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= 040326
(285 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2EC5|A Chain A, Crystal Structures Reveal A Thiol-Protease Like Catalytic
Triad In The C-Terminal Region Of Pasteurella Multocida
Toxin
pdb|2EC5|B Chain B, Crystal Structures Reveal A Thiol-Protease Like Catalytic
Triad In The C-Terminal Region Of Pasteurella Multocida
Toxin
Length = 746
Score = 31.2 bits (69), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 9/63 (14%)
Query: 187 FPDSQNRTLCEETVVNEELFETLSLRVNYMEQDRYGGFCQQNINMDTICTVRANCCDDTE 246
FP Q+R E V+E+L E L +++ ++ D + M+++ ++ A CD
Sbjct: 580 FPTEQSRLPLLENSVSEDLREELMQKIDAIKND---------VKMNSLVSMEAGSCDSVS 630
Query: 247 SKL 249
K+
Sbjct: 631 PKV 633
>pdb|1VH1|A Chain A, Crystal Structure Of Cmp-Kdo Synthetase
pdb|1VH1|B Chain B, Crystal Structure Of Cmp-Kdo Synthetase
pdb|1VH1|C Chain C, Crystal Structure Of Cmp-Kdo Synthetase
pdb|1VH1|D Chain D, Crystal Structure Of Cmp-Kdo Synthetase
Length = 256
Score = 31.2 bits (69), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 23/136 (16%), Positives = 56/136 (41%), Gaps = 4/136 (2%)
Query: 13 LLQLLRRTTMQDRTVIITMVGQEWASPGSVLDLFLESFC---IGEETKHLLNHLLIVALD 69
L +++ + D TVI+ + G E P +++ ++ +G T + H A +
Sbjct: 79 LAEVVEKCAFSDDTVIVNVQGDEPXIPATIIRQVADNLAQRQVGXATLAVPIHNAEEAFN 138
Query: 70 SKAFQYCKTVHPHCFYLSNSSTRYTKKK-QLSLPQLRNKFWQEVIELAYSVVFTEVDVMW 128
A + + Y S ++ + + + L + + F + + Y F V W
Sbjct: 139 PNAVKVVLDAEGYALYFSRATIPWDRDRFAEGLETVGDNFLRHLGIYGYRAGFIRRYVNW 198
Query: 129 LRNPILQVDCLKEMTI 144
+P+ ++ L+++ +
Sbjct: 199 QPSPLEHIEXLEQLRV 214
>pdb|3K8D|A Chain A, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase In Complex With Ctp And 2-Deoxy-Kdo
pdb|3K8D|B Chain B, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase In Complex With Ctp And 2-Deoxy-Kdo
pdb|3K8D|C Chain C, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase In Complex With Ctp And 2-Deoxy-Kdo
pdb|3K8D|D Chain D, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase In Complex With Ctp And 2-Deoxy-Kdo
pdb|3K8E|C Chain C, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase
pdb|3K8E|D Chain D, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase
pdb|3K8E|A Chain A, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase
pdb|3K8E|B Chain B, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase
Length = 264
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/136 (16%), Positives = 56/136 (41%), Gaps = 4/136 (2%)
Query: 13 LLQLLRRTTMQDRTVIITMVGQEWASPGSVLDLFLESFC---IGEETKHLLNHLLIVALD 69
L +++ + D TVI+ + G E P +++ ++ +G T + H A +
Sbjct: 95 LAEVVEKCAFSDDTVIVNVQGDEPMIPATIIRQVADNLAQRQVGMATLAVPIHNAEEAFN 154
Query: 70 SKAFQYCKTVHPHCFYLSNSSTRYTKKK-QLSLPQLRNKFWQEVIELAYSVVFTEVDVMW 128
A + + Y S ++ + + + L + + F + + Y F V W
Sbjct: 155 PNAVKVVLDAEGYALYFSRATIPWDRDRFAEGLETVGDNFLRHLGIYGYRAGFIRRYVNW 214
Query: 129 LRNPILQVDCLKEMTI 144
+P+ ++ L+++ +
Sbjct: 215 QPSPLEHIEMLEQLRV 230
>pdb|2EBF|X Chain X, Crystal Structures Reveal A Thiol-Protease Like Catalytic
Triad In The C-Terminal Region Of Pasteurella Multocida
Toxin
Length = 746
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 9/63 (14%)
Query: 187 FPDSQNRTLCEETVVNEELFETLSLRVNYMEQDRYGGFCQQNINMDTICTVRANCCDDTE 246
FP Q+R E V+E+L E L +++ ++ D + M+++ + A CD
Sbjct: 580 FPTEQSRLPLLENSVSEDLREELMQKIDAIKND---------VKMNSLVCMEAGSCDSVS 630
Query: 247 SKL 249
K+
Sbjct: 631 PKV 633
>pdb|3BW8|A Chain A, Crystal Structure Of The Clostridium Limosum C3 Exoenzyme
pdb|3BW8|B Chain B, Crystal Structure Of The Clostridium Limosum C3 Exoenzyme
Length = 217
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 186 LFPDSQNRTLCEETVVNEELFETLSLRVNYMEQDRYG 222
L PD +N L + +N+ +FE + LR ++ YG
Sbjct: 107 LGPDFENTILNRDGTINKAVFEQVKLRFKGKDRKEYG 143
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
0.323 0.135 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,187,340
Number of Sequences: 62578
Number of extensions: 314170
Number of successful extensions: 656
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 655
Number of HSP's gapped (non-prelim): 6
length of query: 285
length of database: 14,973,337
effective HSP length: 98
effective length of query: 187
effective length of database: 8,840,693
effective search space: 1653209591
effective search space used: 1653209591
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)