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= 042649
(199 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 33.9 bits (76), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 20 RVYGDDRDFKSKNLTAERRRREKLSNRLLTLRSLVPIITN----MNKATIVEDAITYIEK 75
R +R K + ERRRR +++R+ L +L+P + NK TI++ ++ YI K
Sbjct: 19 RALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRK 78
Query: 76 LQ 77
LQ
Sbjct: 79 LQ 80
>pdb|1R05|A Chain A, Solution Structure Of Max B-Hlh-Lz
pdb|1R05|B Chain B, Solution Structure Of Max B-Hlh-Lz
Length = 87
Score = 30.4 bits (67), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 27 DFKSKNLTAERRRREKLSNRLLTLRSLVPIITN--MNKATIVEDAITYIEKLQMTVKVL 83
D ++ + ER+RR+ + + +LR VP + ++A I++ A YI+ ++ V L
Sbjct: 3 DKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTL 61
>pdb|1AN4|A Chain A, Structure And Function Of The BHLHZ DOMAIN OF USF
pdb|1AN4|B Chain B, Structure And Function Of The BHLHZ DOMAIN OF USF
Length = 65
Score = 30.0 bits (66), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 34/61 (55%), Gaps = 6/61 (9%)
Query: 25 DRDFKSKNLTAERRRREKLSNRLLTLRSLVP------IITNMNKATIVEDAITYIEKLQM 78
D ++++ ERRRR+K++N ++ L ++P + +K I+ A YI++L+
Sbjct: 2 DEKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQ 61
Query: 79 T 79
+
Sbjct: 62 S 62
>pdb|1HLO|A Chain A, The Crystal Structure Of An Intact Human Max-Dna
Complex: New Insights Into Mechanisms Of
Transcriptional Control
pdb|1HLO|B Chain B, The Crystal Structure Of An Intact Human Max-Dna
Complex: New Insights Into Mechanisms Of
Transcriptional Control
Length = 80
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 25 DRDFKSKNLTAERRRREKLSNRLLTLRSLVPIIT--NMNKATIVEDAITYIE 74
D D ++ + ER+RR+ + + +LR VP + ++A I++ A YI+
Sbjct: 9 DADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQ 60
>pdb|1A0A|A Chain A, Phosphate System Positive Regulatory Protein Pho4DNA
Complex
pdb|1A0A|B Chain B, Phosphate System Positive Regulatory Protein Pho4DNA
Complex
Length = 63
Score = 27.7 bits (60), Expect = 4.5, Method: Composition-based stats.
Identities = 20/50 (40%), Positives = 26/50 (52%), Gaps = 7/50 (14%)
Query: 35 AERRRREKLSNRLLTLRSLVP-------IITNMNKATIVEDAITYIEKLQ 77
AE+ RR +L+ L L SL+P + +KAT VE A YI LQ
Sbjct: 9 AEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQ 58
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 27.7 bits (60), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 29/46 (63%), Gaps = 4/46 (8%)
Query: 36 ERRRREKLSNRLLTLRSLVPIITNM----NKATIVEDAITYIEKLQ 77
E+RRR+K+++ + L SLVP M +K T++ A+ +++ L+
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 66
>pdb|1AM9|A Chain A, Human Srebp-1a Bound To Ldl Receptor Promoter
pdb|1AM9|B Chain B, Human Srebp-1a Bound To Ldl Receptor Promoter
pdb|1AM9|C Chain C, Human Srebp-1a Bound To Ldl Receptor Promoter
pdb|1AM9|D Chain D, Human Srebp-1a Bound To Ldl Receptor Promoter
Length = 82
Score = 26.9 bits (58), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 36 ERRRREKLSNRLLTLRSLV-PIITNMNKATIVEDAITYIEKLQMTVKVLSDQLLEM 90
E+R R ++++++ L+ LV +NK+ ++ AI YI LQ + + L + L +
Sbjct: 14 EKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSL 69
>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 = 26.6 bits (57), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 29/46 (63%), Gaps = 4/46 (8%)
Query: 36 ERRRREKLSNRLLTLRSLVPIITNM----NKATIVEDAITYIEKLQ 77
E+RRR+K+++ + L SLVP M +K T++ A+ +++ L+
Sbjct: 17 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 62
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 0.130 0.353
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,425,653
Number of Sequences: 62578
Number of extensions: 135247
Number of successful extensions: 381
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 379
Number of HSP's gapped (non-prelim): 10
length of query: 199
length of database: 14,973,337
effective HSP length: 94
effective length of query: 105
effective length of database: 9,091,005
effective search space: 954555525
effective search space used: 954555525
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)