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= 032412
(141 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2RR3|A Chain A, Solution Structure Of The Complex Between Human Vap-A Msp
Domain And Human Osbp Ffat Motif
Length = 130
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 27/43 (62%)
Query: 97 SAVRLKNTSKSHVAFKFQTTAPKSCYMRPPGGVLAPGDSIIAT 139
+ ++L+N S V FK +TTAP+ +RP G++ PG ++ +
Sbjct: 30 TNLKLRNPSDRKVCFKVKTTAPRRYCVRPNSGIIDPGSTVTVS 72
>pdb|1Z9L|A Chain A, 1.7 Angstrom Crystal Structure Of The Rat Vap-A Msp
Homology Domain
Length = 128
Score = 35.8 bits (81), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 23/35 (65%)
Query: 99 VRLKNTSKSHVAFKFQTTAPKSCYMRPPGGVLAPG 133
++L+N S V FK +TTAP+ +RP GV+ PG
Sbjct: 33 LKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPG 67
>pdb|1Z9O|A Chain A, 1.9 Angstrom Crystal Structure Of The Rat Vap-a Msp
Homology Domain In Complex With The Rat Orp1 Ffat Motif
pdb|1Z9O|B Chain B, 1.9 Angstrom Crystal Structure Of The Rat Vap-a Msp
Homology Domain In Complex With The Rat Orp1 Ffat Motif
pdb|1Z9O|C Chain C, 1.9 Angstrom Crystal Structure Of The Rat Vap-a Msp
Homology Domain In Complex With The Rat Orp1 Ffat Motif
pdb|1Z9O|D Chain D, 1.9 Angstrom Crystal Structure Of The Rat Vap-a Msp
Homology Domain In Complex With The Rat Orp1 Ffat Motif
pdb|1Z9O|E Chain E, 1.9 Angstrom Crystal Structure Of The Rat Vap-a Msp
Homology Domain In Complex With The Rat Orp1 Ffat Motif
pdb|1Z9O|F Chain F, 1.9 Angstrom Crystal Structure Of The Rat Vap-a Msp
Homology Domain In Complex With The Rat Orp1 Ffat Motif
Length = 128
Score = 35.8 bits (81), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 23/35 (65%)
Query: 99 VRLKNTSKSHVAFKFQTTAPKSCYMRPPGGVLAPG 133
++L+N S V FK +TTAP+ +RP GV+ PG
Sbjct: 33 LKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPG 67
>pdb|2CRI|A Chain A, Solution Structure Of The Msp Domain Of Mouse Vamp-
Associated Proteina
Length = 147
Score = 35.4 bits (80), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 99 VRLKNTSKSHVAFKFQTTAPKSCYMRPPGGVLAPG 133
++L+N S V FK +TTAP+ +RP G++ PG
Sbjct: 37 LKLQNPSDRKVCFKVKTTAPRRYCVRPNSGIIDPG 71
>pdb|1WIC|A Chain A, Solution Structure Of The Msp Domain Of Riken Cdna
6030424e15
Length = 152
Score = 34.3 bits (77), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%)
Query: 86 YFPYEPGKQTRSAVRLKNTSKSHVAFKFQTTAPKSCYMRPPGGVLAPGDSI 136
YF + ++ + L N +K+ VAFK +TTAP+ ++P PG SI
Sbjct: 28 YFGSIESGEKKTLIVLTNVTKNIVAFKVRTTAPEKYRVKPSNSSCDPGASI 78
>pdb|3IKK|A Chain A, Crystal Structure Analysis Of Msp Domain
pdb|3IKK|B Chain B, Crystal Structure Analysis Of Msp Domain
Length = 127
Score = 33.1 bits (74), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 99 VRLKNTSKSHVAFKFQTTAPKSCYMRPPGGVLAPGDSI 136
++L N + +V FK +TTAP+ +RP G++ G SI
Sbjct: 32 LKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASI 69
>pdb|1GRW|A Chain A, C. Elegans Major Sperm Protein
pdb|1GRW|B Chain B, C. Elegans Major Sperm Protein
pdb|1GRW|C Chain C, C. Elegans Major Sperm Protein
pdb|1GRW|D Chain D, C. Elegans Major Sperm Protein
Length = 126
Score = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 23/39 (58%)
Query: 99 VRLKNTSKSHVAFKFQTTAPKSCYMRPPGGVLAPGDSII 137
+++ N+S + + +TT K + PP GVL P ++++
Sbjct: 31 IKVINSSARRIGYGIKTTNMKRLGVDPPCGVLDPKEAVL 69
>pdb|2MSP|A Chain A, Major Sperm Protein, Beta Isoform, Engineered C59sT90C
Mutant, Putative Subfilament Structure, Ph 8.5
pdb|2MSP|B Chain B, Major Sperm Protein, Beta Isoform, Engineered C59sT90C
Mutant, Putative Subfilament Structure, Ph 8.5
pdb|2MSP|C Chain C, Major Sperm Protein, Beta Isoform, Engineered C59sT90C
Mutant, Putative Subfilament Structure, Ph 8.5
pdb|2MSP|D Chain D, Major Sperm Protein, Beta Isoform, Engineered C59sT90C
Mutant, Putative Subfilament Structure, Ph 8.5
pdb|2MSP|E Chain E, Major Sperm Protein, Beta Isoform, Engineered C59sT90C
Mutant, Putative Subfilament Structure, Ph 8.5
pdb|2MSP|F Chain F, Major Sperm Protein, Beta Isoform, Engineered C59sT90C
Mutant, Putative Subfilament Structure, Ph 8.5
pdb|2MSP|G Chain G, Major Sperm Protein, Beta Isoform, Engineered C59sT90C
Mutant, Putative Subfilament Structure, Ph 8.5
pdb|2MSP|H Chain H, Major Sperm Protein, Beta Isoform, Engineered C59sT90C
Mutant, Putative Subfilament Structure, Ph 8.5
Length = 126
Score = 26.6 bits (57), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 9/39 (23%), Positives = 20/39 (51%)
Query: 99 VRLKNTSKSHVAFKFQTTAPKSCYMRPPGGVLAPGDSII 137
+++ N + + +TT + + PP GVL P + ++
Sbjct: 31 IKITNAGGRRIGWAIKTTNMRRLGVDPPSGVLDPSEKVL 69
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
0.318 0.131 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,054,682
Number of Sequences: 62578
Number of extensions: 71830
Number of successful extensions: 114
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 106
Number of HSP's gapped (non-prelim): 8
length of query: 141
length of database: 14,973,337
effective HSP length: 89
effective length of query: 52
effective length of database: 9,403,895
effective search space: 489002540
effective search space used: 489002540
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: 46 (22.3 bits)