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= 002316
(936 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1EH1|A Chain A, Ribosome Recycling Factor From Thermus Thermophilus
pdb|2V46|Y Chain Y, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 1 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 1.
pdb|2V48|Y Chain Y, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 3 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 2.
pdb|2QBE|6 Chain 6, 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|6 Chain 6, 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|6 Chain 6, 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|6 Chain 6, 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|6 Chain 6, 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|6 Chain 6, 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|3J0D|J Chain J, Models For The T. Thermophilus Ribosome Recycling Factor
Bound To The E. Coli Post-Termination Complex
pdb|3J0E|G Chain G, Models For The T. Thermophilus Ribosome Recycling Factor
And The E. Coli Elongation Factor G Bound To The E. Coli
Post-Termination Complex
Length = 185
Score = 33.5 bits (75), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 30/117 (25%), Positives = 48/117 (41%), Gaps = 10/117 (8%)
Query: 309 NMKRMHEILERKTGGLVIWRSGTAVSLYRGVSYEVPSVQLNKRIYKRNELPASSVSQATD 368
+M++ E+LE GL R+ A+ L+ V Y V LN+ P + V Q+ D
Sbjct: 13 HMQKSLEVLEHNLAGLRTGRANPALLLHLKVEYYGAHVPLNQIATVTAPDPRTLVVQSWD 72
Query: 369 KQIHKQISMSGNSLSAAADKTAQDPSNFDSYNNVHATQVNLETASEEQETDFVREVK 425
+ N+L A + N A +N+ +EE+ D VR V+
Sbjct: 73 Q----------NALKAIEKAIRDSDLGLNPSNKGDALYINIPPLTEERRKDLVRAVR 119
>pdb|3QZM|A Chain A, Staphylococcus Aureus Isda Neat Domain H83a Variant In
Complex With Heme
pdb|3QZM|B Chain B, Staphylococcus Aureus Isda Neat Domain H83a Variant In
Complex With Heme
Length = 127
Score = 33.1 bits (74), Expect = 0.66, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 29/61 (47%)
Query: 360 ASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYNNVHATQVNLETASEEQETD 419
S +SQAT + I+ Q+ G+S +A D Q P NN + Q L AS +E
Sbjct: 1 GSHMSQATSQPINFQVQKDGSSEKSAMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYK 60
Query: 420 F 420
F
Sbjct: 61 F 61
>pdb|1RQ8|A Chain A, Solution Structure Of The Hypothetical Protein Sav1595
From Staphylococcus Aureus, A Putative Rna Binding
Protein
Length = 104
Score = 32.7 bits (73), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 42/88 (47%), Gaps = 4/88 (4%)
Query: 692 ITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKI 751
+T +++ R L + +G+ G+ + ++ + + REL+K+ V FD K++
Sbjct: 2 LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKEL 61
Query: 752 ALALEAESGGVLVSVDKISKGYAMVVYR 779
A L + LV V G +V+YR
Sbjct: 62 AETLSEATRSELVQV----IGSMIVIYR 85
>pdb|2O1A|A Chain A, Crystal Structure Of Iron-regulated Surface Determinant
Protein A From Staphylococcus Aureus- Targeted Domain
47...188
Length = 142
Score = 32.0 bits (71), Expect = 1.7, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 29/61 (47%)
Query: 360 ASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYNNVHATQVNLETASEEQETD 419
++ VSQAT + I+ Q+ G+S + D Q P NN + Q L AS +E
Sbjct: 12 STQVSQATSQPINFQVQKDGSSEKSHXDDYXQHPGKVIKQNNKYYFQTVLNNASFWKEYK 71
Query: 420 F 420
F
Sbjct: 72 F 72
>pdb|3QZL|A Chain A, Staphylococcus Aureus Isda Neat Domain K75a Variant In
Complex With Heme
Length = 127
Score = 31.2 bits (69), Expect = 2.5, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 28/61 (45%)
Query: 360 ASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYNNVHATQVNLETASEEQETD 419
S +SQAT + I+ Q+ G+S + D Q P NN + Q L AS +E
Sbjct: 1 GSHMSQATSQPINFQVQADGSSEKSHMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYK 60
Query: 420 F 420
