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= 042904
(320 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 = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 79 KRQKTAATSAVNSSDEANNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFY--VKRG 136
KR+ TA S A + Q++ +H +ER RR +N+ + L +L+P R
Sbjct: 4 KRELTACIFPTESEARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRW 63
Query: 137 DQASIIGGVVDYINELQQVLQ 157
++ +I+ VDYI +LQ+ Q
Sbjct: 64 NKGTILKASVDYIRKLQREQQ 84
>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 = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 26/52 (50%)
Query: 98 TDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYI 149
+D +R H +ER RR + ++ LR +P ++ +A I+ +YI
Sbjct: 8 SDADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYI 59
>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 = 0.39, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 31/59 (52%)
Query: 102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLE 160
+R H +ER RR + ++ LR +P ++ +A I+ +YI +++ + +L+
Sbjct: 4 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTLQ 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 = 31.2 bits (69), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 99 DGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVV----DYINELQQ 154
D ++R H VER RR ++N + L ++P ++ GG++ DYI EL+Q
Sbjct: 2 DEKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQ 61
>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
BHLHZ DOMAIN
Length = 86
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 27/53 (50%)
Query: 102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQ 154
+R H +ER RR + ++ LR +P ++ +A I+ +YI +++
Sbjct: 3 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRR 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 = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 27/53 (50%)
Query: 102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQ 154
+R H +ER RR + ++ LR +P ++ +A I+ +YI +++
Sbjct: 1 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRR 53
>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 = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 13/53 (24%), Positives = 27/53 (50%)
Query: 102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQ 154
+R H +ER RR + ++ LR +P ++ +A I+ +YI +++
Sbjct: 2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRR 54
>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 = 28.1 bits (61), Expect = 7.1, Method: Composition-based stats.
Identities = 15/65 (23%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 96 NNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQV 155
++ D +R+S E+ RR Q N + L S++P ++ D+++++ +D++ + +++
Sbjct: 2 DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPG-NARKMDKSTVLQKSIDFLRKHKEI 60
Query: 156 LQSLE 160
LE
Sbjct: 61 TAWLE 65
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 27.7 bits (60), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 16/75 (21%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 94 EANNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQ 153
E ++ D +R+S E+ RR Q N + L S++P ++ D+++++ +D++ + +
Sbjct: 4 EEDDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPG-NARKMDKSTVLQKSIDFLRKHK 62
Query: 154 QVLQSLEAKKQRKVY 168
+ +A + R+ +
Sbjct: 63 ETTAQSDASEIRQDW 77
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 0.127 0.339
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,757,660
Number of Sequences: 62578
Number of extensions: 196792
Number of successful extensions: 413
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 405
Number of HSP's gapped (non-prelim): 12
length of query: 320
length of database: 14,973,337
effective HSP length: 99
effective length of query: 221
effective length of database: 8,778,115
effective search space: 1939963415
effective search space used: 1939963415
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: 51 (24.3 bits)