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= 014485
(423 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 = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 309 ELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSD----K 364
EL + +S AK + + HNL ERRRR IN++++ L LIP+ N D K
Sbjct: 6 ELTACIFPTESEARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNK 65
Query: 365 ASMLDEAIEYLKSLQLQVQ 383
++L +++Y++ LQ + Q
Sbjct: 66 GTILKASVDYIRKLQREQQ 84
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 35/54 (64%), Gaps = 4/54 (7%)
Query: 330 AAEVHNLSERRRRDRINEKMRALQELIPRCN----KSDKASMLDEAIEYLKSLQ 379
A E H+ E+RRRD++N + L L+P CN K DK ++L A++++K+L+
Sbjct: 13 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 66
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 35/54 (64%), Gaps = 4/54 (7%)
Query: 330 AAEVHNLSERRRRDRINEKMRALQELIPRCN----KSDKASMLDEAIEYLKSLQ 379
A E H+ E+RRRD++N + L L+P CN K DK ++L A++++K+L+
Sbjct: 9 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 62
>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 = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 35/54 (64%), Gaps = 2/54 (3%)
Query: 334 HNLSERRRRDRINEKMRALQELIP--RCNKSDKASMLDEAIEYLKSLQLQVQMM 385
HN ER+RRD I + +L++ +P + K+ +A +LD+A EY++ ++ +V +
Sbjct: 8 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTL 61
>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 = 37.0 bits (84), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 45/77 (58%), Gaps = 16/77 (20%)
Query: 305 SEDVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIP--RCNKS 362
++D+E+ES DA K++ HN ER+RRD I + +L++ +P + K+
Sbjct: 1 NDDIEVES-DADKRAH-------------HNALERKRRDHIKDSFHSLRDSVPSLQGEKA 46
Query: 363 DKASMLDEAIEYLKSLQ 379
+A +LD+A EY++ ++
Sbjct: 47 SRAQILDKATEYIQYMR 63
>pdb|1NLW|B Chain B, Crystal Structure Of Mad-Max Recognizing Dna
pdb|1NLW|E Chain E, Crystal Structure Of Mad-Max Recognizing Dna
Length = 76
Score = 35.8 bits (81), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 31/47 (65%), Gaps = 2/47 (4%)
Query: 334 HNLSERRRRDRINEKMRALQELIP--RCNKSDKASMLDEAIEYLKSL 378
HN ER+RRD I + +L++ +P + K+ +A +LD+A EY++ +
Sbjct: 5 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYM 51
>pdb|1NKP|B Chain B, Crystal Structure Of Myc-Max Recognizing Dna
pdb|1NKP|E Chain E, Crystal Structure Of Myc-Max Recognizing Dna
Length = 83
Score = 35.8 bits (81), Expect = 0.053, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 32/48 (66%), Gaps = 2/48 (4%)
Query: 334 HNLSERRRRDRINEKMRALQELIP--RCNKSDKASMLDEAIEYLKSLQ 379
HN ER+RRD I + +L++ +P + K+ +A +LD+A EY++ ++
Sbjct: 6 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 53
>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
BHLHZ DOMAIN
Length = 86
Score = 35.4 bits (80), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 31/47 (65%), Gaps = 2/47 (4%)
Query: 334 HNLSERRRRDRINEKMRALQELIP--RCNKSDKASMLDEAIEYLKSL 378
HN ER+RRD I + +L++ +P + K+ +A +LD+A EY++ +
Sbjct: 7 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYM 53
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 30/43 (69%), Gaps = 1/43 (2%)
Query: 335 NLSERRRRDRINEKMRALQELIP-RCNKSDKASMLDEAIEYLK 376
N SE++RRD+ N ++ L ++P K DK+++L ++I++L+
Sbjct: 17 NKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 59
>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 = 33.5 bits (75), Expect = 0.21, Method: Composition-based stats.
Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 8/69 (11%)
Query: 318 QSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCN-KSDKASMLDEAIEYLK 376
QSRG KR+ HN E+R R IN+K+ L++L+ K +K+++L +AI+Y++
Sbjct: 1 QSRGE---KRT----AHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIR 53
Query: 377 SLQLQVQMM 385
LQ Q +
Sbjct: 54 FLQHSNQKL 62
>pdb|3U5V|A Chain A, Crystal Structure Of Max-E47
Length = 76
Score = 33.1 bits (74), Expect = 0.29, Method: Composition-based stats.
Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 334 HNLSERRRRDRINEKMRALQELIPRCNKSDKAS----MLDEAIEYLKSLQLQVQ 383
HN ER+RR INE R L + KSDKA +L +A++ + L+ QV+
Sbjct: 9 HNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVR 62
>pdb|1NKP|A Chain A, Crystal Structure Of Myc-Max Recognizing Dna
pdb|1NKP|D Chain D, Crystal Structure Of Myc-Max Recognizing Dna
Length = 88
Score = 32.3 bits (72), Expect = 0.46, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 3/55 (5%)
Query: 334 HNLSERRRRDRINEKMRALQELIPRCNKSDKAS---MLDEAIEYLKSLQLQVQMM 385
HN+ ER+RR+ + AL++ IP ++KA +L +A Y+ S+Q + Q +
Sbjct: 10 HNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKL 64
>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 = 32.0 bits (71), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 6/52 (11%)
Query: 334 HNLSERRRRDRINEKMRALQELIP----RCNKS--DKASMLDEAIEYLKSLQ 379
HN ERRRRD+IN + L ++IP KS K +L +A +Y++ L+
Sbjct: 9 HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60
>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 = 0.98, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 30/43 (69%), Gaps = 1/43 (2%)
Query: 335 NLSERRRRDRINEKMRALQELIP-RCNKSDKASMLDEAIEYLK 376
N SE++RRD+ N ++ L ++P K DK+++L ++I++L+
Sbjct: 13 NKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 55
>pdb|4ATH|A Chain A, Mitf Apo Structure
pdb|4ATH|B Chain B, Mitf Apo Structure
Length = 83
Score = 29.6 bits (65), Expect = 3.5, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 4/46 (8%)
Query: 342 RDRINEKMRALQELIPRCNKSD----KASMLDEAIEYLKSLQLQVQ 383
R IN++++ L LIP+ N D K ++L +++Y++ LQ + Q
Sbjct: 4 RFNINDRIKELGTLIPKSNDPDXRWNKGTILKASVDYIRKLQREQQ 49
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 0.126 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,129,216
Number of Sequences: 62578
Number of extensions: 274802
Number of successful extensions: 474
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 458
Number of HSP's gapped (non-prelim): 15
length of query: 423
length of database: 14,973,337
effective HSP length: 101
effective length of query: 322
effective length of database: 8,652,959
effective search space: 2786252798
effective search space used: 2786252798
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (25.0 bits)