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= 016577
(387 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 36/58 (62%), Gaps = 4/58 (6%)
Query: 329 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQ 382
R A E H+ E+RRRD++N + L L+P CN K DK ++L A++++K+L+
Sbjct: 9 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 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 = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 35/54 (64%), Gaps = 4/54 (7%)
Query: 333 AAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQ 382
A E H+ E+RRRD++N + L L+P CN K DK ++L A++++K+L+
Sbjct: 9 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 62
>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 = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 22/54 (40%), Positives = 34/54 (62%), Gaps = 4/54 (7%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCNKTD----KASMLDEAIEYLKSLQLQLQ 386
HNL ERRRR IN++++ L LIP N D K ++L +++Y++ LQ + Q
Sbjct: 31 HNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQ 84
>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 = 35.8 bits (81), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQ 382
HN ER+RRD I + +L++ +P K +A +LD+A EY++ ++
Sbjct: 8 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 55
>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 = 35.4 bits (80), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQ 382
HN ER+RRD I + +L++ +P K +A +LD+A EY++ ++
Sbjct: 16 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 63
>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 = 35.4 bits (80), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQ 382
HN ER+RRD I + +L++ +P K +A +LD+A EY++ ++
Sbjct: 6 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 53
>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 = 35.4 bits (80), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQ 382
HN ER+RRD I + +L++ +P K +A +LD+A EY++ ++
Sbjct: 5 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 52
>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 = 0.059, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQ 382
HN ER+RRD I + +L++ +P K +A +LD+A EY++ ++
Sbjct: 7 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 54
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 31/43 (72%), Gaps = 1/43 (2%)
Query: 338 NLSERRRRDRINEKMRALQELIP-HCNKTDKASMLDEAIEYLK 379
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 = 0.19, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 330 RSRAAEVHNLSERRRRDRINEKMRALQELIPHCN-KTDKASMLDEAIEYLKSLQ 382
R HN E+R R IN+K+ L++L+ K +K+++L +AI+Y++ LQ
Sbjct: 3 RGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQ 56
>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 = 32.3 bits (72), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 31/43 (72%), Gaps = 1/43 (2%)
Query: 338 NLSERRRRDRINEKMRALQELIP-HCNKTDKASMLDEAIEYLK 379
N SE++RRD+ N ++ L ++P + K DK+++L ++I++L+
Sbjct: 13 NKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 55
>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 = 31.6 bits (70), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCNK------TDKASMLDEAIEYLKSLQ 382
HN ERRRRD+IN + L ++IP + K +L +A +Y++ L+
Sbjct: 9 HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60
>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 = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCNKTDKA---SMLDEAIEYLKSLQ 382
HN+ ER+RR+ + AL++ IP +KA +L +A Y+ S+Q
Sbjct: 10 HNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQ 58
>pdb|3U5V|A Chain A, Crystal Structure Of Max-E47
Length = 76
Score = 28.5 bits (62), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCNKTDKAS----MLDEAIEYLKSLQLQLQ 386
HN ER+RR INE R L + K+DKA +L +A++ + L+ Q++
Sbjct: 9 HNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVR 62
>pdb|4ATH|A Chain A, Mitf Apo Structure
pdb|4ATH|B Chain B, Mitf Apo Structure
Length = 83
Score = 28.1 bits (61), Expect = 9.8, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 345 RDRINEKMRALQELIPHCNKTD----KASMLDEAIEYLKSLQLQLQ 386
R IN++++ L LIP N D K ++L +++Y++ LQ + Q
Sbjct: 4 RFNINDRIKELGTLIPKSNDPDXRWNKGTILKASVDYIRKLQREQQ 49
>pdb|3SFW|A Chain A, Crystal Structure Of Dihydropyrimidinase From
Brevibacillus Agri Nchu1002
pdb|3SFW|B Chain B, Crystal Structure Of Dihydropyrimidinase From
Brevibacillus Agri Nchu1002
Length = 461
Score = 27.7 bits (60), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 83 ETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDKHTRQLRE 125
+TV HCP S +K+ + F+++P GP+ D+ T E
Sbjct: 310 QTVGSDHCPFNFSGQKELGRRDFTKIPNGGPIIEDRMTILFSE 352
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
0.311 0.128 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,016,654
Number of Sequences: 62578
Number of extensions: 431203
Number of successful extensions: 647
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 629
Number of HSP's gapped (non-prelim): 17
length of query: 387
length of database: 14,973,337
effective HSP length: 101
effective length of query: 286
effective length of database: 8,652,959
effective search space: 2474746274
effective search space used: 2474746274
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)