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= psy6072
(107 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1A0P|A Chain A, Site-Specific Recombinase, Xerd
Length = 290
Score = 29.6 bits (65), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 34/79 (43%)
Query: 1 MSRLRNLYEALSRKKIDVGDDDVSIAEGKNPAGGADGAGKLPLESASDAPQLARVLGLVD 60
+S +R L++ L R+K D +A K P + +E AP + + L L D
Sbjct: 74 LSAVRRLFQYLYREKFREDDPSAHLASPKLPQRLPKDLSEAQVERLLQAPLIDQPLELRD 133
Query: 61 LTMLGVGATLGVGVYVLAG 79
ML V G+ V L G
Sbjct: 134 KAMLEVLYATGLRVSELVG 152
>pdb|1P85|N Chain N, Real Space Refined Coordinates Of The 50s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp
State Of E. Coli 70s Ribosome
pdb|1P86|N Chain N, Real Space Refined Coordinates Of The 50s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The
Initiation-Like State Of E. Coli 70s Ribosome
pdb|2AW4|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File Contains
The 50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2AWB|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File Contains
The 50s Subunit Of The Second 70s Ribosome. The Entire
Crystal Structure Contains Two 70s Ribosomes And Is
Described In Remark 400.
pdb|2GYA|N Chain N, Structure Of The 50s Subunit Of A Pre-Translocational E.
Coli Ribosome Obtained By Fitting Atomic Models For Rna
And Protein Components Into Cryo-Em Map Emd-1056
pdb|2GYC|N Chain N, Structure Of The 50s Subunit Of A Secm-Stalled E. Coli
Ribosome Complex Obtained By Fitting Atomic Models For
Rna And Protein Components Into Cryo-Em Map Emd-1143
pdb|2I2T|P Chain P, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2I2V|P Chain P, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2J28|P Chain P, Model Of E. Coli Srp Bound To 70s Rncs
pdb|2QOV|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 50s Subunit Of The First 70s Ribosome.
The Entire Crystal Structure Contains Two 70s Ribosomes.
pdb|2QOX|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 50s Subunit Of The Second 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|2QOZ|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 50s Subunit Of The
First 70s Ribosome, With Neomycin Bound. The Entire
Crystal Structure Contains Two 70s Ribosomes.
pdb|2QP1|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome, With Neomycin Bound. The Entire
Crystal Structure Contains Two 70s Ribosomes.
pdb|2QAM|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 50s Subunit Of The First 70s Ribosome, With
Neomycin Bound. The Entire Crystal Structure Contains
Two 70s Ribosomes And Is Described In Remark 400.
pdb|2QAO|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 50s Subunit Of The Second 70s Ribosome,
With Neomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBA|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 50s Subunit Of The First 70s Ribosome, With
Gentamicin Bound. The Entire Crystal Structure Contains
Two 70s Ribosomes And Is Described In Remark 400.
pdb|2QBC|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 50s Subunit Of The Second 70s Ribosome,
With Gentamicin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBE|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 50s Subunit Of The
First 70s Ribosome, With Rrf Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QBG|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 50s Subunit Of The
Second 70s Ribosome, With Rrf Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QBI|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 50s
Subunit Of The First 70s Ribosome, With Gentamicin And
Rrf Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2QBK|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 50s
Subunit Of The Second 70s Ribosome, With Gentamicin And
Rrf Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4L|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
50s Subunit Of The First 70s Ribosome, With Paromomycin
And Rrf Bound. The Entire Crystal Structure Contains Two
70s Ribosomes And Is Described In Remark 400.
pdb|2Z4N|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
50s Subunit Of The Second 70s Ribosome, With Paromomycin
And Rrf Bound. The Entire Crystal Structure Contains Two
70s Ribosomes And Is Described In Remark 400.
pdb|2VHM|P Chain P, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 1 Of 4)
pdb|2VHN|P Chain P, Structure Of Pdf Binding Helix In Complex With The
Ribosome. (Part 2 Of 4)
pdb|2RDO|P Chain P, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound
pdb|3DF2|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This File
Contains The 50s Subunit Of The First 70s Ribosome. The
Entire Crystal Structure Contains Two 70s Ribosomes.
pdb|3DF4|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This File
Contains The 50s Subunit Of The Second 70s Ribosome. The
Entire Crystal Structure Contains Two 70s Ribosomes.
pdb|3BBX|P Chain P, The Hsp15 Protein Fitted Into The Low Resolution Cryo-Em
Map 50s.Nc-Trna.Hsp15 Complex
pdb|3FIK|P Chain P, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry
Consists Of The 50s Subunit.
pdb|2WWQ|P Chain P, E.Coli 70s Ribosome Stalled During Translation Of Tnac
Leader Peptide. This File Contains The 50s, The P-Site
Trna And The Tnac Leader Peptide (Part 2 Of 2).
pdb|3OFQ|P Chain P, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3OFR|P Chain P, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 50s Subunit Of The
First 70s Ribosome With Erthromycin Bound.
pdb|3OFC|P Chain P, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 50s Subunit Of
The First 70s Ribosome With Chloramphenicol Bound.
pdb|3OFD|P Chain P, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 50s Subunit Of
The Second 70s Ribosome.
pdb|3OFZ|P Chain P, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 50s Subunit Of The
First 70s Ribosome Bound To Clindamycin.
pdb|3OG0|P Chain P, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3OAS|P Chain P, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3OAT|P Chain P, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 50s Subunit Of The
First 70s Ribosome With Telithromycin Bound.
