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= 028956
(201 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 = 8e-05, Method: Compositional matrix adjust.
Identities = 31/103 (30%), Positives = 51/103 (49%), Gaps = 5/103 (4%)
Query: 32 VRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKFVELPENNEKPM 91
V + +K+ N + +V FK +TTAP+ +RP I+ G S+ +V L + P
Sbjct: 28 VTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASINVSVM----LQPFDYDP- 82
Query: 92 YQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVF 134
+KS+ KF + SM D + ++ E K + + LR VF
Sbjct: 83 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 = 30/107 (28%), Positives = 52/107 (48%), Gaps = 5/107 (4%)
Query: 32 VRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKFVELPENNEKPM 91
V + +K++N S V FK +TTAP+ +RP I+ PG ++ +V L + P
Sbjct: 28 VTTNLKLRNPSDRKVCFKVKTTAPRRYCVRPNSGIIDPGSTVTVSVM----LQPFDYDP- 82
Query: 92 YQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVFLNPE 138
+KS+ KF + ++ + + ++ E K + LR VF P
Sbjct: 83 NEKSKHKFMVQTIFAPPNTSDMEAVWKEAKPDELMDSKLRCVFEMPN 129
>pdb|2CRI|A Chain A, Solution Structure Of The Msp Domain Of Mouse Vamp-
Associated Proteina
Length = 147
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 30/107 (28%), Positives = 52/107 (48%), Gaps = 5/107 (4%)
Query: 32 VRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKFVELPENNEKPM 91
V + +K++N S V FK +TTAP+ +RP I+ PG + +V L + P
Sbjct: 33 VTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGIIDPGSIVTVSVM----LQPFDYDP- 87
Query: 92 YQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVFLNPE 138
+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 = 28/103 (27%), Positives = 51/103 (49%), Gaps = 5/103 (4%)
Query: 32 VRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKFVELPENNEKPM 91
V + +K++N S V FK +TTAP+ +RP ++ PG + +V L + P
Sbjct: 29 VTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPGSIVTVSVM----LQPFDYDP- 83
Query: 92 YQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVF 134
+KS+ KF + ++ ++ + ++ E K + LR VF
Sbjct: 84 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 = 31/103 (30%), Positives = 51/103 (49%), Gaps = 5/103 (4%)
Query: 32 VRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKFVELPENNEKPM 91
V + +K++N S V FK +TTAP+ +RP ++ PG I TV V L + P
Sbjct: 29 VTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPGS--IVTV--SVXLQPFDYDPN 84
Query: 92 YQKSRDKFKIISMKVKADVDYVPELFDEQKDQTAAEQILRVVF 134
+KS+ KF + ++ ++ ++ E K + LR VF
Sbjct: 85 -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: 36 IKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATV----FKFVELPENNEK 89
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 = 0.55, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 26/41 (63%)
Query: 33 RSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESL 73
++ 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 = 3.1, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 20/42 (47%)
Query: 36 IKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATV 77
IKI N + + +TT + + PP +L P E ++ V
Sbjct: 31 IKITNAGGRRIGWAIKTTNMRRLGVDPPSGVLDPSEKVLMAV 72
>pdb|3GKH|A Chain A, Npc1(ntd)
pdb|3GKI|A Chain A, Npc1(Ntd):cholesterol
pdb|3GKJ|A Chain A, Npc1d(ntd):25hydroxycholesterol
Length = 232
Score = 26.9 bits (58), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 19/43 (44%)
Query: 16 NGAVSSLILPISSTFPVRSAIKIKNTSKSHVAFKFQTTAPKSC 58
NG I P+ S FPV + N +K + TAP SC
Sbjct: 178 NGQAPFTITPVFSDFPVHGMEPMNNATKGCDESVDEVTAPCSC 220
>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 = 9.0, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 113 VPELFDEQKDQTAAEQILRVVFLN---PERPEPALEKLKRQL 151
P L Q+ + AE++L +V + P +P+P L ++KR L
Sbjct: 243 CPVLAVAQRHRDVAERVLEIVLASLDEPRKPKPGLTRIKRNL 284
>pdb|3OP5|A Chain A, Human Vaccinia-Related Kinase 1
pdb|3OP5|B Chain B, Human Vaccinia-Related Kinase 1
pdb|3OP5|C Chain C, Human Vaccinia-Related Kinase 1
pdb|3OP5|D Chain D, Human Vaccinia-Related Kinase 1
Length = 364
Score = 26.6 bits (57), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 68 APGESLIATVFKFVELPENNEKPMYQKSRD 97
APGE IA + V+L + EKP+Y+ RD
Sbjct: 295 APGE--IAKYMETVKLLDYTEKPLYENLRD 322
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 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,885,987
Number of Sequences: 62578
Number of extensions: 215845
Number of successful extensions: 438
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 428
Number of HSP's gapped (non-prelim): 14
length of query: 201
length of database: 14,973,337
effective HSP length: 94
effective length of query: 107
effective length of database: 9,091,005
effective search space: 972737535
effective search space used: 972737535
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)