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= 025361
(254 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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 34/122 (27%), Positives = 56/122 (45%), Gaps = 5/122 (4%)
Query: 78 DPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIAT 137
DP L F V + +K++N S V FK +TTAP+ +RP I+ PG ++ +
Sbjct: 13 DPPTDLKFKGPFTDVVTTNLKLRNPSDRKVCFKVKTTAPRRYCVRPNSGIIDPGSTVTVS 72
Query: 138 VFKFVELPENNEKPMYQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVFLN 197
V L + P +KS+ KF + ++ + + ++ E K + LR VF
Sbjct: 73 VM----LQPFDYDP-NEKSKHKFMVQTIFAPPNTSDMEAVWKEAKPDELMDSKLRCVFEM 127
Query: 198 PE 199
P
Sbjct: 128 PN 129
>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 = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 34/118 (28%), Positives = 57/118 (48%), Gaps = 5/118 (4%)
Query: 78 DPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIAT 137
+P ++L F V + +K+ N + +V FK +TTAP+ +RP I+ G S+ +
Sbjct: 13 EPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASINVS 72
Query: 138 VFKFVELPENNEKPMYQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVF 195
V L + P +KS+ KF + SM D + ++ E K + + LR VF
Sbjct: 73 VM----LQPFDYDP-NEKSKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSKLRCVF 125
>pdb|2CRI|A Chain A, Solution Structure Of The Msp Domain Of Mouse Vamp-
Associated Proteina
Length = 147
Score = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 34/122 (27%), Positives = 57/122 (46%), Gaps = 5/122 (4%)
Query: 78 DPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIAT 137
DP + L F V + +K++N S V FK +TTAP+ +RP I+ PG + +
Sbjct: 18 DPPSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGIIDPGSIVTVS 77
Query: 138 VFKFVELPENNEKPMYQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVFLN 197
V L + P +KS+ KF + ++ ++ + ++ E K + LR VF
Sbjct: 78 VM----LQPFDYDP-NEKSKHKFMVQTIFAPPNISDMEAVWKEAKPDELMDSKLRCVFEM 132
Query: 198 PE 199
P
Sbjct: 133 PN 134
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 32/118 (27%), Positives = 56/118 (47%), Gaps = 5/118 (4%)
Query: 78 DPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIAT 137
DP + L F V + +K++N S V FK +TTAP+ +RP ++ PG + +
Sbjct: 14 DPPSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPGSIVTVS 73
Query: 138 VFKFVELPENNEKPMYQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVF 195
V L + P +KS+ KF + ++ ++ + ++ E K + LR VF
Sbjct: 74 VM----LQPFDYDP-NEKSKHKFMVQTIFAPPNISDMEAVWKEAKPDELMDSKLRCVF 126
>pdb|1Z9L|A Chain A, 1.7 Angstrom Crystal Structure Of The Rat Vap-A Msp
Homology Domain
Length = 128
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 35/118 (29%), Positives = 56/118 (47%), Gaps = 5/118 (4%)
Query: 78 DPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIAT 137
DP + L F V + +K++N S V FK +TTAP+ +RP ++ PG I T
Sbjct: 14 DPPSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPGS--IVT 71
Query: 138 VFKFVELPENNEKPMYQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVF 195
V V L + P +KS+ KF + ++ ++ ++ E K + LR VF
Sbjct: 72 V--SVXLQPFDYDP-NEKSKHKFXVQTIFAPPNISDXEAVWKEAKPDELXDSKLRCVF 126
>pdb|1WIC|A Chain A, Solution Structure Of The Msp Domain Of Riken Cdna
6030424e15
Length = 152
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 33/57 (57%)
Query: 78 DPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESL 134
PA +LYF + ++ I + N +K+ VAFK +TTAP+ ++P + PG S+
Sbjct: 22 SPAEELYFGSIESGEKKTLIVLTNVTKNIVAFKVRTTAPEKYRVKPSNSSCDPGASI 78
>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 = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 79 PANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATV 138
P K+ F + IK+ N+S + + +TT K + PP +L P E+++ V
Sbjct: 13 PGTKIVFNAPYDDKHTYHIKVINSSARRIGYGIKTTNMKRLGVDPPCGVLDPKEAVLLAV 72
Query: 139 ----FKFVELPENNEK 150
F F + NN++
Sbjct: 73 SCDAFAFGQEDTNNDR 88
>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 = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 26/60 (43%)
Query: 79 PANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATV 138
P +K+ F + IKI N + + +TT + + PP +L P E ++ V
Sbjct: 13 PGSKIVFNAPYDDKHTYHIKITNAGGRRIGWAIKTTNMRRLGVDPPSGVLDPSEKVLMAV 72
>pdb|2IKS|A Chain A, Crystal Structure Of N-Terminal Truncated Dna-Binding
Transcriptional Dual Regulator From Escherichia Coli K12
pdb|2IKS|B Chain B, Crystal Structure Of N-Terminal Truncated Dna-Binding
Transcriptional Dual Regulator From Escherichia Coli K12
Length = 293
Score = 27.3 bits (59), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 174 VPELFDEQKDQTAAEQILRVVFLN---PERPEPALEKLKRQL 212
P L Q+ + AE++L +V + P +P+P L ++KR L
Sbjct: 243 CPVLAVAQRHRDVAERVLEIVLASLDEPRKPKPGLTRIKRNL 284
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 0.135 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,972,903
Number of Sequences: 62578
Number of extensions: 200631
Number of successful extensions: 357
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 350
Number of HSP's gapped (non-prelim): 10
length of query: 254
length of database: 14,973,337
effective HSP length: 97
effective length of query: 157
effective length of database: 8,903,271
effective search space: 1397813547
effective search space used: 1397813547
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: 50 (23.9 bits)