pdb|3J01|P Chain P, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
pdb|3R8S|P Chain P, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|3R8T|P Chain P, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|3J0T|R Chain R, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class2 Of The Six
Classes)
pdb|3J0W|R Chain R, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 4a Of The Six
Classes)
pdb|3J0Y|R Chain R, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 4b Of The Six
Classes)
pdb|3J11|R Chain R, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 3 Of The Six
Classes)
pdb|3J12|R Chain R, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 5 Of The Six
Classes)
pdb|3J14|R Chain R, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 6 Of The Six
Classes)
pdb|3J19|P Chain P, Structure Of The Bacterial Ribosome Complexed By
Tmrna-Smpb And Ef-G During Translocation And Mld-Loading
(50s Subunit)
Length = 114
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 60 DLTMLGVGATLGVGVYVLAGSVARNQAGPSVVISFAIAAVTSLFSVQ 106
D+ G T+ V V+V+ GS R QA VVI+ + S F+V+
Sbjct: 15 DVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAFTVR 61
>pdb|1VS6|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|1VS8|P Chain P, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|3E1B|I Chain I, Structure Of The 50s Subunit Of E. Coli Ribosome In
Pre-Accommodation State
pdb|3E1D|I Chain I, Structure Of The 50s Subunit Of E. Coli Ribosome In
Post-Accommodation State
pdb|3I1N|P Chain P, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1P|P Chain P, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1R|P Chain P, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1T|P Chain P, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I20|P Chain P, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I22|P Chain P, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3KCR|P Chain P, Ribosome-Secy Complex. This Entry 3kcr Contains 50s
Ribosomal Subnit. The 30s Ribosomal Subunit Can Be Found
In Pdb Entry 3kc4
pdb|1VT2|P Chain P, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3ORB|P Chain P, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 50s Subunit Of The First
70s Ribosome Bound To Cem-101.
pdb|3IZT|Q Chain Q, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding. This Entry Contains The
Large Subunit Of A Ribosome Programmed With A
Near-Cognate Codon.
pdb|3IZU|Q Chain Q, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding. This Entry Contains The
Large Subunit Of A Ribosome Programmed With A Cognate
Codon
pdb|3SGF|T Chain T, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3UOS|T Chain T, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
pdb|4GAR|P Chain P, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
pdb|4GAU|P Chain P, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
Length = 115
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 60 DLTMLGVGATLGVGVYVLAGSVARNQAGPSVVISFAIAAVTSLFSVQ 106
D+ G T+ V V+V+ GS R QA VVI+ + S F+V+
Sbjct: 16 DVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAFTVR 62
>pdb|3U55|A Chain A, Crystal Structure (Type-2) Of Saicar Synthetase From
Pyrococcus Horikoshii Ot3
Length = 238
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 1 MSRLRNLYEALSRKKIDVGDDDVSIAEGKNPAGGADGAGK 40
M +L +YE ++K I + DDD I E K+ A DG K
Sbjct: 1 MVKLMEVYEGKAKKMIPI-DDDKLIMEFKDDATAFDGTKK 39
>pdb|2DG6|A Chain A, Crystal Structure Of The Putative Transcriptional
Regulator Sco5550 From Streptomyces Coelicolor A3(2)
Length = 222
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 39 GKLPLESASDAPQLARVLGLVDLTMLGVGATLGVGVYVLAGSVARNQAGPSV 90
GK+P+ +A + VLG VD LG LG ++ L ++A P+V
Sbjct: 57 GKVPVATARE------VLGHVDDDSLGRTVRLGAALWALPQDAEPDEADPAV 102
>pdb|2YYB|A Chain A, Crystal Structure Of Ttha1606 From Thermus Thermophilus
Hb8
pdb|2YYB|B Chain B, Crystal Structure Of Ttha1606 From Thermus Thermophilus
Hb8
Length = 242
Score = 25.4 bits (54), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 38 AGKLPLESASDAPQ---LARVLGLVDLTMLGVG 67
A LPL++ + LAR LGLVDLT VG
Sbjct: 95 AAHLPLDAHEEVGNNFVLARELGLVDLTPWDVG 127
>pdb|3U54|A Chain A, Crystal Structure (Type-1) Of Saicar Synthetase From
Pyrococcus Horikoshii Ot3
pdb|3U54|B Chain B, Crystal Structure (Type-1) Of Saicar Synthetase From
Pyrococcus Horikoshii Ot3
Length = 238
Score = 25.4 bits (54), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 3 RLRNLYEALSRKKIDVGDDDVSIAEGKNPAGGADGAGK 40
+L +YE ++K I + DDD I E K+ A DG K
Sbjct: 3 KLXEVYEGKAKKMIPI-DDDKLIXEFKDDATAFDGTKK 39
>pdb|1LLQ|A Chain A, Crystal Structure Of Malic Enzyme From Ascaris Suum
Complexed With Nicotinamide Adenine Dinucleotide
pdb|1LLQ|B Chain B, Crystal Structure Of Malic Enzyme From Ascaris Suum
Complexed With Nicotinamide Adenine Dinucleotide
pdb|1O0S|A Chain A, Crystal Structure Of Ascaris Suum Malic Enzyme Complexed
With Nadh
pdb|1O0S|B Chain B, Crystal Structure Of Ascaris Suum Malic Enzyme Complexed
With Nadh
Length = 605
Score = 25.4 bits (54), Expect = 9.4, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 54 RVLGLVDLTMLGVGATLG-VGVYVLAGSV 81
R+LGL DL G+G +G + +YV G V
Sbjct: 181 RILGLGDLGAYGIGIPVGKLALYVALGGV 209
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
0.315 0.134 0.361
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,962,146
Number of Sequences: 62578
Number of extensions: 114768
Number of successful extensions: 319
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 310
Number of HSP's gapped (non-prelim): 28
length of query: 107
length of database: 14,973,337
effective HSP length: 72
effective length of query: 35
effective length of database: 10,467,721
effective search space: 366370235
effective search space used: 366370235
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: 45 (21.9 bits)