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= 044652
(553 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 = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 30/89 (33%), Positives = 44/89 (49%), Gaps = 9/89 (10%)
Query: 351 ARRGQATDSHSLAERVRREKISERMKLLQDLVPGCNKVT---GKALMLDEIINYVQSLQR 407
A+ Q D+H+L ER RR I++R+K L L+P N K +L ++Y++ LQR
Sbjct: 22 AKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQR 81
Query: 408 Q------VEFLSMKLASVNTRLELNVDAL 430
+ +E KL N L L V L
Sbjct: 82 EQQRAKDLENRQKKLEHANRHLLLRVQEL 110
>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 = 35.0 bits (79), Expect = 0.097, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 360 HSLAERVRREKISERMKLLQDLVPGCN-KVTGKALMLDEIINYVQSLQRQVEFLSMKLAS 418
H+ ER RR+ I + L+D VP + +A +LD+ Y+Q ++R+V L +
Sbjct: 8 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTLQQDIDD 67
Query: 419 V---NTRLELNVDAL 430
+ N LE V AL
Sbjct: 68 LKRQNALLEQQVRAL 82
>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 = 34.7 bits (78), Expect = 0.15, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 38/69 (55%)
Query: 353 RGQATDSHSLAERVRREKISERMKLLQDLVPGCNKVTGKALMLDEIINYVQSLQRQVEFL 412
RG+ +H+ E+ R I++++ L+DLV G K+ +L + I+Y++ LQ + L
Sbjct: 3 RGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKL 62
Query: 413 SMKLASVNT 421
+ S+ T
Sbjct: 63 KQENLSLRT 71
>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 = 31.6 bits (70), Expect = 1.1, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 31/57 (54%)
Query: 350 RARRGQATDSHSLAERVRREKISERMKLLQDLVPGCNKVTGKALMLDEIINYVQSLQ 406
+ R A ++HS E+ RR+K++ + L LVP CN ++ K L + VQ ++
Sbjct: 3 QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 59
>pdb|3EYB|A Chain A, Structural And Functional Insights Into The Ligand Binding
Domain Of A Non-Duplicated Rxr From The Invertebrate
Chordate Amphioxus
pdb|3EYB|B Chain B, Structural And Functional Insights Into The Ligand Binding
Domain Of A Non-Duplicated Rxr From The Invertebrate
Chordate Amphioxus
pdb|3EYB|C Chain C, Structural And Functional Insights Into The Ligand Binding
Domain Of A Non-Duplicated Rxr From The Invertebrate
Chordate Amphioxus
pdb|3EYB|D Chain D, Structural And Functional Insights Into The Ligand Binding
Domain Of A Non-Duplicated Rxr From The Invertebrate
Chordate Amphioxus
Length = 219
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 473 NGTMTQCPVDPLDNALCRNLSMQLPQLEQFTETIPQFQNFGEDDLQSIVQMGFGQ 527
+G M + P DP+ N +C+ QL L ++ + IP F + DD +++ G+ +
Sbjct: 18 DGNMVEQPNDPVTN-ICQAADKQLVTLVEWAKRIPHFSDLPIDDQVILLRAGWNE 71
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%)
Query: 346 YIHVRARRGQATDSHSLAERVRREKISERMKLLQDLVPGCNKVTGKALMLDEIINYVQSL 405
Y + R A ++HS E+ RR+K++ + L LVP CN ++ K L + VQ +
Sbjct: 3 YAEHQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHM 62
Query: 406 Q 406
+
Sbjct: 63 K 63
>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 = 30.4 bits (67), Expect = 2.6, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 360 HSLAERVRREKISERMKLLQDLVPGCN-KVTGKALMLDEIINYVQSLQRQ 408
H+ ER RR+ I + L+D VP + +A +LD+ Y+Q ++R+
Sbjct: 6 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 55
>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
BHLHZ DOMAIN
Length = 86
Score = 29.6 bits (65), Expect = 4.2, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 360 HSLAERVRREKISERMKLLQDLVPGCN-KVTGKALMLDEIINYVQSLQRQ 408
H+ ER RR+ I + L+D VP + +A +LD+ Y+Q ++R+
Sbjct: 7 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 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 = 29.6 bits (65), Expect = 4.2, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 360 HSLAERVRREKISERMKLLQDLVPGCN-KVTGKALMLDEIINYVQSLQRQ 408
H+ ER RR+ I + L+D VP + +A +LD+ Y+Q ++R+
Sbjct: 5 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 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 = 29.6 bits (65), Expect = 4.9, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 360 HSLAERVRREKISERMKLLQDLVPGCN-KVTGKALMLDEIINYVQSLQRQ 408
H+ ER RR+ I + L+D VP + +A +LD+ Y+Q ++R+
Sbjct: 16 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 65
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 0.126 0.362
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,905,241
Number of Sequences: 62578
Number of extensions: 409486
Number of successful extensions: 643
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 638
Number of HSP's gapped (non-prelim): 12
length of query: 553
length of database: 14,973,337
effective HSP length: 104
effective length of query: 449
effective length of database: 8,465,225
effective search space: 3800886025
effective search space used: 3800886025
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: 54 (25.4 bits)