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= psy14439
(245 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 46/77 (59%), Gaps = 5/77 (6%)
Query: 79 RREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFLVQQK 138
+R H E+KRRD IK + SL+D VP+ G K S+A +L K+ +YIQ++ ++
Sbjct: 4 KRAHHNALERKRRDHIKDSFHSLRDSVPSL-----QGEKASRAQILDKATEYIQYMRRKV 58
Query: 139 KKLEEERNGLRKEVVAL 155
L+++ + L+++ L
Sbjct: 59 HTLQQDIDDLKRQNALL 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 = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 35/55 (63%), Gaps = 3/55 (5%)
Query: 80 REAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFL 134
REAH+Q E++RRD + D L LVPTC ++ KL K TVL+ ++ +++ L
Sbjct: 10 REAHSQIEKRRRDKMNSFIDELASLVPTC---NAMSRKLDKLTVLRMAVQHMKTL 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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 44/73 (60%), Gaps = 5/73 (6%)
Query: 79 RREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFLVQQK 138
+R H E+KRRD IK + SL+D VP+ G K S+A +L K+ +YIQ++ ++
Sbjct: 12 KRAHHNALERKRRDHIKDSFHSLRDSVPSL-----QGEKASRAQILDKATEYIQYMRRKN 66
Query: 139 KKLEEERNGLRKE 151
+++ + L+++
Sbjct: 67 HTHQQDIDDLKRQ 79
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 45/77 (58%), Gaps = 5/77 (6%)
Query: 79 RREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFLVQQK 138
+R H E+KRRD IK + SL+D VP+ G K S+A +L K+ +YIQ++ ++
Sbjct: 1 KRAHHNALERKRRDHIKDSFHSLRDSVPSL-----QGEKASRAQILDKATEYIQYMRRKN 55
Query: 139 KKLEEERNGLRKEVVAL 155
+++ + L+++ L
Sbjct: 56 HTHQQDIDDLKRQNALL 72
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 45/77 (58%), Gaps = 5/77 (6%)
Query: 79 RREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFLVQQK 138
+R H E+KRRD IK + SL+D VP+ G K S+A +L K+ +YIQ++ ++
Sbjct: 2 KRAHHNALERKRRDHIKDSFHSLRDSVPSL-----QGEKASRAQILDKATEYIQYMRRKN 56
Query: 139 KKLEEERNGLRKEVVAL 155
+++ + L+++ L
Sbjct: 57 HTHQQDIDDLKRQNALL 73
>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
BHLHZ DOMAIN
Length = 86
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 45/77 (58%), Gaps = 5/77 (6%)
Query: 79 RREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFLVQQK 138
+R H E+KRRD IK + SL+D VP+ G K S+A +L K+ +YIQ++ ++
Sbjct: 3 KRAHHNALERKRRDHIKDSFHSLRDSVPSL-----QGEKASRAQILDKATEYIQYMRRKN 57
Query: 139 KKLEEERNGLRKEVVAL 155
+++ + L+++ L
Sbjct: 58 HTHQQDIDDLKRQNALL 74
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 35/55 (63%), Gaps = 3/55 (5%)
Query: 80 REAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFL 134
REAH+Q E++RRD + D L LVPTC ++ KL K TVL+ ++ +++ L
Sbjct: 14 REAHSQIEKRRRDKMNSFIDELASLVPTC---NAMSRKLDKLTVLRMAVQHMKTL 65
>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 = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 79 RREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFLVQQK 138
+R AH E++ R +I L+DLV + KL+K+ VL+K+IDYI+FL
Sbjct: 6 KRTAHNAIEKRYRSSINDKIIELKDLVV------GTEAKLNKSAVLRKAIDYIRFLQHSN 59
Query: 139 KKLEEERNGLRKEV 152
+KL++E LR V
Sbjct: 60 QKLKQENLSLRTAV 73
>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 = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 77 ERRREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFLVQ 136
E+RR H + E++RRD I L ++P +S+ SK +L K+ DYIQ L Q
Sbjct: 3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDS-SMESTKSGQSKGGILSKASDYIQELRQ 61
>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 = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 79 RREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFLVQ 136
+RE+H AEQ RR+ + L L+P + + SKAT ++ + YI+ L Q
Sbjct: 2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQ 59
