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= 040035
(228 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1W6J|A Chain A, Structure Of Human Osc In Complex With Ro 48-8071
Length = 732
Score = 156 bits (394), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 86/240 (35%), Positives = 132/240 (55%), Gaps = 25/240 (10%)
Query: 1 MFGTVFNYICMRLLGEGPDGGENNACARARKWILDRGGAMGI----------LGVYDWSG 50
+FGT NY+ +R+LG GPD + RAR + +GGA+ I L VY W G
Sbjct: 151 VFGTALNYVSLRILGVGPD---DPDLVRARNILHKKGGAVAIPSWGKFWLAVLNVYSWEG 207
Query: 51 CNPMPPEFWKIPSFLPISPGKLNCYCRVTYMPMSYLYGKRFVGPITPLILQLREEIYTQP 110
N + PE W P + P P L C+CR Y+PMSY Y R PL+ LR+E+Y +
Sbjct: 208 LNTLFPEMWLFPDWAPAHPSTLWCHCRQVYLPMSYCYAVRLSAAEDPLVQSLRQELYVED 267
Query: 111 YTDIDWSKMRHFCAKEDIFFPHTTVQNLLWDTLYNVVEPILNRWPLN---KLREKSLEIA 167
+ IDW R+ A ++++ PH+ W L VV +LN + + LR+++++
Sbjct: 268 FASIDWLAQRNNVAPDELYTPHS------W--LLRVVYALLNLYEHHHSAHLRQRAVQKL 319
Query: 168 MNHIHYEDEASRYMTIECVEKPLNMLCCW-IEDPNSDYFKKHLPRIGEYLWVGEDGMKVQ 226
HI +D ++ ++I + K +NML W ++ P S F++H+ RI +YLW+G DGMK+Q
Sbjct: 320 YEHIVADDRFTKSISIGPISKTINMLVRWYVDGPASTAFQEHVSRIPDYLWMGLDGMKMQ 379
>pdb|1W6K|A Chain A, Structure Of Human Osc In Complex With Lanosterol
Length = 732
Score = 156 bits (394), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 86/240 (35%), Positives = 132/240 (55%), Gaps = 25/240 (10%)
Query: 1 MFGTVFNYICMRLLGEGPDGGENNACARARKWILDRGGAMGI----------LGVYDWSG 50
+FGT NY+ +R+LG GPD + RAR + +GGA+ I L VY W G
Sbjct: 151 VFGTALNYVSLRILGVGPD---DPDLVRARNILHKKGGAVAIPSWGKFWLAVLNVYSWEG 207
Query: 51 CNPMPPEFWKIPSFLPISPGKLNCYCRVTYMPMSYLYGKRFVGPITPLILQLREEIYTQP 110
N + PE W P + P P L C+CR Y+PMSY Y R PL+ LR+E+Y +
Sbjct: 208 LNTLFPEMWLFPDWAPAHPSTLWCHCRQVYLPMSYCYAVRLSAAEDPLVQSLRQELYVED 267
Query: 111 YTDIDWSKMRHFCAKEDIFFPHTTVQNLLWDTLYNVVEPILNRWPLN---KLREKSLEIA 167
+ IDW R+ A ++++ PH+ W L VV +LN + + LR+++++
Sbjct: 268 FASIDWLAQRNNVAPDELYTPHS------W--LLRVVYALLNLYEHHHSAHLRQRAVQKL 319
Query: 168 MNHIHYEDEASRYMTIECVEKPLNMLCCW-IEDPNSDYFKKHLPRIGEYLWVGEDGMKVQ 226
HI +D ++ ++I + K +NML W ++ P S F++H+ RI +YLW+G DGMK+Q
Sbjct: 320 YEHIVADDRFTKSISIGPISKTINMLVRWYVDGPASTAFQEHVSRIPDYLWMGLDGMKMQ 379
>pdb|1GSZ|A Chain A, Crystal Structure Of A Squalene Cyclase In Complex With
The Potential Anticholesteremic Drug Ro48-8071
pdb|1GSZ|B Chain B, Crystal Structure Of A Squalene Cyclase In Complex With
The Potential Anticholesteremic Drug Ro48-8071
pdb|1GSZ|C Chain C, Crystal Structure Of A Squalene Cyclase In Complex With
The Potential Anticholesteremic Drug Ro48-8071
pdb|1H35|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H35|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H35|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H36|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H36|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H36|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H37|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H37|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H37|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H39|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H39|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H39|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H3A|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H3A|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H3A|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H3B|A Chain A, Squalene-Hopene Cyclase
pdb|1H3B|B Chain B, Squalene-Hopene Cyclase
pdb|1H3B|C Chain C, Squalene-Hopene Cyclase
pdb|1H3C|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H3C|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H3C|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O6H|A Chain A, Squalene-Hopene Cyclase
pdb|1O6H|B Chain B, Squalene-Hopene Cyclase
pdb|1O6H|C Chain C, Squalene-Hopene Cyclase
pdb|1O6Q|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O6Q|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O6Q|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O6R|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O6R|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O6R|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O79|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O79|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O79|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1UMP|A Chain A, Geometry Of Triterpene Conversion To Pentacarbocyclic
