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= psy14432
(189 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1J26|A Chain A, Solution Structure Of A Putative Peptidyl-Trna Hydrolase
Domain In A Mouse Hypothetical Protein
Length = 112
Score = 90.5 bits (223), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 41/96 (42%), Positives = 70/96 (72%), Gaps = 1/96 (1%)
Query: 81 SYI-TEELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNK 139
SYI + L I+Y RSSGPGGQ+VN V++K ++RF + +A+W+ E V++++ +KN++NK
Sbjct: 15 SYIPLDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINK 74
Query: 140 DGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAKPA 175
G L++ S+ +R Q NLA+ + +R+MI +A+ P+
Sbjct: 75 AGELVLTSESSRYQFRNLAECLQKIRDMIAEASGPS 110
>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 = 69.3 bits (168), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 35/88 (39%), Positives = 60/88 (68%), Gaps = 1/88 (1%)
Query: 86 ELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLII 145
E+++T R+ G GGQ+VN VS+ + +RF +NA++ L K++L+ LN +R+ DG +++
Sbjct: 14 EIELTAIRAQGAGGQNVNKVSSAMHLRFDINASS-LPPFYKERLLALNDSRITSDGVIVL 72
Query: 146 KSDRTRSQQLNLADAMTTLRNMIWKAAK 173
K+ + R+Q+ N ADA+ L +I AAK
Sbjct: 73 KAQQYRTQEQNRADALLRLSELIVNAAK 100
>pdb|4DH9|Y Chain Y, Crystal Structure Of Yaej Bound To The 70s Ribosome
Length = 140
Score = 68.2 bits (165), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 38/95 (40%), Positives = 59/95 (62%), Gaps = 2/95 (2%)
Query: 75 VVIPRFSYITE-ELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELN 133
+VI R I + EL+IT R+ G GGQHVN ST + +RF + A++ L E K++L+ +
Sbjct: 2 IVISRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASS-LPEYYKERLLAAS 60
Query: 134 KNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMI 168
+ ++ DG ++IK+ RSQ+LN A+ L MI
Sbjct: 61 HHLISSDGVIVIKAQEYRSQELNREAALARLVAMI 95
>pdb|2JY9|A Chain A, Nmr Structure Of Putative Trna Hydrolase Domain From
Salmonella Typhimurium. Northeast Structural Genomics
Consortium Target Str220
Length = 148
Score = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 35/91 (38%), Positives = 55/91 (60%), Gaps = 2/91 (2%)
Query: 75 VVIPRFSYITE-ELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELN 133
+ I R I + EL+IT R+ G GGQHVN S+ + +RF + A+ L E K++L+ +
Sbjct: 2 IAISRTVSIADNELEITAIRAQGAGGQHVNKTSSAIHLRFDIR-ASGLPEYYKQRLLTAS 60
Query: 134 KNRLNKDGYLIIKSDRTRSQQLNLADAMTTL 164
+ ++ DG +IIK+ RSQ+LN A+ L
Sbjct: 61 HHLISDDGVIIIKAQEFRSQELNREAAIARL 91
>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 = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
EEL I R+SGPGGQ VN+ + V +
Sbjct: 238 EELRIDVMRASGPGGQGVNTTDSAVRV 264
>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 = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
EEL I R+SGPGGQ VN+ + V +
Sbjct: 220 EELRIDVMRASGPGGQGVNTTDSAVRV 246
>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 = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
EEL I R+SGPGGQ VN+ + V +
Sbjct: 225 EELRIDVMRASGPGGQGVNTTDSAVRV 251
>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 = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
EEL I R+SGPGGQ VN+ + V +
Sbjct: 220 EELRIDVMRASGPGGQGVNTTDSAVRV 246
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 32.0 bits (71), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
EEL I R+SGPGGQ VN+ + V +
Sbjct: 225 EELRIDVMRASGPGGQGVNTTDSAVRV 251
>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 = 30.4 bits (67), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 59 IPVKAPDGLKFNGVIPV-VIPR-----FSYITEELDITYSRSSGPGGQHVNSVSTKVDI 111
+PV G V V+P+ F+ +E+ I R+SGPGGQ VN+ + V +
Sbjct: 183 VPVTETQGRIHTSTATVAVLPKAEEEDFALNMDEIRIDVMRASGPGGQGVNTTDSAVRV 241
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 360
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 86 ELDITYSRSSGPGGQHVNSVSTKVDI 111
+L I RSSG GGQHVN+ + + I
Sbjct: 221 DLRIDTFRSSGAGGQHVNTTDSAIRI 246
>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 = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 86 ELDITYSRSSGPGGQHVNSVSTKVDI 111
+L I R+SG GGQHVN + V I
Sbjct: 238 DLRIDVYRASGAGGQHVNRTESAVRI 263
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 86 ELDITYSRSSGPGGQHVNSVSTKVDI 111
+L I R+SG GGQHVN + V I
Sbjct: 238 DLRIDVYRTSGAGGQHVNRTESAVRI 263
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 86 ELDITYSRSSGPGGQHVNSVSTKVDI 111
+L I R+SG GGQHVN + V I
Sbjct: 238 DLRIDVYRASGAGGQHVNRTESAVRI 263
>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 = 28.5 bits (62), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
E+L I R+SG GGQ+VN + V I
Sbjct: 196 EDLKIETFRASGHGGQYVNKTESAVRI 222
>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 = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
E+L I R+SG GGQ+VN + V I
Sbjct: 196 EDLKIETFRASGHGGQYVNKTESAVRI 222
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 0.134 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,551,176
Number of Sequences: 62578
Number of extensions: 227684
Number of successful extensions: 522
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: 501
Number of HSP's gapped (non-prelim): 22
length of query: 189
length of database: 14,973,337
effective HSP length: 93
effective length of query: 96
effective length of database: 9,153,583
effective search space: 878743968
effective search space used: 878743968
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)