSGPGGQHRNKRESAVRLKHV 94
TD +L +E +D Y+ S QH +K+ A +K V
Sbjct: 121 TDYQLSKEYTLDVYRLSSVVTQHDSKKAGAEVVKQV 156
>pdb|3Q6Z|A Chain A, Human Parp14 (Artd8)-Macro Domain 1 In Complex With
Adenosine-5- Diphosphoribose
Length = 214
Score = 25.4 bits (54), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 91 LKHVPTGVIALAA-EDRSQHKNRASALSHSFGPQSEEQCE 129
L +P V+ A+ ED + A+ALS + GP+ + C+
Sbjct: 46 LARLPVDVVVNASNEDLKHYGGLAAALSKAAGPELQADCD 85
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
0.317 0.132 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,243,304
Number of Sequences: 62578
Number of extensions: 91633
Number of successful extensions: 204
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 186
Number of HSP's gapped (non-prelim): 22
length of query: 130
length of database: 14,973,337
effective HSP length: 88
effective length of query: 42
effective length of database: 9,466,473
effective search space: 397591866
effective search space used: 397591866
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: 45 (21.9 bits)