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= 005721
(681 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2E4M|A Chain A, Crystal Structure Of Hemagglutinin Subcomponent Complex
(Ha- 33HA-17) From Clostridium Botulinum Serotype D
Strain 4947
pdb|2E4M|B Chain B, Crystal Structure Of Hemagglutinin Subcomponent Complex
(Ha- 33HA-17) From Clostridium Botulinum Serotype D
Strain 4947
Length = 286
Score = 33.9 bits (76), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 24/33 (72%), Gaps = 1/33 (3%)
Query: 538 LNDFIGKSVMLEPFDSPGMLVIQHETDDELVVT 570
L D+I ++V+L + +P LV+Q+ TDD L+V+
Sbjct: 96 LQDYISRNVILRNYMNPN-LVLQYNTDDTLIVS 127
>pdb|2XJ4|A Chain A, Structure Of The Bacterial Cell Division Regulator Protein
Mipz
Length = 286
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 30/133 (22%), Positives = 54/133 (40%), Gaps = 12/133 (9%)
Query: 360 RVTLTFSSKGSGLTTSLNLRIPTWTSSNGAKATLNGQDLPLPSPGNFLSVTKTWSSDDKL 419
RV + + KG +++ + + T GAK + DL + F + W + K+
Sbjct: 5 RVIVVGNEKGGAGKSTIAVHLVTALLYGGAKVAVIDLDLRQRTSARFFENRRAWLDNKKI 64
Query: 420 TIQLPLTLR---TEAIQDDRPEYASI--------QAILYGPYVLAGHSIGDWDITESATS 468
+ PL L + +RPE + +A+ ++L GD IT A
Sbjct: 65 ELPEPLALNLSDNDVALAERPEEEQVAGFEAAFARAMAECDFILIDTPGGDSAITRMAHG 124
Query: 469 LSDW-ITPIPASY 480
+D +TP+ S+
Sbjct: 125 RADLVVTPMNDSF 137
>pdb|2XIT|A Chain A, Crystal Structure Of Monomeric Mipz
pdb|2XIT|B Chain B, Crystal Structure Of Monomeric Mipz
Length = 294
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 30/133 (22%), Positives = 54/133 (40%), Gaps = 12/133 (9%)
Query: 360 RVTLTFSSKGSGLTTSLNLRIPTWTSSNGAKATLNGQDLPLPSPGNFLSVTKTWSSDDKL 419
RV + + KG +++ + + T GAK + DL + F + W + K+
Sbjct: 5 RVIVVGNEKGGAGKSTIAVHLVTALLYGGAKVAVIDLDLRQRTSARFFENRRAWLDNKKI 64
Query: 420 TIQLPLTLR---TEAIQDDRPEYASI--------QAILYGPYVLAGHSIGDWDITESATS 468
+ PL L + +RPE + +A+ ++L GD IT A
Sbjct: 65 ELPEPLALNLSDNDVALAERPEEEQVAGFEAAFARAMAECDFILIDTPGGDSAITRMAHG 124
Query: 469 LSDW-ITPIPASY 480
+D +TP+ S+
Sbjct: 125 RADLVVTPMNDSF 137
>pdb|2QFZ|A Chain A, Crystal Structure Of Human Tbc1 Domain Family Member 22a
pdb|2QFZ|B Chain B, Crystal Structure Of Human Tbc1 Domain Family Member 22a
Length = 345
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 22/95 (23%), Positives = 45/95 (47%), Gaps = 7/95 (7%)
Query: 26 KEIGSGYLSAFPTEQFDRLEALIPVWAPYYTIHKILAGLLDQYTYADNAEALRMTTWMVE 85
+E+ + +S P E +EA Y+ + K+L G+ D YT+A ++M M+E
Sbjct: 169 EEVDTVDVSGVPAEVLCNIEA-----DTYWCMSKLLDGIQDNYTFAQ--PGIQMKVKMLE 221
Query: 86 YFYNRVQNVIKKYSIERHWQTLNEEAGGMNDVLYK 120
+R+ + ++ + + L MN++L +
Sbjct: 222 ELVSRIDEQVHRHLDQHEVRYLQFAFRWMNNLLMR 256
>pdb|3IFL|L Chain L, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
7:12a11) Complex
pdb|3IFN|L Chain L, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
40:12a11) Complex
Length = 219
Score = 29.3 bits (64), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 143 LGLLALQADDISGFHS--NTHIPIVIGSQMRYEVTGDQLHKTISMFFMDIVNSSHTYATG 200
L + ++A+D+ ++ ++H+P+ G+ + E+ G T+S+F SS +G
Sbjct: 78 LKISRVEAEDLGIYYCFQSSHVPLTFGAGTKLELKGADAAPTVSIF----PPSSEQLTSG 133
Query: 201 GTSVGEFWSD--PKRL 214
G SV F ++ PK +
Sbjct: 134 GASVVCFLNNFYPKDI 149
>pdb|3GNM|L Chain L, The Crystal Structure Of The Jaa-f11 Monoclonal Antibody
Fab Fragment
Length = 219
Score = 29.3 bits (64), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 143 LGLLALQADDISGFHS--NTHIPIVIGSQMRYEVTGDQLHKTISMFFMDIVNSSHTYATG 200
L + ++ADD+ ++ +H+P GS + E+ T+S+F SS +G
Sbjct: 78 LKISRVEADDLGVYYCFQGSHVPFTFGSGTKLEIKRADAAPTVSIF----PPSSEQLTSG 133
Query: 201 GTSVGEFWSD--PKRL 214
G SV F ++ PK +
Sbjct: 134 GASVVCFLNNFYPKDI 149
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
0.317 0.133 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,103,083
Number of Sequences: 62578
Number of extensions: 899803
Number of successful extensions: 2216
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 2216
Number of HSP's gapped (non-prelim): 13
length of query: 681
length of database: 14,973,337
effective HSP length: 105
effective length of query: 576
effective length of database: 8,402,647
effective search space: 4839924672
effective search space used: 4839924672
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: 55 (25.8 bits)