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= 043635
(560 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2G0B|A Chain A, The Structure Of Feem, An N-Acyl Amino Acid Synthase From
Uncultured Soil Microbes
pdb|2G0B|B Chain B, The Structure Of Feem, An N-Acyl Amino Acid Synthase From
Uncultured Soil Microbes
pdb|2G0B|C Chain C, The Structure Of Feem, An N-Acyl Amino Acid Synthase From
Uncultured Soil Microbes
pdb|2G0B|D Chain D, The Structure Of Feem, An N-Acyl Amino Acid Synthase From
Uncultured Soil Microbes
pdb|2G0B|E Chain E, The Structure Of Feem, An N-Acyl Amino Acid Synthase From
Uncultured Soil Microbes
pdb|2G0B|F Chain F, The Structure Of Feem, An N-Acyl Amino Acid Synthase From
Uncultured Soil Microbes
pdb|2G0B|G Chain G, The Structure Of Feem, An N-Acyl Amino Acid Synthase From
Uncultured Soil Microbes
pdb|2G0B|H Chain H, The Structure Of Feem, An N-Acyl Amino Acid Synthase From
Uncultured Soil Microbes
Length = 198
Score = 32.0 bits (71), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 18/33 (54%)
Query: 333 QFGMDQDLPACVAPANESPKSACSSFCKLVTYA 365
QF MD L VA A SP A S F ++TYA
Sbjct: 99 QFAMDHTLYEAVAGAKPSPFEAASLFTMVLTYA 131
>pdb|1LOP|A Chain A, Cyclophilin A Complexed With
Succinyl-Ala-Pro-Ala-P-Nitroanilide
Length = 164
Score = 30.4 bits (67), Expect = 2.9, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 295 LVDGDL----PEELQSWGQCLRVSELLGLDHVEQYFPHRITRQFGMDQDLP 341
+VD D E LQ WG C+ + G+D V++ T + GM QD+P
Sbjct: 102 VVDNDFLNFSGESLQGWGYCVFAEVVDGMDEVDK-IKGVATGRSGMHQDVP 151
>pdb|3U5C|HH Chain h, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
Length = 273
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 470 IPPETESVKKIMKNVPVNVGSEMAVEDSTDGKAGNPSHDMV 510
+PP + K KN P G+E A+ D T G+ N S D+
Sbjct: 37 VPPPSADPSKARKNRPRPSGNEGAIRDKTAGRRNNRSKDVT 77
>pdb|3U5G|HH Chain h, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 273
Score = 29.6 bits (65), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 470 IPPETESVKKIMKNVPVNVGSEMAVEDSTDGKAGNPSHDMV 510
+PP + K KN P G+E A+ D T G+ N S D+
Sbjct: 37 VPPPSADPSKARKNRPRPSGNEGAIRDKTAGRRNNRSKDVT 77
>pdb|3ULQ|B Chain B, Crystal Structure Of The Anti-Activator Rapf Complexed
With The Response Regulator Coma Dna Binding Domain
Length = 90
Score = 29.6 bits (65), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 409 PKSNHVVTTDSTEEDCLTIAELMKSRKKHDGFWNERVANAENLPDQSEAFSSTAEWEVVK 468
P+ +H+ + E+D LT E + ++ GF N+ +A+A +L +S +S T+ + +
Sbjct: 16 PRGSHM--SSQKEQDVLTPRECLILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFNKLN 73
Query: 469 VIPPETESV 477
V TE+V
Sbjct: 74 V-GSRTEAV 81
>pdb|3SBF|A Chain A, Crystal Structure Of The Mutant P311a Of Enolase
Superfamily Member From Vibrionales Bacterium Complexed
With Mg And D-Arabinonate
pdb|3SBF|B Chain B, Crystal Structure Of The Mutant P311a Of Enolase
Superfamily Member From Vibrionales Bacterium Complexed
With Mg And D-Arabinonate
pdb|3SBF|C Chain C, Crystal Structure Of The Mutant P311a Of Enolase
Superfamily Member From Vibrionales Bacterium Complexed
With Mg And D-Arabinonate
pdb|3SBF|D Chain D, Crystal Structure Of The Mutant P311a Of Enolase
Superfamily Member From Vibrionales Bacterium Complexed
With Mg And D-Arabinonate
Length = 401
Score = 29.6 bits (65), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 18 ISPNGGPKPTKRLGHLLKPCINFIKGQVFELPTHCLSSLAPIFEPKSWPLNVNFH 72
+S GG P +LGHL C NF + HC + PI + LNV+ H
Sbjct: 283 VSQIGGITPALKLGHL---CQNF----GVRIAWHCAPDMTPIGAAVNTHLNVHLH 330
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
0.318 0.135 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,088,526
Number of Sequences: 62578
Number of extensions: 774050
Number of successful extensions: 1626
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1621
Number of HSP's gapped (non-prelim): 9
length of query: 560
length of database: 14,973,337
effective HSP length: 104
effective length of query: 456
effective length of database: 8,465,225
effective search space: 3860142600
effective search space used: 3860142600
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: 54 (25.4 bits)