>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 = 34.7 bits (78), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 4/72 (5%)
Query: 79 RREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFLVQQK 138
+R H E++RR+ +K+ + +L+D +P + K K +L+K+ YI + ++
Sbjct: 6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNE----KAPKVVILKKATAYILSVQAEE 61
Query: 139 KKLEEERNGLRK 150
+KL E + LRK
Sbjct: 62 QKLISEEDLLRK 73
>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 = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 53/99 (53%), Gaps = 10/99 (10%)
Query: 76 KER-RREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFL 134
KER +++ H E++RR I L L+P + D + +K T+L+ S+DYI+ L
Sbjct: 23 KERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPD---MRWNKGTILKASVDYIRKL 79
Query: 135 VQQKKKLEEERNGLRKEVVALRIMQANYDIMVKAQQTPL 173
+++++ ++ N +K + AN ++++ Q+ +
Sbjct: 80 QREQQRAKDLENRQKK------LEHANRHLLLRVQELEM 112
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 6/54 (11%)
Query: 79 RREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQ 132
+R + ++E+KRRD L ++P + K+ K+TVLQKSID+++
Sbjct: 12 KRVSRNKSEKKRRDQFNVLIKELGSMLP------GNARKMDKSTVLQKSIDFLR 59
>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 = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 6/54 (11%)
Query: 79 RREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQ 132
+R + ++E+KRRD L ++P + K+ K+TVLQKSID+++
Sbjct: 8 KRVSRNKSEKKRRDQFNVLIKELGSMLP------GNARKMDKSTVLQKSIDFLR 55
>pdb|1UKL|C Chain C, Crystal Structure Of Importin-Beta And Srebp-2 Complex
pdb|1UKL|D Chain D, Crystal Structure Of Importin-Beta And Srebp-2 Complex
pdb|1UKL|E Chain E, Crystal Structure Of Importin-Beta And Srebp-2 Complex
pdb|1UKL|F Chain F, Crystal Structure Of Importin-Beta And Srebp-2 Complex
Length = 61
Score = 30.4 bits (67), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 6/59 (10%)
Query: 91 RDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFLVQQKKKLEEERNGLR 149
R +I L+DLV TD+ K K+ VL+K+IDYI++L Q KL +E L+
Sbjct: 1 RSSINDKIIELKDLVXG---TDA---KXHKSGVLRKAIDYIKYLQQVNHKLRQENXVLK 53
>pdb|4ATH|A Chain A, Mitf Apo Structure
pdb|4ATH|B Chain B, Mitf Apo Structure
Length = 83
Score = 27.7 bits (60), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 39/70 (55%), Gaps = 9/70 (12%)
Query: 101 LQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFLVQQKKKLEEERNGLRKEVVALRIMQA 160
L L+P + D + +K T+L+ S+DYI+ L +++++ ++ N +K + A
Sbjct: 14 LGTLIPKSNDPDX---RWNKGTILKASVDYIRKLQREQQRAKDLENRQKK------LEHA 64
Query: 161 NYDIMVKAQQ 170
N ++++ Q+
Sbjct: 65 NRHLLLRVQE 74
>pdb|4AYA|A Chain A, Crystal Structure Of Id2 Hlh Homodimer At 2.1a Resolution
pdb|4AYA|B Chain B, Crystal Structure Of Id2 Hlh Homodimer At 2.1a Resolution
Length = 97
Score = 27.3 bits (59), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 4/34 (11%)
Query: 98 YDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYI 131
Y L++LVP+ Q K+SK +LQ IDYI
Sbjct: 44 YSKLKELVPSIPQNK----KVSKMEILQHVIDYI 73
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
0.314 0.127 0.352
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,812,912
Number of Sequences: 62578
Number of extensions: 187953
Number of successful extensions: 372
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 353
Number of HSP's gapped (non-prelim): 23
length of query: 245
length of database: 14,973,337
effective HSP length: 96
effective length of query: 149
effective length of database: 8,965,849
effective search space: 1335911501
effective search space used: 1335911501
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: 50 (23.9 bits)