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= 028668
(205 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 32/108 (29%), Positives = 52/108 (48%), Gaps = 5/108 (4%)
Query: 31 PAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKFVELPEN 90
P V + +K+ N + +V FK +TTAP+ +RP I+ G S+ +V L
Sbjct: 23 PFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASINVSVM----LQPF 78
Query: 91 NEKPMYQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVF 138
+ P +KS+ KF + SM D + ++ E K + + LR VF
Sbjct: 79 DYDP-NEKSKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSKLRCVF 125
>pdb|2RR3|A Chain A, Solution Structure Of The Complex Between Human Vap-A Msp
Domain And Human Osbp Ffat Motif
Length = 130
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 31/112 (27%), Positives = 53/112 (47%), Gaps = 5/112 (4%)
Query: 31 PAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKFVELPEN 90
P V + +K++N S V FK +TTAP+ +RP I+ PG ++ +V L
Sbjct: 23 PFTDVVTTNLKLRNPSDRKVCFKVKTTAPRRYCVRPNSGIIDPGSTVTVSVM----LQPF 78
Query: 91 NEKPMYQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVFLNPE 142
+ P +KS+ KF + ++ + + ++ E K + LR VF P
Sbjct: 79 DYDP-NEKSKHKFMVQTIFAPPNTSDMEAVWKEAKPDELMDSKLRCVFEMPN 129
>pdb|2CRI|A Chain A, Solution Structure Of The Msp Domain Of Mouse Vamp-
Associated Proteina
Length = 147
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 30/107 (28%), Positives = 52/107 (48%), Gaps = 5/107 (4%)
Query: 36 VRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKFVELPENNEKPM 95
V + +K++N S V FK +TTAP+ +RP I+ PG + +V L + P
Sbjct: 33 VTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGIIDPGSIVTVSVM----LQPFDYDP- 87
Query: 96 YQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVFLNPE 142
+KS+ KF + ++ ++ + ++ E K + LR VF P
Sbjct: 88 NEKSKHKFMVQTIFAPPNISDMEAVWKEAKPDELMDSKLRCVFEMPN 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 = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 52/108 (48%), Gaps = 5/108 (4%)
Query: 31 PAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKFVELPEN 90
P V + +K++N S V FK +TTAP+ +RP ++ PG + +V L
Sbjct: 24 PFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPGSIVTVSVM----LQPF 79
Query: 91 NEKPMYQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVF 138
+ P +KS+ KF + ++ ++ + ++ E K + LR VF
Sbjct: 80 DYDP-NEKSKHKFMVQTIFAPPNISDMEAVWKEAKPDELMDSKLRCVF 126
>pdb|1Z9L|A Chain A, 1.7 Angstrom Crystal Structure Of The Rat Vap-A Msp
Homology Domain
Length = 128
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 32/108 (29%), Positives = 52/108 (48%), Gaps = 5/108 (4%)
Query: 31 PAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKFVELPEN 90
P V + +K++N S V FK +TTAP+ +RP ++ PG I TV V L
Sbjct: 24 PFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPGS--IVTV--SVXLQPF 79
Query: 91 NEKPMYQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVF 138
+ P +KS+ KF + ++ ++ ++ E K + LR VF
Sbjct: 80 DYDPN-EKSKHKFXVQTIFAPPNISDXEAVWKEAKPDELXDSKLRCVF 126
>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 = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 40 IKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATV----FKFVELPENNEK 93
IK+ N+S + + +TT K + PP +L P E+++ V F F + NN++
Sbjct: 31 IKVINSSARRIGYGIKTTNMKRLGVDPPCGVLDPKEAVLLAVSCDAFAFGQEDTNNDR 88
>pdb|1WIC|A Chain A, Solution Structure Of The Msp Domain Of Riken Cdna
6030424e15
Length = 152
Score = 30.8 bits (68), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 26/41 (63%)
Query: 37 RSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESL 77
++ I + N +K+ VAFK +TTAP+ ++P + PG S+
Sbjct: 38 KTLIVLTNVTKNIVAFKVRTTAPEKYRVKPSNSSCDPGASI 78
>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 = 28.1 bits (61), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 20/42 (47%)
Query: 40 IKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATV 81
IKI N + + +TT + + PP +L P E ++ V
Sbjct: 31 IKITNAGGRRIGWAIKTTNMRRLGVDPPSGVLDPSEKVLMAV 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 = 26.6 bits (57), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 117 VPELFDEQKDQTAAEQILRVVFLN---PERPEPALEKLKRQL 155
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
0.318 0.136 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,030,619
Number of Sequences: 62578
Number of extensions: 222224
Number of successful extensions: 461
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 452
Number of HSP's gapped (non-prelim): 10
length of query: 205
length of database: 14,973,337
effective HSP length: 94
effective length of query: 111
effective length of database: 9,091,005
effective search space: 1009101555
effective search space used: 1009101555
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: 49 (23.5 bits)