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= 026943
(230 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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 34/46 (73%), Gaps = 1/46 (2%)
Query: 55 NQSERRRRDRINQKMKALQKLVP-NASKTDKASMLDEVIDYLKQLK 99
N+SE++RRD+ N +K L ++P NA K DK+++L + ID+L++ K
Sbjct: 17 NKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHK 62
>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 = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 36/60 (60%), Gaps = 9/60 (15%)
Query: 46 KRRRTAAVHNQSERRRRDRINQKMKALQKLVPNA------SKTDKASMLDEVIDYLKQLK 99
KRR A HN+ ERRRRD+IN + L K++P++ S K +L + DY+++L+
Sbjct: 4 KRR---AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 33/44 (75%), Gaps = 1/44 (2%)
Query: 55 NQSERRRRDRINQKMKALQKLVP-NASKTDKASMLDEVIDYLKQ 97
N+SE++RRD+ N +K L ++P NA K DK+++L + ID+L++
Sbjct: 13 NKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRK 56
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 4/62 (6%)
Query: 43 HSSKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNAS----KTDKASMLDEVIDYLKQL 98
H + + H+Q E+RRRD++N + L LVP + K DK ++L + ++K L
Sbjct: 6 HQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTL 65
Query: 99 KA 100
+
Sbjct: 66 RG 67
>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 = 0.006, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 34/58 (58%), Gaps = 4/58 (6%)
Query: 45 SKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNASKTD----KASMLDEVIDYLKQL 98
+K R+ HN ERRRR IN ++K L L+P ++ D K ++L +DY+++L
Sbjct: 22 AKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKL 79
>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 = 35.4 bits (80), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 4/62 (6%)
Query: 43 HSSKRRRTAAVHNQSERRRRDRINQKMKALQKLVPNAS----KTDKASMLDEVIDYLKQL 98
H + + H+Q E+RRRD++N + L LVP + K DK ++L + ++K L
Sbjct: 2 HQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTL 61
Query: 99 KA 100
+
Sbjct: 62 RG 63
>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 = 33.9 bits (76), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 33/52 (63%), Gaps = 3/52 (5%)
Query: 48 RRTAAVHNQSERRRRDRINQKMKALQKLVPNA-SKTDKASMLDEVIDYLKQL 98
+RTA HN E+R R IN K+ L+ LV +K +K+++L + IDY++ L
Sbjct: 6 KRTA--HNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFL 55
>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 = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 52 AVHNQSERRRRDRINQKMKALQKLVPN--ASKTDKASMLDEVIDYLKQLK 99
A HN ER+RRD I +L+ VP+ K +A +LD+ +Y++ ++
Sbjct: 4 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 53
>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 = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 52 AVHNQSERRRRDRINQKMKALQKLVPN--ASKTDKASMLDEVIDYLKQLK 99
A HN ER+RRD I +L+ VP+ K +A +LD+ +Y++ ++
Sbjct: 6 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 55
>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 = 32.0 bits (71), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 52 AVHNQSERRRRDRINQKMKALQKLVPN--ASKTDKASMLDEVIDYLKQLK 99
A HN ER+RRD I +L+ VP+ K +A +LD+ +Y++ ++
Sbjct: 3 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 52
>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
BHLHZ DOMAIN
Length = 86
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 52 AVHNQSERRRRDRINQKMKALQKLVPN--ASKTDKASMLDEVIDYLKQLK 99
A HN ER+RRD I +L+ VP+ K +A +LD+ +Y++ ++
Sbjct: 5 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 54
>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 = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 52 AVHNQSERRRRDRINQKMKALQKLVPN--ASKTDKASMLDEVIDYLKQLK 99
A HN ER+RRD I +L+ VP+ K +A +LD+ +Y++ ++
Sbjct: 14 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 63
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
0.310 0.121 0.332
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,260,613
Number of Sequences: 62578
Number of extensions: 114187
Number of successful extensions: 236
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 217
Number of HSP's gapped (non-prelim): 20
length of query: 230
length of database: 14,973,337
effective HSP length: 96
effective length of query: 134
effective length of database: 8,965,849
effective search space: 1201423766
effective search space used: 1201423766
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)