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= 007246
(611 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3GFV|A Chain A, Crystal Structure Of Petrobactin-Binding Protein Yclq From
Bacillu Subtilis
pdb|3GFV|B Chain B, Crystal Structure Of Petrobactin-Binding Protein Yclq From
Bacillu Subtilis
Length = 303
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 13/74 (17%)
Query: 535 VVLSTEGKIVGFQPTSRVGVNHWAASPLAKEMYGGRKLSPGLIEPSLKIHLPNEVVLIEL 594
V+ + +GKI F P SR G+ H +++G ++P + ++K + V E
Sbjct: 176 VIXANDGKISAFGPKSRYGLIH--------DVFG---VAPA--DQNIKASTHGQSVSYEY 222
Query: 595 LMSVNPDSCFALAR 608
+ NPD F + R
Sbjct: 223 ISKTNPDYLFVIDR 236
>pdb|3BLW|A Chain A, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLW|C Chain C, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLW|E Chain E, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLW|G Chain G, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLW|I Chain I, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLW|K Chain K, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLW|M Chain M, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLW|O Chain O, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLX|A Chain A, Yeast Isocitrate Dehydrogenase (Apo Form)
pdb|3BLX|C Chain C, Yeast Isocitrate Dehydrogenase (Apo Form)
pdb|3BLX|E Chain E, Yeast Isocitrate Dehydrogenase (Apo Form)
pdb|3BLX|G Chain G, Yeast Isocitrate Dehydrogenase (Apo Form)
pdb|3BLX|I Chain I, Yeast Isocitrate Dehydrogenase (Apo Form)
pdb|3BLX|K Chain K, Yeast Isocitrate Dehydrogenase (Apo Form)
pdb|3BLX|M Chain M, Yeast Isocitrate Dehydrogenase (Apo Form)
pdb|3BLX|O Chain O, Yeast Isocitrate Dehydrogenase (Apo Form)
Length = 349
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 34/150 (22%), Positives = 66/150 (44%), Gaps = 12/150 (8%)
Query: 284 ESIKPVKMRSKHLWWTP---SAHSKLEKIGGREFSIWTSENVPAYR-LEIDVSRYNDVKL 339
ES+K K+ K LW TP + H L ++ I+ NV ++ L+ +R D+ L
Sbjct: 68 ESLKRNKIGLKGLWHTPADQTGHGSLNVALRKQLDIYA--NVALFKSLKGVKTRIPDIDL 125
Query: 340 EGWRKSAENRWEILLTHSQMVGLADILDMYYEDIFSLPNKQLSCSVVTNYTNLPSKKRDS 399
R++ E + L H + G+ + L + + P + ++ ++K +
Sbjct: 126 IVIRENTEGEFS-GLEHESVPGVVESL-----KVMTRPKTERIARFAFDFAKKYNRKSVT 179
Query: 400 SFLKILSVTLASGIFLVAISALGQRSSPHL 429
+ K + L G+F I+ +GQ+ P +
Sbjct: 180 AVHKANIMKLGDGLFRNIITEIGQKEYPDI 209
>pdb|3BKY|L Chain L, Crystal Structure Of Chimeric Antibody C2h7 Fab In Complex
With A Cd20 Peptide
Length = 213
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 170 QLWSFELVLFRPGTERNMEDLGNQREVPASFALTSSDERVISVLAEVVCL 219
Q WSF F GT+ +L P+ F SDE++ S A VVCL
Sbjct: 88 QQWSFNPPTFGAGTKL---ELKRTVAAPSVFIFPPSDEQLKSGTASVVCL 134
>pdb|3BLV|A Chain A, Yeast Isocitrate Dehydrogenase With Citrate Bound In The
Regulatory Subunits
pdb|3BLV|C Chain C, Yeast Isocitrate Dehydrogenase With Citrate Bound In The
Regulatory Subunits
pdb|3BLV|E Chain E, Yeast Isocitrate Dehydrogenase With Citrate Bound In The
Regulatory Subunits
pdb|3BLV|G Chain G, Yeast Isocitrate Dehydrogenase With Citrate Bound In The
Regulatory Subunits
Length = 354
Score = 30.0 bits (66), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 34/150 (22%), Positives = 65/150 (43%), Gaps = 12/150 (8%)
Query: 284 ESIKPVKMRSKHLWWTP---SAHSKLEKIGGREFSIWTSENVPAYR-LEIDVSRYNDVKL 339
ES+K K+ K LW TP + H L ++ I+ NV ++ L+ +R D+ L
Sbjct: 68 ESLKRNKIGLKGLWHTPADQTGHGSLNVALRKQLDIYA--NVALFKSLKGVKTRIPDIDL 125
Query: 340 EGWRKSAENRWEILLTHSQMVGLADILDMYYEDIFSLPNKQLSCSVVTNYTNLPSKKRDS 399
R++ E + L H + G+ + L + + P + ++ ++K +
Sbjct: 126 IVIRENTEGEFS-GLEHESVPGVVESL-----KVXTRPKTERIARFAFDFAKKYNRKSVT 179
Query: 400 SFLKILSVTLASGIFLVAISALGQRSSPHL 429
+ K L G+F I+ +GQ+ P +
Sbjct: 180 AVHKANIXKLGDGLFRNIITEIGQKEYPDI 209
>pdb|3S34|H Chain H, Structure Of The 1121b Fab Fragment
pdb|3S36|H Chain H, Structural Basis For The Function Of Two Anti-Vegf
Receptor Antibodies
pdb|3S37|H Chain H, Structural Basis For The Function Of Two Anti-Vegf
Receptor Antibodies
Length = 221
Score = 28.9 bits (63), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 449 NALRQPVDAVKLEEMCVSIIKRIKDTFD-WPGDIMTEMSIGAWIGEIPNYLKLSHEDDST 507
N+L +++++ E+ V R+ D FD W M +S + G P+ L+ ST
Sbjct: 77 NSLYLQMNSLRAEDTAVYYCARVTDAFDIWGQGTMVTVSSASTKG--PSVFPLAPSSKST 134
Query: 508 SEGNLTAALEKIDPD 522
S G TAAL + D
Sbjct: 135 SGG--TAALGCLVKD 147
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 0.131 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,751,040
Number of Sequences: 62578
Number of extensions: 646086
Number of successful extensions: 1861
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1860
Number of HSP's gapped (non-prelim): 10
length of query: 611
length of database: 14,973,337
effective HSP length: 105
effective length of query: 506
effective length of database: 8,402,647
effective search space: 4251739382
effective search space used: 4251739382
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)