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= 027513
(222 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 = 58.5 bits (140), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 40/121 (33%), Positives = 67/121 (55%), Gaps = 7/121 (5%)
Query: 8 QLISVHPE-ELKFIFELEKQGFCDLKVINNTEHHVAFKVKTTSPKKYFVRPNTGVVQPWD 66
Q++S+ P+ ELKF +LK+ N T+ +V FKVKTT+P++Y VRPN+G++
Sbjct: 8 QVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGA 67
Query: 67 SCIIRAQRE---SPPDMQCKDKFLLQSTIVPSNTDVDDLPPDTFNKDSGKTIEECKLRVV 123
S + + P+ + K KF++QS P TD D+ + + + + + KLR V
Sbjct: 68 SINVSVMLQPFDYDPNEKSKHKFMVQSMFAP--TDTSDMEA-VWKEAKPEDLMDSKLRCV 124
Query: 124 Y 124
+
Sbjct: 125 F 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 = 57.4 bits (137), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 38/132 (28%), Positives = 69/132 (52%), Gaps = 8/132 (6%)
Query: 1 MTADGGNQLISVHPEELKFIFELEKQGFCDLKVINNTEHHVAFKVKTTSPKKYFVRPNTG 60
+ +D L+ P +LKF +LK+ N ++ V FKVKTT+P++Y VRPN+G
Sbjct: 2 LGSDHEQILVLDPPTDLKFKGPFTDVVTTNLKLRNPSDRKVCFKVKTTAPRRYCVRPNSG 61
Query: 61 VVQPWDSCIIRAQRE---SPPDMQCKDKFLLQSTIVPSNT-DVDDLPPDTFNKDSGKTIE 116
++ P + + + P+ + K KF++Q+ P NT D++ + + + +
Sbjct: 62 IIDPGSTVTVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNTSDMEAV----WKEAKPDELM 117
Query: 117 ECKLRVVYVSPS 128
+ KLR V+ P+
Sbjct: 118 DSKLRCVFEMPN 129
>pdb|2CRI|A Chain A, Solution Structure Of The Msp Domain Of Mouse Vamp-
Associated Proteina
Length = 147
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 38/128 (29%), Positives = 64/128 (50%), Gaps = 7/128 (5%)
Query: 14 PEELKFIFELEKQGFCDLKVINNTEHHVAFKVKTTSPKKYFVRPNTGVVQPWDSCIIRAQ 73
P +LKF +LK+ N ++ V FKVKTT+P++Y VRPN+G++ P +
Sbjct: 20 PSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGIIDPGSIVTVSVM 79
Query: 74 RE---SPPDMQCKDKFLLQSTIVPSNTDVDDLPPDTFNKDSGKTIEECKLRVVYVSPSSA 130
+ P+ + K KF++Q+ P N + D+ + + + + KLR V+ P+
Sbjct: 80 LQPFDYDPNEKSKHKFMVQTIFAPPN--ISDMEA-VWKEAKPDELMDSKLRCVFEMPNE- 135
Query: 131 QGNLEDEG 138
L D G
Sbjct: 136 NDKLNDSG 143
>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 = 53.9 bits (128), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 30/86 (34%), Positives = 47/86 (54%), Gaps = 3/86 (3%)
Query: 14 PEELKFIFELEKQGFCDLKVINNTEHHVAFKVKTTSPKKYFVRPNTGVVQPWDSCIIRAQ 73
P +LKF +LK+ N ++ V FKVKTT+P++Y VRPN+GV+ P +
Sbjct: 16 PSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPGSIVTVSVM 75
Query: 74 RE---SPPDMQCKDKFLLQSTIVPSN 96
+ P+ + K KF++Q+ P N
Sbjct: 76 LQPFDYDPNEKSKHKFMVQTIFAPPN 101
>pdb|1Z9L|A Chain A, 1.7 Angstrom Crystal Structure Of The Rat Vap-A Msp
Homology Domain
Length = 128
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/86 (34%), Positives = 46/86 (53%), Gaps = 3/86 (3%)
Query: 14 PEELKFIFELEKQGFCDLKVINNTEHHVAFKVKTTSPKKYFVRPNTGVVQPWDSCIIRAQ 73
P +LKF +LK+ N ++ V FKVKTT+P++Y VRPN+GV+ P +
Sbjct: 16 PSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPGSIVTVSVX 75
Query: 74 RE---SPPDMQCKDKFLLQSTIVPSN 96
+ P+ + K KF +Q+ P N
Sbjct: 76 LQPFDYDPNEKSKHKFXVQTIFAPPN 101
>pdb|1WIC|A Chain A, Solution Structure Of The Msp Domain Of Riken Cdna
6030424e15
Length = 152
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 9 LISVHPEELKFIFELEKQGFCDLKVINN-TEHHVAFKVKTTSPKKYFVRPNTGVVQPWDS 67
L+ + P E + +E L V+ N T++ VAFKV+TT+P+KY V+P+ P S
Sbjct: 18 LLHISPAEELYFGSIESGEKKTLIVLTNVTKNIVAFKVRTTAPEKYRVKPSNSSCDPGAS 77
Query: 68 CIIRAQRESPPDMQCKDKFLLQS 90
I + +D+FL+ +
Sbjct: 78 IDIIVSPHGGLTVSAQDRFLIMA 100
>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 = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 26/40 (65%)
Query: 31 LKVINNTEHHVAFKVKTTSPKKYFVRPNTGVVQPWDSCII 70
+KVIN++ + + +KTT+ K+ V P GV+ P ++ ++
Sbjct: 31 IKVINSSARRIGYGIKTTNMKRLGVDPPCGVLDPKEAVLL 70
>pdb|1M1S|A Chain A, Structure Of Wr4, A C.Elegans Msp Family Member
Length = 116
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 27 GFCDLKVINNTEHHVAFKVKTTSPKKYFVRPNTGVVQPWDSCIIRAQRESPPDMQCKDKF 86
G + + ++ +AFKVK+++ + Y VRP G V + R P + DK
Sbjct: 25 GNSTHNITSESDSRLAFKVKSSNNEHYRVRPVYGFVDAKGKSKLDINRLPGPPKE--DKI 82
Query: 87 LLQSTIVPS 95
++Q VP+
Sbjct: 83 VIQYAEVPA 91
>pdb|3DLI|A Chain A, Crystal Structure Of A Sam Dependent Methyltransferase
From Archaeoglobus Fulgidus
pdb|3DLI|B Chain B, Crystal Structure Of A Sam Dependent Methyltransferase
From Archaeoglobus Fulgidus
pdb|3DLI|C Chain C, Crystal Structure Of A Sam Dependent Methyltransferase
From Archaeoglobus Fulgidus
Length = 240
Score = 26.9 bits (58), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 14/22 (63%), Positives = 16/22 (72%), Gaps = 2/22 (9%)
Query: 12 VHPEELKFIFELEKQGFCDLKV 33
VHPE LKFI LE GF D+K+
Sbjct: 162 VHPETLKFI--LEYLGFRDVKI 181
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
0.316 0.133 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,090,789
Number of Sequences: 62578
Number of extensions: 229831
Number of successful extensions: 364
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 351
Number of HSP's gapped (non-prelim): 18
length of query: 222
length of database: 14,973,337
effective HSP length: 95
effective length of query: 127
effective length of database: 9,028,427
effective search space: 1146610229
effective search space used: 1146610229
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)