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= 026702
(235 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRD 127
EK RRD+ N EL S+L PG KMDK+ +L ++ + + ++
Sbjct: 20 EKKRRDQFNVLIKELGSML-PGNARKMDKSTVLQKSIDFLRKHKE 63
>pdb|4H10|B Chain B, Intermolecular Recognition Revealed By The Complex
Structure Of Human Clock-bmal1 Basic Helix-loop-helix
Domains With E-box Dna
Length = 71
Score = 31.6 bits (70), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRD 127
EK RRD+ N EL S+L PG KMDK+ +L ++ + + ++
Sbjct: 16 EKKRRDQFNVLIKELGSML-PGNARKMDKSTVLQKSIDFLRKHKE 59
>pdb|4ATI|A Chain A, Mitf:m-Box Complex
pdb|4ATI|B Chain B, Mitf:m-Box Complex
pdb|4ATK|A Chain A, Mitf:e-Box Complex
pdb|4ATK|B Chain B, Mitf:e-Box Complex
Length = 118
Score = 31.2 bits (69), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 12/79 (15%)
Query: 83 EKMRRDRLNDRFMELASILDPGRPPKM--DKTVLLADAVQMVTQLRDEAQ---------- 130
E+ RR +NDR EL +++ P M +K +L +V + +L+ E Q
Sbjct: 35 ERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENRQK 94
Query: 131 KLKVSNEKLLGKINELKCE 149
KL+ +N LL ++ EL+ +
Sbjct: 95 KLEHANRHLLLRVQELEMQ 113
>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 = 30.8 bits (68), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 26/46 (56%)
Query: 83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDE 128
EK+RR L+++ + L PG PP +D T+ A++ + RDE
Sbjct: 62 EKIRRYLLHEQREDGTWALYPGGPPDLDTTIEAYVALKYIGMSRDE 107
>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 = 30.8 bits (68), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 26/46 (56%)
Query: 83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDE 128
EK+RR L+++ + L PG PP +D T+ A++ + RDE
Sbjct: 62 EKIRRYLLHEQREDGTWALYPGGPPDLDTTIEAYVALKYIGMSRDE 107
>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 = 30.8 bits (68), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 26/46 (56%)
Query: 83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDE 128
EK+RR L+++ + L PG PP +D T+ A++ + RDE
Sbjct: 62 EKIRRYLLHEQREDGTWALYPGGPPDLDTTIEAYVALKYIGMSRDE 107
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 30.4 bits (67), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 83 EKMRRDRLNDRFMELASILDP--GRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEK 138
EK RRD++N ELAS++ K+DK +L AVQ + LR +N K
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTEANYK 78
>pdb|4H10|A Chain A, Intermolecular Recognition Revealed By The Complex
Structure Of Human Clock-bmal1 Basic Helix-loop-helix
Domains With E-box Dna
Length = 73
Score = 30.0 bits (66), Expect = 1.2, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 83 EKMRRDRLNDRFMELASILDP--GRPPKMDKTVLLADAVQMVTQLR 126
EK RRD++N ELAS++ K+DK +L AVQ + LR
Sbjct: 17 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 62
>pdb|2W83|C Chain C, Crystal Structure Of The Arf6 Gtpase In Complex With A
Specific Effector, Jip4
pdb|2W83|D Chain D, Crystal Structure Of The Arf6 Gtpase In Complex With A
Specific Effector, Jip4
Length = 77
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 123 TQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEK 164
TQL + L + L+ K++EL CEK+ L+ E + +K K
Sbjct: 19 TQLLETKNALNIVKNDLIAKVDELTCEKDVLQGELEAVKQAK 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
0.313 0.133 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,255,826
Number of Sequences: 62578
Number of extensions: 210274
Number of successful extensions: 453
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 435
Number of HSP's gapped (non-prelim): 30
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)