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= 004904
(724 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A8X|B Chain B, Structure Of The Core Asap Complex
Length = 40
Score = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 20/30 (66%), Positives = 23/30 (76%)
Query: 685 IVTLDDLFRKTKATPRIYYLPLSEEQVAAK 714
I LDDLFRKTK TP IY+LPL+ E +A K
Sbjct: 7 IRLLDDLFRKTKGTPCIYWLPLTPEAIAEK 36
>pdb|2VDD|A Chain A, Crystal Structure Of The Open State Of Tolc Outer Membrane
Component Of Mutlidrug Efflux Pumps
pdb|2VDD|B Chain B, Crystal Structure Of The Open State Of Tolc Outer Membrane
Component Of Mutlidrug Efflux Pumps
pdb|2VDD|C Chain C, Crystal Structure Of The Open State Of Tolc Outer Membrane
Component Of Mutlidrug Efflux Pumps
pdb|2VDE|A Chain A, Crystal Structure Of The Open State Of Tolc Outer Membrane
Component Of Mutlidrug Efflux Pumps
pdb|2VDE|B Chain B, Crystal Structure Of The Open State Of Tolc Outer Membrane
Component Of Mutlidrug Efflux Pumps
pdb|2VDE|C Chain C, Crystal Structure Of The Open State Of Tolc Outer Membrane
Component Of Mutlidrug Efflux Pumps
Length = 460
Score = 33.1 bits (74), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 13/81 (16%)
Query: 69 DAFHGANITSQPVVEVKDAEVSVGSETAKDVLDV-----DAKR---NEKVENVVVQLDIN 120
+A+ A +++Q ++ +A SVG+ET DVLD +AK+ N + ++ QL+I
Sbjct: 364 NAYKQAVVSAQSSLDAMEAGFSVGTETIVDVLDATTTLYNAKQELANARYNYLINQLNIK 423
Query: 121 SFAPGFGPGEHQERDIRGDNN 141
S G E+D+ NN
Sbjct: 424 S-----ALGTLNEQDLLALNN 439
>pdb|3DOJ|A Chain A, Structure Of Glyoxylate Reductase 1 From Arabidopsis
(Atglyr1)
Length = 310
Score = 32.3 bits (72), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 9/70 (12%)
Query: 93 SETAKDVLDVDAKRNEKVENVVVQLDINSFAPGFGPGEHQERDIR-----GDNNEN---V 144
S+T D+LD+ A N + ++ +S+ P F P +HQ++D+R GD N V
Sbjct: 219 SDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPAF-PLKHQQKDMRLALALGDENAVSMPV 277
Query: 145 AALGQEKFQE 154
AA E F++
Sbjct: 278 AAAANEAFKK 287
>pdb|3DDR|A Chain A, Structure Of The Serratia Marcescens Hemophore Receptor
Hasr-Ile671gly Mutant In Complex With Its Hemophore Hasa
And Heme
pdb|3DDR|B Chain B, Structure Of The Serratia Marcescens Hemophore Receptor
Hasr-Ile671gly Mutant In Complex With Its Hemophore Hasa
And Heme
Length = 865
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 288 KIELKDNIIADNVKLELDVNKSGMVEPSSGNVTAV 322
K+ D + + + L +D NK G+V+PS GN V
Sbjct: 643 KVAYFDTKVDNYINLAIDRNKPGLVQPSGGNAAYV 677
>pdb|1TQQ|A Chain A, Structure Of Tolc In Complex With Hexamminecobalt
pdb|1TQQ|B Chain B, Structure Of Tolc In Complex With Hexamminecobalt
pdb|1TQQ|C Chain C, Structure Of Tolc In Complex With Hexamminecobalt
Length = 471
Score = 30.4 bits (67), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 13/81 (16%)
Query: 69 DAFHGANITSQPVVEVKDAEVSVGSETAKDVLDV-----DAKR---NEKVENVVVQLDIN 120
+A+ A +++Q ++ +A SVG+ T DVLD +AK+ N + ++ QL+I
Sbjct: 342 NAYKQAVVSAQSSLDAMEAGYSVGTRTIVDVLDATTTLYNAKQELANARYNYLINQLNIK 401
Query: 121 SFAPGFGPGEHQERDIRGDNN 141
S G E+D+ NN
Sbjct: 402 S-----ALGTLNEQDLLALNN 417
>pdb|3CSL|A Chain A, Structure Of The Serratia Marcescens Hemophore Receptor
Hasr In Complex With Its Hemophore Hasa And Heme
pdb|3CSL|B Chain B, Structure Of The Serratia Marcescens Hemophore Receptor
Hasr In Complex With Its Hemophore Hasa And Heme
pdb|3CSN|A Chain A, Structure Of The Serratia Marcescens Hemophore Receptor
Hasr In Complex With Its Hemophore Hasa
pdb|3CSN|B Chain B, Structure Of The Serratia Marcescens Hemophore Receptor
Hasr In Complex With Its Hemophore Hasa
Length = 865
Score = 30.4 bits (67), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 288 KIELKDNIIADNVKLELDVNKSGMVEPSSGNVTAV 322
K+ D + + + L +D NK G+V+PS GN V
Sbjct: 643 KVAYFDTKVDNYINLAIDRNKPGLVQPSIGNAAYV 677
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
0.307 0.126 0.346
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,854,627
Number of Sequences: 62578
Number of extensions: 714795
Number of successful extensions: 1994
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1991
Number of HSP's gapped (non-prelim): 8
length of query: 724
length of database: 14,973,337
effective HSP length: 106
effective length of query: 618
effective length of database: 8,340,069
effective search space: 5154162642
effective search space used: 5154162642
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 55 (25.8 bits)