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= psy5198
(186 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ZHT|A Chain A, Structure Of Yeast Oxysterol Binding Protein Osh4 In
Complex With 7-Hydroxycholesterol
pdb|1ZHW|A Chain A, Structure Of Yeast Oxysterol Binding Protein Osh4 In
Complex With 20-hydroxycholesterol
pdb|1ZHX|A Chain A, Structure Of Yeast Oxysterol Binding Protein Osh4 In
Complex With 25-Hydroxycholesterol
pdb|1ZHY|A Chain A, Structure Of Yeast Oxysterol Binding Protein Osh4 In
Complex With Cholesterol
pdb|1ZHZ|A Chain A, Structure Of Yeast Oxysterol Binding Protein Osh4 In
Complex With Ergosterol
Length = 438
Score = 43.1 bits (100), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 43/144 (29%), Positives = 61/144 (42%), Gaps = 31/144 (21%)
Query: 17 SLSLWNLLCKNIGK---DLSQVSMPVALNEPLNMLQRMCEELEYSELL--------DKAA 65
S S W K+I DLS +S P + P+++ + E+ EL D
Sbjct: 10 SSSSWTSFLKSIASFNGDLSSLSAPPFILSPISLTEFSQYWAEHPELFLEPSFINDDNYK 69
Query: 66 E--LSDP------YERMVYVAAFAVSSYGSSY------FRAASKPFNPLLGETYECVRED 111
E L DP RM+ V + +S+ S Y + KP NP LGE + E+
Sbjct: 70 EHCLIDPEVESPELARMLAVTKWFISTLKSQYCSRNESLGSEKKPLNPFLGELFVGKWEN 129
Query: 112 KGFK------FVAEQVSHHPPVSV 129
K ++EQVSHHPPV+
Sbjct: 130 KEHPEFGETVLLSEQVSHHPPVTA 153
>pdb|3SPW|A Chain A, Structure Of Osh4pKES1P IN COMPLEX WITH
PHOSPHATIDYLINOSITOL 4- Phosphate
pdb|3SPW|B Chain B, Structure Of Osh4pKES1P IN COMPLEX WITH
PHOSPHATIDYLINOSITOL 4- Phosphate
Length = 436
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/140 (29%), Positives = 59/140 (42%), Gaps = 31/140 (22%)
Query: 21 WNLLCKNIGK---DLSQVSMPVALNEPLNMLQRMCEELEYSELL--------DKAAE--L 67
W K+I DLS +S P + P+++ + E+ EL D E L
Sbjct: 12 WTSFLKSIASFNGDLSSLSAPPFILSPISLTEFSQYWAEHPELFLEPSFINDDNYKEHCL 71
Query: 68 SDP------YERMVYVAAFAVSSYGSSY------FRAASKPFNPLLGETYECVREDKGFK 115
DP RM+ V + +S+ S Y + KP NP LGE + E+K
Sbjct: 72 IDPEVESPELARMLAVTKWFISTLKSQYCSRNESLGSEKKPLNPFLGELFVGKWENKEHP 131
Query: 116 ------FVAEQVSHHPPVSV 129
++EQVSHHPPV+
Sbjct: 132 EFGETVLLSEQVSHHPPVTA 151
>pdb|1ZI7|A Chain A, Structure Of Truncated Yeast Oxysterol Binding Protein
Osh4
pdb|1ZI7|B Chain B, Structure Of Truncated Yeast Oxysterol Binding Protein
Osh4
pdb|1ZI7|C Chain C, Structure Of Truncated Yeast Oxysterol Binding Protein
Osh4
Length = 406
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 12/69 (17%)
Query: 73 RMVYVAAFAVSSYGSSY------FRAASKPFNPLLGETYECVREDKGFK------FVAEQ 120
RM+ V + +S+ S Y + KP NP LGE + E+K ++EQ
Sbjct: 56 RMLAVTKWFISTLKSQYCSRNESLGSEKKPLNPFLGELFVGKWENKEHPEFGETVLLSEQ 115
Query: 121 VSHHPPVSV 129
VSHHPPV+
Sbjct: 116 VSHHPPVTA 124
>pdb|2E6K|A Chain A, X-Ray Structure Of Thermus Thermopilus Hb8 Tt0505
pdb|2E6K|B Chain B, X-Ray Structure Of Thermus Thermopilus Hb8 Tt0505
pdb|2E6K|C Chain C, X-Ray Structure Of Thermus Thermopilus Hb8 Tt0505
pdb|2E6K|D Chain D, X-Ray Structure Of Thermus Thermopilus Hb8 Tt0505
Length = 651
Score = 28.1 bits (61), Expect = 2.7, Method: Composition-based stats.
Identities = 27/120 (22%), Positives = 50/120 (41%), Gaps = 8/120 (6%)
Query: 53 EELEYSELLDKAAELSDPYERMVYVAAFAVSSYGSSYFRAASKPFNPLLGETYECVREDK 112
E++ E L KA +L+ ER +A + +GS +A PL E E R +
Sbjct: 220 EDVNDLEALRKAIKLAKLDERPTLIAVRSHIGFGSPKQDSAKAHGEPLGPEAVEATRRNL 279
Query: 113 GFKFVAEQVSHHPPVSVCHAESKNFIFWQDVRIKTKFWGKSMEFQPNELNELNAEMKKQI 172
G+ + PP V ++ + R + W K++E +L+ E+ +++
Sbjct: 280 GWPY--------PPFVVPEEVYRHXDXREKGRAWQEAWEKALEAYARAYPDLHQELXRRL 331
>pdb|4A15|A Chain A, Crystal Structure Of An Xpd Dna Complex
Length = 620
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 8 LPCPRPDTESLSLWNLLCKNIGKDLS-QVSMPVALN--EPLNMLQRMCEELEYSELLDKA 64
LP PRPD + SL++ + GK V P A+ + + L R E+ +LDK
Sbjct: 525 LPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDKR 584
Query: 65 A 65
A
Sbjct: 585 A 585
>pdb|2VSF|A Chain A, Structure Of Xpd From Thermoplasma Acidophilum
Length = 602
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 8 LPCPRPDTESLSLWNLLCKNIGKDLS-QVSMPVALN--EPLNMLQRMCEELEYSELLDKA 64
LP PRPD + SL++ + GK V P A+ + + L R E+ +LDK
Sbjct: 507 LPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDKR 566
Query: 65 A 65
A
Sbjct: 567 A 567
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 0.131 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,490,649
Number of Sequences: 62578
Number of extensions: 201228
Number of successful extensions: 407
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 403
Number of HSP's gapped (non-prelim): 7
length of query: 186
length of database: 14,973,337
effective HSP length: 93
effective length of query: 93
effective length of database: 9,153,583
effective search space: 851283219
effective search space used: 851283219
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: 48 (23.1 bits)