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= 007974
(583 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 = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 4/53 (7%)
Query: 329 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEY 377
R A E H+ E+RRRD++N + L L+P CN K DK ++L A+++
Sbjct: 9 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQH 61
>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 = 37.7 bits (86), Expect = 0.020, Method: Composition-based stats.
Identities = 19/45 (42%), Positives = 28/45 (62%), Gaps = 4/45 (8%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCNKTD----KASMLDEAIEY 377
HNL ERRRR IN++++ L LIP N D K ++L +++Y
Sbjct: 31 HNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDY 75
>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 = 36.6 bits (83), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 4/49 (8%)
Query: 333 AAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEY 377
A E H+ E+RRRD++N + L L+P CN K DK ++L A+++
Sbjct: 9 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQH 57
>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 = 0.065, Method: Composition-based stats.
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEY 377
HN ER+RRD I + +L++ +P K +A +LD+A EY
Sbjct: 8 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEY 50
>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 = 0.075, Method: Composition-based stats.
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEY 377
HN ER+RRD I + +L++ +P K +A +LD+A EY
Sbjct: 6 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEY 48
>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 = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEY 377
HN ER+RRD I + +L++ +P K +A +LD+A EY
Sbjct: 5 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEY 47
>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 = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEY 377
HN ER+RRD I + +L++ +P K +A +LD+A EY
Sbjct: 16 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEY 58
>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
BHLHZ DOMAIN
Length = 86
Score = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEY 377
HN ER+RRD I + +L++ +P K +A +LD+A EY
Sbjct: 7 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEY 49
>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 = 32.0 bits (71), Expect = 1.0, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 29/41 (70%), Gaps = 1/41 (2%)
Query: 338 NLSERRRRDRINEKMRALQELIP-HCNKTDKASMLDEAIEY 377
N SE++RRD+ N ++ L ++P + K DK+++L ++I++
Sbjct: 13 NKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDF 53
>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 = 31.6 bits (70), Expect = 1.1, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 330 RSRAAEVHNLSERRRRDRINEKMRALQELIPHCN-KTDKASMLDEAIEY 377
R HN E+R R IN+K+ L++L+ K +K+++L +AI+Y
Sbjct: 3 RGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDY 51
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 29/41 (70%), Gaps = 1/41 (2%)
Query: 338 NLSERRRRDRINEKMRALQELIP-HCNKTDKASMLDEAIEY 377
N SE++RRD+ N ++ L ++P + K DK+++L ++I++
Sbjct: 17 NKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDF 57
>pdb|3U5V|A Chain A, Crystal Structure Of Max-E47
Length = 76
Score = 28.9 bits (63), Expect = 8.4, Method: Composition-based stats.
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCNKTDKAS----MLDEAIE 376
HN ER+RR INE R L + K+DKA +L +A++
Sbjct: 9 HNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQ 52
>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 = 28.9 bits (63), Expect = 8.8, Method: Composition-based stats.
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCNKTDKA 368
HN+ ER+RR+ + AL++ IP +KA
Sbjct: 10 HNVLERQRRNELKRSFFALRDQIPELENNEKA 41
>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 = 28.9 bits (63), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 337 HNLSERRRRDRINEKMRALQELIP 360
HN ERRRRD+IN + L ++IP
Sbjct: 9 HNEVERRRRDKINNWIVQLSKIIP 32
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
0.315 0.129 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,446,385
Number of Sequences: 62578
Number of extensions: 633891
Number of successful extensions: 1109
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1102
Number of HSP's gapped (non-prelim): 16
length of query: 583
length of database: 14,973,337
effective HSP length: 104
effective length of query: 479
effective length of database: 8,465,225
effective search space: 4054842775
effective search space used: 4054842775
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: 54 (25.4 bits)