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= 007527
(600 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 = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 44/68 (64%), Gaps = 7/68 (10%)
Query: 440 NHVKSERRQRGKLNERFVILKSMVPSVS----KFDKVSILDDTIEYVQELER---KVKEL 492
NH ERR+R +N+R L +++P + +++K +IL +++Y+++L+R + K+L
Sbjct: 30 NHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDL 89
Query: 493 ESCRAKLE 500
E+ + KLE
Sbjct: 90 ENRQKKLE 97
>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 = 36.6 bits (83), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 439 TNHVKSERRQRGKLNERFVILKSMVPSVS--KFDKVSILDDTIEYVQELERKVKELE 493
+H ER++R + + F L+ VPS+ K + ILD EY+Q + RKV L+
Sbjct: 6 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTLQ 62
>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 = 33.9 bits (76), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 439 TNHVKSERRQRGKLNERFVILKSMVPSVS--KFDKVSILDDTIEYVQELERK 488
+H ER++R + + F L+ VPS+ K + ILD EY+Q + RK
Sbjct: 4 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 55
>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 = 33.5 bits (75), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 427 DDVSRLEAEETATNHVKSERRQRGKLNERFVILKSMVPSVS--KFDKVSILDDTIEYVQE 484
DD+ + +H ER++R + + F L+ VPS+ K + ILD EY+Q
Sbjct: 2 DDIEVESDADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQY 61
Query: 485 LERK 488
+ RK
Sbjct: 62 MRRK 65
>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
BHLHZ DOMAIN
Length = 86
Score = 33.1 bits (74), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 439 TNHVKSERRQRGKLNERFVILKSMVPSVS--KFDKVSILDDTIEYVQELERK 488
+H ER++R + + F L+ VPS+ K + ILD EY+Q + RK
Sbjct: 5 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 56
>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 = 33.1 bits (74), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 439 TNHVKSERRQRGKLNERFVILKSMVPSVS--KFDKVSILDDTIEYVQELERK 488
+H ER++R + + F L+ VPS+ K + ILD EY+Q + RK
Sbjct: 3 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 54
>pdb|2XZA|H Chain H, Crystal Structure Of Recombinant A.17 Antibody Fab
Fragment
pdb|2XZC|H Chain H, Crystal Structure Of Phosphonate-Modified Recombinant
A.17 Antibody Fab Fragment
Length = 222
Score = 32.3 bits (72), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 37/85 (43%), Gaps = 13/85 (15%)
Query: 6 IQNQKRVPESLKKQ----LALAVRSIQWSYAIFWTISDTQPG-VLEW-------GDGYYN 53
+Q Q+ P +K L AV S +W PG LEW G YYN
Sbjct: 2 VQLQESGPGLVKPSETLSLTCAVSGYSISSGYYWGWIRQPPGKGLEWIGSIYHSGSTYYN 61
Query: 54 GDIKTRKTIQSVELSSNQLGLQRSE 78
+K+R TI SV+ S NQ L+ S
Sbjct: 62 PSLKSRVTI-SVDTSKNQFSLKLSS 85
>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 = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 436 ETATNHVKSERRQRGKLNERFVILKSMVPSV-SKFDKVSILDDTIEYVQELE 486
E T H E+R R +N++ + LK +V +K +K ++L I+Y++ L+
Sbjct: 5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQ 56
>pdb|4ATH|A Chain A, Mitf Apo Structure
pdb|4ATH|B Chain B, Mitf Apo Structure
Length = 83
Score = 30.0 bits (66), Expect = 4.0, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 38/59 (64%), Gaps = 7/59 (11%)
Query: 449 RGKLNERFVILKSMVPSVS----KFDKVSILDDTIEYVQELER---KVKELESCRAKLE 500
R +N+R L +++P + +++K +IL +++Y+++L+R + K+LE+ + KLE
Sbjct: 4 RFNINDRIKELGTLIPKSNDPDXRWNKGTILKASVDYIRKLQREQQRAKDLENRQKKLE 62
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 29.6 bits (65), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 441 HVKSERRQRGKLNERFVILKSMVPSVS----KFDKVSILDDTIEYVQELE 486
H + E+R+R K+N L S+VP+ + K DK+++L +++++ L
Sbjct: 17 HSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 66
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1752
Score = 29.6 bits (65), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 383 KGGLVSCKKQRDGVSQKLLKKILFEVPRIINYRLLESSEDNHIKDDVSRLEAEETATNHV 442
+GGLV + G ++ K + R++NY LL + I D ++ + + T V
Sbjct: 632 QGGLVHTIWKEKG--PEICKGFFNGIQRVVNYWLLHNGFSIGIGDTIADADTMKEVTRTV 689
Query: 443 KSERRQ 448
K RRQ
Sbjct: 690 KEARRQ 695
>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 = 5.4, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 30/49 (61%), Gaps = 4/49 (8%)
Query: 441 HVKSERRQRGKLNERFVILKSMVPSVS----KFDKVSILDDTIEYVQEL 485
H + E+R+R K+N L S+VP+ + K DK+++L +++++ L
Sbjct: 13 HSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTL 61
>pdb|3B0J|A Chain A, M175e Mutant Of Assimilatory Nitrite Reductase (Nii3) From
Tobbaco Leaf
Length = 584
Score = 29.3 bits (64), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 22/47 (46%)
Query: 86 SLSAGESNPQAASKRPSAALSPEDLTDTEWYYLVCMSFVFNIGEGLP 132
SL +GE N + P A + PE++ DT Y + F+ G P
Sbjct: 199 SLQSGEDNVRNPVGNPLAGIDPEEIVDTRPYTNLLSQFITGNSRGNP 245
>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 = 29.3 bits (64), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 435 EETATNHVKSERRQRGKLNERFVILKSMVP------SVSKFDKVSILDDTIEYVQEL 485
E+ H + ERR+R K+N V L ++P + S K IL +Y+QEL
Sbjct: 3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59
>pdb|1MDY|B Chain B, Crystal Structure Of Myod Bhlh Domain Bound To Dna:
Perspectives On Dna Recognition And Implications For
Transcriptional Activation
pdb|1MDY|C Chain C, Crystal Structure Of Myod Bhlh Domain Bound To Dna:
Perspectives On Dna Recognition And Implications For
Transcriptional Activation
pdb|1MDY|D Chain D, Crystal Structure Of Myod Bhlh Domain Bound To Dna:
Perspectives On Dna Recognition And Implications For
Transcriptional Activation
Length = 62
Score = 28.9 bits (63), Expect = 9.7, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 445 ERRQRGKLNERFVILKSMVPS--VSKFDKVSILDDTIEYVQELERKVKE 491
ERR+ K+NE F LK S + KV IL + I Y++ L+ +++
Sbjct: 14 ERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLRD 62
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 0.130 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,360,139
Number of Sequences: 62578
Number of extensions: 625933
Number of successful extensions: 1515
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 1503
Number of HSP's gapped (non-prelim): 20
length of query: 600
length of database: 14,973,337
effective HSP length: 104
effective length of query: 496
effective length of database: 8,465,225
effective search space: 4198751600
effective search space used: 4198751600
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)