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= psy11481
(561 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
BHLHZ DOMAIN
Length = 86
Score = 46.2 bits (108), Expect = 5e-05, Method: Composition-based stats.
Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Query: 186 REVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQFLXXXXXXXXX 245
R HN LE+ RR H+K+ F L+ VP Q E K+S IL A YIQ++
Sbjct: 4 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGE-KASRAQILDKATEYIQYMRRKNHTHQQ 62
Query: 246 XXXXLAREKIHAQQRLALLKKELS 269
L R+ +Q++ L+K S
Sbjct: 63 DIDDLKRQNALLEQQVRALEKARS 86
>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 = 45.4 bits (106), Expect = 8e-05, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 186 REVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQFLXXXXXXXXX 245
R HN LE+ RR H+K+ F L+ VP Q E K+S IL A YIQ++
Sbjct: 5 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGE-KASRAQILDKATEYIQYMRRKVHTLQQ 63
Query: 246 XXXXLAREKIHAQQRLALLK 265
L R+ +Q++ L+
Sbjct: 64 DIDDLKRQNALLEQQVRALE 83
>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 = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 186 REVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQFLXXXXXXXXX 245
R HN LE+ RR H+K+ F L+ VP Q E K+S IL A YIQ++
Sbjct: 3 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGE-KASRAQILDKATEYIQYMRRKNHTHQQ 61
Query: 246 XXXXLAREKIHAQQRLALL 264
L R+ +Q++ L
Sbjct: 62 DIDDLKRQNALLEQQVRAL 80
>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 = 43.1 bits (100), Expect = 4e-04, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 186 REVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQFLXXXXXXXXX 245
R HN LE+ RR H+K+ F L+ VP Q E K+S IL A YIQ++
Sbjct: 2 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGE-KASRAQILDKATEYIQYMRRKNHTHQQ 60
Query: 246 XXXXLAREKIHAQQRL 261
L R+ +Q++
Sbjct: 61 DIDDLKRQNALLEQQV 76
>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 = 42.7 bits (99), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/51 (45%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 186 REVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQFL 236
R HN LE+ RR H+K+ F L+ VP Q E K+S IL A YIQ++
Sbjct: 13 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGE-KASRAQILDKATEYIQYM 62
>pdb|1NLW|A Chain A, Crystal Structure Of Mad-Max Recognizing Dna
pdb|1NLW|D Chain D, Crystal Structure Of Mad-Max Recognizing Dna
Length = 80
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 41/79 (51%)
Query: 186 REVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQFLXXXXXXXXX 245
R HN++EKNRRAHL+ E LK VP + + + LS+L A +I+ L
Sbjct: 2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVH 61
Query: 246 XXXXLAREKIHAQQRLALL 264
L RE+ H +++L L
Sbjct: 62 QIDQLQREQRHLKRQLEKL 80
>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 = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 26/48 (54%)
Query: 186 REVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYI 233
R HN LE+ RR LK F L+ Q+P + +K+ + IL A YI
Sbjct: 7 RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYI 54
>pdb|1MDY|A Chain A, Crystal Structure Of Myod Bhlh Domain Bound To Dna:
Perspectives On Dna Recognition And Implications For
Transcriptional Activation
Length = 68
Score = 30.4 bits (67), Expect = 2.5, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 176 IKKRSGISGIREVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQF 235
+K+++ + R+ E+ R + + E FE LKR + ++ + IL +AIRYI+
Sbjct: 3 LKRKTTNADRRKAATMRERRRLSKVNEAFETLKRST-SSNPNQRLPKVEILRNAIRYIEG 61
Query: 236 L 236
L
Sbjct: 62 L 62
>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 = 29.6 bits (65), Expect = 4.9, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 182 ISGIREVHNKLEKNRRAHLKECFEILKRQVPPAQE-EKKSSNLSILHSAIRYIQFL 236
I RE H+++EK RR + + L VP +K L++L A+++++ L
Sbjct: 6 IKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTL 61
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
0.312 0.126 0.357
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,928,092
Number of Sequences: 62578
Number of extensions: 433517
Number of successful extensions: 1837
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1824
Number of HSP's gapped (non-prelim): 18
length of query: 561
length of database: 14,973,337
effective HSP length: 104
effective length of query: 457
effective length of database: 8,465,225
effective search space: 3868607825
effective search space used: 3868607825
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: 54 (25.4 bits)