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= 028377
(210 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 = 68.9 bits (167), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 45/123 (36%), Positives = 73/123 (59%), Gaps = 7/123 (5%)
Query: 5 ELLSIEPL-ELKFPFELKKQISCSLQLSNKTDNYVAFKVKTTNPKKYCVRPNTGIVLPRS 63
++LS+EP ELKF ++ +L+L N TD V FKVKTT P++YCVRPN+GI+ +
Sbjct: 8 QVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGA 67
Query: 64 TCDIIVTMQAQKEAPPDMQCKDKFLLQSVKTNDGTTAKDINAEMFNKEA-GHVVEECKLR 122
+ ++ V +Q + P+ + K KF++QS+ T+ + E KEA + + KLR
Sbjct: 68 SINVSVMLQPF-DYDPNEKSKHKFMVQSMFAPTDTS----DMEAVWKEAKPEDLMDSKLR 122
Query: 123 VIY 125
++
Sbjct: 123 CVF 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 = 68.6 bits (166), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 42/116 (36%), Positives = 67/116 (57%), Gaps = 6/116 (5%)
Query: 11 PLELKFPFELKKQISCSLQLSNKTDNYVAFKVKTTNPKKYCVRPNTGIVLPRSTCDIIVT 70
P +LKF ++ +L+L N +D V FKVKTT P++YCVRPN+GI+ P ST + V
Sbjct: 15 PTDLKFKGPFTDVVTTNLKLRNPSDRKVCFKVKTTAPRRYCVRPNSGIIDPGSTVTVSVM 74
Query: 71 MQAQKEAPPDMQCKDKFLLQSVKTNDGTTAKDINAEMFNKEA-GHVVEECKLRVIY 125
+Q + P+ + K KF++Q++ T+ + E KEA + + KLR ++
Sbjct: 75 LQPF-DYDPNEKSKHKFMVQTIFAPPNTS----DMEAVWKEAKPDELMDSKLRCVF 125
>pdb|2CRI|A Chain A, Solution Structure Of The Msp Domain Of Mouse Vamp-
Associated Proteina
Length = 147
Score = 65.9 bits (159), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 33/82 (40%), Positives = 52/82 (63%), Gaps = 1/82 (1%)
Query: 11 PLELKFPFELKKQISCSLQLSNKTDNYVAFKVKTTNPKKYCVRPNTGIVLPRSTCDIIVT 70
P +LKF ++ +L+L N +D V FKVKTT P++YCVRPN+GI+ P S + V
Sbjct: 20 PSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGIIDPGSIVTVSVM 79
Query: 71 MQAQKEAPPDMQCKDKFLLQSV 92
+Q + P+ + K KF++Q++
Sbjct: 80 LQPF-DYDPNEKSKHKFMVQTI 100
>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 = 64.7 bits (156), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 32/82 (39%), Positives = 52/82 (63%), Gaps = 1/82 (1%)
Query: 11 PLELKFPFELKKQISCSLQLSNKTDNYVAFKVKTTNPKKYCVRPNTGIVLPRSTCDIIVT 70
P +LKF ++ +L+L N +D V FKVKTT P++YCVRPN+G++ P S + V
Sbjct: 16 PSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPGSIVTVSVM 75
Query: 71 MQAQKEAPPDMQCKDKFLLQSV 92
+Q + P+ + K KF++Q++
Sbjct: 76 LQPF-DYDPNEKSKHKFMVQTI 96
>pdb|1Z9L|A Chain A, 1.7 Angstrom Crystal Structure Of The Rat Vap-A Msp
Homology Domain
Length = 128
Score = 63.2 bits (152), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 32/82 (39%), Positives = 51/82 (62%), Gaps = 1/82 (1%)
Query: 11 PLELKFPFELKKQISCSLQLSNKTDNYVAFKVKTTNPKKYCVRPNTGIVLPRSTCDIIVT 70
P +LKF ++ +L+L N +D V FKVKTT P++YCVRPN+G++ P S + V
Sbjct: 16 PSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPGSIVTVSVX 75
Query: 71 MQAQKEAPPDMQCKDKFLLQSV 92
+Q + P+ + K KF +Q++
Sbjct: 76 LQPF-DYDPNEKSKHKFXVQTI 96
>pdb|1WIC|A Chain A, Solution Structure Of The Msp Domain Of Riken Cdna
6030424e15
Length = 152
Score = 50.8 bits (120), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 35/109 (32%), Positives = 52/109 (47%), Gaps = 5/109 (4%)
Query: 4 GELLSIEPLE-LKFPFELKKQISCSLQLSNKTDNYVAFKVKTTNPKKYCVRPNTGIVLPR 62
G LL I P E L F + + L+N T N VAFKV+TT P+KY V+P+ P
Sbjct: 16 GPLLHISPAEELYFGSIESGEKKTLIVLTNVTKNIVAFKVRTTAPEKYRVKPSNSSCDPG 75
Query: 63 STCDIIVTMQAQKEAPPDMQCKDKFLLQSVKTNDGTTAKDINAEMFNKE 111
++ DIIV+ + +D+FL+ + + + F KE
Sbjct: 76 ASIDIIVSPHGGL----TVSAQDRFLIMAAEMEQSSGTGPAELSQFWKE 120
>pdb|1ROW|A Chain A, Structure Of Ssp-19, An Msp-Domain Protein Like Family
Member In Caenorhabditis Elegans
pdb|1ROW|B Chain B, Structure Of Ssp-19, An Msp-Domain Protein Like Family
Member In Caenorhabditis Elegans
Length = 109
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 7 LSIEPLELKFPFELKKQISCSLQLSNKTDNYVAFKVKTTNPKKYCVRPNTGIVLPRSTCD 66
L+ +P P +S + +L N + FK+K++N +Y + P G V P + D
Sbjct: 3 LTADPPACTVP---AAGVSSTHKLVNGGAEKIVFKIKSSNNNEYRIAPVFGFVDPSGSKD 59
Query: 67 IIVTMQA 73
+++T A
Sbjct: 60 VVITRTA 66
>pdb|1M1S|A Chain A, Structure Of Wr4, A C.Elegans Msp Family Member
Length = 116
Score = 30.4 bits (67), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 23/30 (76%)
Query: 30 LSNKTDNYVAFKVKTTNPKKYCVRPNTGIV 59
+++++D+ +AFKVK++N + Y VRP G V
Sbjct: 31 ITSESDSRLAFKVKSSNNEHYRVRPVYGFV 60
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
0.314 0.129 0.362
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,721,736
Number of Sequences: 62578
Number of extensions: 147343
Number of successful extensions: 205
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: 196
Number of HSP's gapped (non-prelim): 10
length of query: 210
length of database: 14,973,337
effective HSP length: 95
effective length of query: 115
effective length of database: 9,028,427
effective search space: 1038269105
effective search space used: 1038269105
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)