Hopene
pdb|1UMP|B Chain B, Geometry Of Triterpene Conversion To Pentacarbocyclic
Hopene
pdb|1UMP|C Chain C, Geometry Of Triterpene Conversion To Pentacarbocyclic
Hopene
pdb|1SQC|A Chain A, Squalene-Hopene-Cyclase From Alicyclobacillus
Acidocaldarius
Length = 631
Score = 30.4 bits (67), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 20/102 (19%), Positives = 45/102 (44%), Gaps = 13/102 (12%)
Query: 4 TVFNYICMRLLGEGPDGGENNACARARKWILDRGGA----------MGILGVYDWSGCNP 53
T+ Y+ ++ +G D +A ++I +GG + ++G Y W
Sbjct: 91 TIEAYVALKYIGMSRD---EEPMQKALRFIQSQGGIESSRVFTRMWLALVGEYPWEKVPM 147
Query: 54 MPPEFWKIPSFLPISPGKLNCYCRVTYMPMSYLYGKRFVGPI 95
+PPE + +P++ + + R T + +S + ++ V P+
Sbjct: 148 VPPEIMFLGKRMPLNIYEFGSWARATVVALSIVMSRQPVFPL 189
>pdb|2SQC|A Chain A, Squalene-Hopene Cyclase From Alicyclobacillus
Acidocaldarius
pdb|2SQC|B Chain B, Squalene-Hopene Cyclase From Alicyclobacillus
Acidocaldarius
Length = 631
Score = 30.4 bits (67), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 20/102 (19%), Positives = 45/102 (44%), Gaps = 13/102 (12%)
Query: 4 TVFNYICMRLLGEGPDGGENNACARARKWILDRGGA----------MGILGVYDWSGCNP 53
T+ Y+ ++ +G D +A ++I +GG + ++G Y W
Sbjct: 91 TIEAYVALKYIGMSRD---EEPMQKALRFIQSQGGIESSRVFTRMWLALVGEYPWEKVPM 147
Query: 54 MPPEFWKIPSFLPISPGKLNCYCRVTYMPMSYLYGKRFVGPI 95
+PPE + +P++ + + R T + +S + ++ V P+
Sbjct: 148 VPPEIMFLGKRMPLNIYEFGSWARATVVALSIVMSRQPVFPL 189
>pdb|3SQC|A Chain A, Squalene-Hopene Cyclase
pdb|3SQC|B Chain B, Squalene-Hopene Cyclase
pdb|3SQC|C Chain C, Squalene-Hopene Cyclase
Length = 631
Score = 30.4 bits (67), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 20/102 (19%), Positives = 45/102 (44%), Gaps = 13/102 (12%)
Query: 4 TVFNYICMRLLGEGPDGGENNACARARKWILDRGGA----------MGILGVYDWSGCNP 53
T+ Y+ ++ +G D +A ++I +GG + ++G Y W
Sbjct: 91 TIEAYVALKYIGMSRD---EEPMQKALRFIQSQGGIESSRVFTRMWLALVGEYPWEKVPM 147
Query: 54 MPPEFWKIPSFLPISPGKLNCYCRVTYMPMSYLYGKRFVGPI 95
+PPE + +P++ + + R T + +S + ++ V P+
Sbjct: 148 VPPEIMFLGKRMPLNIYEFGSWARATVVALSIVMSRQPVFPL 189
>pdb|1US1|A Chain A, Crystal Structure Of Human Vascular Adhesion Protein-1
pdb|1US1|B Chain B, Crystal Structure Of Human Vascular Adhesion Protein-1
pdb|1PU4|A Chain A, Crystal Structure Of Human Vascular Adhesion Protein-1
pdb|1PU4|B Chain B, Crystal Structure Of Human Vascular Adhesion Protein-1
pdb|2Y73|A Chain A, The Native Structures Of Soluble Human Primary Amine
Oxidase Aoc3
pdb|2Y73|B Chain B, The Native Structures Of Soluble Human Primary Amine
Oxidase Aoc3
pdb|2Y74|A Chain A, The Crystal Structure Of Human Soluble Primary Amine
Oxidase Aoc3 In The Off-Copper Conformation
pdb|2Y74|B Chain B, The Crystal Structure Of Human Soluble Primary Amine
Oxidase Aoc3 In The Off-Copper Conformation
Length = 763
Score = 27.3 bits (59), Expect = 6.6, Method: Composition-based stats.
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 4 TVFNYICMRLLGEGPDGGE 22
T+F +C+ L+G G DGGE
Sbjct: 16 TIFALVCVLLVGRGGDGGE 34
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 27.3 bits (59), Expect = 6.7, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 30 RKWILDRGGAMG-----ILG--VYDWSGCNPMPPEFWKIPSFLPISPGKLNCYCRVTYMP 82
+K+ +D+ G ILG V D S P+P EF IP+F ++ + N V P
Sbjct: 318 KKFAIDKKSISGYLYYKILGHQVVDISFDVPLPKEF-SIPNFAQLNSSQSNAVSHVLQRP 376
Query: 83 MSYLYG 88
+S + G
Sbjct: 377 LSLIQG 382
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
0.324 0.143 0.488
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,153,076
Number of Sequences: 62578
Number of extensions: 359385
Number of successful extensions: 808
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 792
Number of HSP's gapped (non-prelim): 12
length of query: 228
length of database: 14,973,337
effective HSP length: 95
effective length of query: 133
effective length of database: 9,028,427
effective search space: 1200780791
effective search space used: 1200780791
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 50 (23.9 bits)