F
Sbjct: 61 F 61
>pdb|3QZO|A Chain A, Staphylococcus Aureus Isda Neat Domain In Complex With
Heme, Reduced Crystal
pdb|3QZO|B Chain B, Staphylococcus Aureus Isda Neat Domain In Complex With
Heme, Reduced Crystal
pdb|3QZO|C Chain C, Staphylococcus Aureus Isda Neat Domain In Complex With
Heme, Reduced Crystal
pdb|3QZO|D Chain D, Staphylococcus Aureus Isda Neat Domain In Complex With
Heme, Reduced Crystal
pdb|3QZP|A Chain A, Staphylococcus Aureus Isda Neat Domain In Complex With
Cobalt- Protoporphyrin Ix
pdb|3QZP|B Chain B, Staphylococcus Aureus Isda Neat Domain In Complex With
Cobalt- Protoporphyrin Ix
Length = 127
Score = 31.2 bits (69), Expect = 3.0, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 28/61 (45%)
Query: 360 ASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYNNVHATQVNLETASEEQETD 419
S +SQAT + I+ Q+ G+S + D Q P NN + Q L AS +E
Sbjct: 1 GSHMSQATSQPINFQVQKDGSSEKSHMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYK 60
Query: 420 F 420
F
Sbjct: 61 F 61
>pdb|3QZN|A Chain A, Staphylococcus Aureus Isda Neat Domain Y166a Variant In
Complex With Heme
pdb|3QZN|B Chain B, Staphylococcus Aureus Isda Neat Domain Y166a Variant In
Complex With Heme
pdb|3QZN|C Chain C, Staphylococcus Aureus Isda Neat Domain Y166a Variant In
Complex With Heme
Length = 127
Score = 31.2 bits (69), Expect = 3.0, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 28/61 (45%)
Query: 360 ASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYNNVHATQVNLETASEEQETD 419
S +SQAT + I+ Q+ G+S + D Q P NN + Q L AS +E
Sbjct: 1 GSHMSQATSQPINFQVQKDGSSEKSHMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYK 60
Query: 420 F 420
F
Sbjct: 61 F 61
>pdb|2ITE|A Chain A, Crystal Structure Of The Isda Neat Domain From
Staphylococcus Aureus
pdb|2ITE|B Chain B, Crystal Structure Of The Isda Neat Domain From
Staphylococcus Aureus
pdb|2ITF|A Chain A, Crystal Structure Isda Neat Domain From Staphylococcus
Aureus With Heme Bound
pdb|2ITF|B Chain B, Crystal Structure Isda Neat Domain From Staphylococcus
Aureus With Heme Bound
pdb|2ITF|C Chain C, Crystal Structure Isda Neat Domain From Staphylococcus
Aureus With Heme Bound
pdb|2ITF|D Chain D, Crystal Structure Isda Neat Domain From Staphylococcus
Aureus With Heme Bound
Length = 127
Score = 30.4 bits (67), Expect = 4.6, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 27/61 (44%)
Query: 360 ASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYNNVHATQVNLETASEEQETD 419
S SQAT + I+ Q+ G+S + D Q P NN + Q L AS +E
Sbjct: 1 GSHXSQATSQPINFQVQKDGSSEKSHXDDYXQHPGKVIKQNNKYYFQTVLNNASFWKEYK 60
Query: 420 F 420
F
Sbjct: 61 F 61
>pdb|1LN4|A Chain A, Crystal Structure Of E. Coli Yhby
Length = 104
Score = 30.0 bits (66), Expect = 6.4, Method: Composition-based stats.
Identities = 25/90 (27%), Positives = 46/90 (51%), Gaps = 8/90 (8%)
Query: 692 ITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKK- 750
++ +++ + L +K +LLG G+ +G + + ++ EL+K VK+ T D+ K
Sbjct: 3 LSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIK--VKIATEDRETKT 60
Query: 751 -IALALEAESGGVLVSVDKISKGYAMVVYR 779
I A+ E+G V V G +V+YR
Sbjct: 61 LIVEAIVRETGACNVQV----IGKTLVLYR 86
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 0.131 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,659,242
Number of Sequences: 62578
Number of extensions: 1027256
Number of successful extensions: 2459
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 2445
Number of HSP's gapped (non-prelim): 30
length of query: 936
length of database: 14,973,337
effective HSP length: 108
effective length of query: 828
effective length of database: 8,214,913
effective search space: 6801947964
effective search space used: 6801947964
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 56 (26.2 bits)