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= 007396
(605 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2EF0|A Chain A, Crystal Structure Of Ornithine Carbamoyltransferase From
Thermus Thermophilus
Length = 301
Score = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 29/95 (30%), Positives = 41/95 (43%), Gaps = 4/95 (4%)
Query: 509 LKFEGYSPDISQVLRDVDEDEKRERLKGHSQK---LAIAFALIHLSQGSPIRIARNLRMC 565
L F GY P Q L D+ E KRER +G K LA+ F L + + +A
Sbjct: 13 LDFSGYGPKELQALLDLAEQLKRERYRGEDLKGKVLALLFEKPSLRTRTTLEVAMVHLGG 72
Query: 566 NDCHTYTKLISVIYEREIIVRDRKRFHRFKDGTCS 600
+ + K + I ERE + K RF +G +
Sbjct: 73 HAVYLDQKQVG-IGEREPVRDVAKNLERFVEGIAA 106
>pdb|3DKW|A Chain A, Crystal Structure Of Dnr From Pseudomonas Aeruginosa.
pdb|3DKW|B Chain B, Crystal Structure Of Dnr From Pseudomonas Aeruginosa.
pdb|3DKW|C Chain C, Crystal Structure Of Dnr From Pseudomonas Aeruginosa.
pdb|3DKW|D Chain D, Crystal Structure Of Dnr From Pseudomonas Aeruginosa.
pdb|3DKW|E Chain E, Crystal Structure Of Dnr From Pseudomonas Aeruginosa.
pdb|3DKW|F Chain F, Crystal Structure Of Dnr From Pseudomonas Aeruginosa.
pdb|3DKW|G Chain G, Crystal Structure Of Dnr From Pseudomonas Aeruginosa.
pdb|3DKW|H Chain H, Crystal Structure Of Dnr From Pseudomonas Aeruginosa.
pdb|3DKW|I Chain I, Crystal Structure Of Dnr From Pseudomonas Aeruginosa.
pdb|3DKW|J Chain J, Crystal Structure Of Dnr From Pseudomonas Aeruginosa
Length = 227
Score = 33.5 bits (75), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 2/63 (3%)
Query: 46 EFKKVHAHVLKWGFFWNPFCASNLVATCALSHWGSMDYACSIFRQIDEPGAFDFNTLIRG 105
EF++VH +L+ + P L A S ++D +FRQ + AF + LI G
Sbjct: 2 EFQRVHQQLLQSHHLFEPLSPVQLQELLASSDLVNLDKGAYVFRQGEPAHAFYY--LISG 59
Query: 106 FVK 108
VK
Sbjct: 60 CVK 62
>pdb|1S5A|A Chain A, Crystal Structure Of Putative Isomerase From Bacillus
Subtilis
pdb|1S5A|B Chain B, Crystal Structure Of Putative Isomerase From Bacillus
Subtilis
pdb|1S5A|C Chain C, Crystal Structure Of Putative Isomerase From Bacillus
Subtilis
pdb|1S5A|D Chain D, Crystal Structure Of Putative Isomerase From Bacillus
Subtilis
Length = 150
Score = 33.5 bits (75), Expect = 0.35, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 92 DEPGAFDFNTLIRGFVKEVEFEEALFLYNEMFERGVEPDNFTFPALFKACAKLQALKEGM 151
DE F+F G K +E + A++ Y + + + + +FT P ++++ + E
Sbjct: 36 DENAVFEFPYAPEGSPKRIEGKAAIYDYIKDYPKQIHLSSFTAPTVYRSADSNTVIAE-F 94
Query: 152 QIHGHVFKVGF 162
Q GHV + G
Sbjct: 95 QCDGHVIETGL 105
>pdb|2NYD|A Chain A, Crystal Structure Of Staphylococcus Aureus Hypothetical
Protein Sa1388
pdb|2NYD|B Chain B, Crystal Structure Of Staphylococcus Aureus Hypothetical
Protein Sa1388
Length = 370
Score = 33.1 bits (74), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 415 HHNLEIGEIAAKNLFQINSHHPSDYVLLSNMYARAQRWYDVAKIRTEMASKGLNQSP 471
HH+ +I NL IN H S+YV+ + W+++ KI ++ + +N P
Sbjct: 312 HHDALDAKIHGVNLIDIN--HYSEYVMKEGLKTLLMNWFNIEKINIDVEASTINTDP 366
>pdb|3LNL|A Chain A, Crystal Structure Of Staphylococcus Aureus Protein Sa1388
pdb|3LNL|B Chain B, Crystal Structure Of Staphylococcus Aureus Protein Sa1388
Length = 370
Score = 33.1 bits (74), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 415 HHNLEIGEIAAKNLFQINSHHPSDYVLLSNMYARAQRWYDVAKIRTEMASKGLNQSP 471
HH+ +I NL IN H S+YV+ + W+++ KI ++ + +N P
Sbjct: 312 HHDALDAKIHGVNLIDIN--HYSEYVMKEGLKTLLMNWFNIEKINIDVEASTINTDP 366
>pdb|2Z69|A Chain A, Crystal Structure Of The Sensor Domain Of The
Transcriptional Regulator Dnr From Pseudomonas
Aeruginosa
pdb|2Z69|B Chain B, Crystal Structure Of The Sensor Domain Of The
Transcriptional Regulator Dnr From Pseudomonas
Aeruginosa
pdb|2Z69|C Chain C, Crystal Structure Of The Sensor Domain Of The
Transcriptional Regulator Dnr From Pseudomonas
Aeruginosa
Length = 154
Score = 30.4 bits (67), Expect = 2.7, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 30/63 (47%), Gaps = 2/63 (3%)
Query: 46 EFKKVHAHVLKWGFFWNPFCASNLVATCALSHWGSMDYACSIFRQIDEPGAFDFNTLIRG 105
EF++VH +L+ + P L A S ++D +FRQ EP A F LI G
Sbjct: 5 EFQRVHQQLLQSHHLFEPLSPVQLQELLASSDLVNLDKGAYVFRQ-GEP-AHAFYYLISG 62
Query: 106 FVK 108
VK
Sbjct: 63 CVK 65
>pdb|3S6B|A Chain A, Crystal Structure Of Methionine Aminopeptidase 1b From
Plasmodium Falciparum, Pf10_0150
Length = 368
Score = 29.6 bits (65), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 22/32 (68%)
Query: 470 SPGFSLVEVARKVYKFVSQDRSHPAWDNIYEM 501
SPG + E+ RKV++F+ ++ ++P+ N Y+
Sbjct: 131 SPGVTTDEIDRKVHEFIIKNNAYPSTLNYYKF 162
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
0.324 0.137 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,209,607
Number of Sequences: 62578
Number of extensions: 668867
Number of successful extensions: 1997
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1991
Number of HSP's gapped (non-prelim): 9
length of query: 605
length of database: 14,973,337
effective HSP length: 104
effective length of query: 501
effective length of database: 8,465,225
effective search space: 4241077725
effective search space used: 4241077725
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 54 (25.4 bits)