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= 010053
(519 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 = 37.4 bits (85), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 40/69 (57%), Gaps = 2/69 (2%)
Query: 342 NHVEAERQRRERLNHRFYALRSVVPNVS--KMDKASLLADAVAYIKELRAKVDELEAKLR 399
+H ER+RR+ + F++LR VP++ K +A +L A YI+ +R KV L+ +
Sbjct: 7 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTLQQDID 66
Query: 400 EQARKSKVV 408
+ R++ ++
Sbjct: 67 DLKRQNALL 75
>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 = 35.4 bits (80), Expect = 0.077, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 12/74 (16%)
Query: 342 NHVEAERQRRERLNHRFYALRSVVPNVS--KMDKASLLADAVAYIKELRAK-------VD 392
+H ER+RR+ + F++LR VP++ K +A +L A YI+ +R K +D
Sbjct: 5 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDID 64
Query: 393 ELE---AKLREQAR 403
+L+ A L +Q R
Sbjct: 65 DLKRQNALLEQQVR 78
>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 = 0.12, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 3/51 (5%)
Query: 347 ERQRRERLNHRFYALRSVVPNVSKMDKAS---LLADAVAYIKELRAKVDEL 394
ERQRR L F+ALR +P + +KA +L A AYI ++A+ +L
Sbjct: 14 ERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKL 64
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 33.9 bits (76), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 4/54 (7%)
Query: 343 HVEAERQRRERLNHRFYALRSVVPNVS----KMDKASLLADAVAYIKELRAKVD 392
H + E++RR+++N L S+VP + K+DK ++L AV ++K LR +
Sbjct: 17 HSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATN 70
>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 = 33.9 bits (76), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 342 NHVEAERQRRERLNHRFYALRSVVPNV--SKMDKASLLADAVAYIKELRAK 390
+H ER+RR+ + F++LR VP++ K +A +L A YI+ +R K
Sbjct: 15 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 65
>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 = 33.9 bits (76), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 343 HVEAERQRRERLNHRFYALRSVVPNV------SKMDKASLLADAVAYIKELR 388
H E ER+RR+++N+ L ++P+ S K +L+ A YI+ELR
Sbjct: 9 HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60
>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 = 33.5 bits (75), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 342 NHVEAERQRRERLNHRFYALRSVVPNVS--KMDKASLLADAVAYIKELRAK 390
+H ER+RR+ + F++LR VP++ K +A +L A YI+ +R K
Sbjct: 4 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 54
>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 = 33.5 bits (75), Expect = 0.32, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 31/51 (60%), Gaps = 4/51 (7%)
Query: 343 HVEAERQRRERLNHRFYALRSVVPNVS----KMDKASLLADAVAYIKELRA 389
H + E++RR+++N L S+VP + K+DK ++L AV ++K LR
Sbjct: 13 HSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG 63
>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 = 0.39, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 342 NHVEAERQRRERLNHRFYALRSVVPNVS--KMDKASLLADAVAYIKELRAK 390
+H ER+RR+ + F++LR VP++ K +A +L A YI+ +R K
Sbjct: 6 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 56
>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 = 32.3 bits (72), Expect = 0.70, Method: Composition-based stats.
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 9/88 (10%)
Query: 326 SKKRGRKPTSGRESPLNHVEAERQRRERLNHRFYALRSVVPNVSKMD----KASLLADAV 381
++ R R+ NH ER+RR +N R L +++P + D K ++L +V
Sbjct: 14 TESEARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASV 73
Query: 382 AYIKEL-----RAKVDELEAKLREQARK 404
YI++L RAK E K E A +
Sbjct: 74 DYIRKLQREQQRAKDLENRQKKLEHANR 101
>pdb|2L30|A Chain A, Human Parp-1 Zinc Finger 1
Length = 108
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 13/58 (22%)
Query: 17 CQETSPTLQQRLQFIVQNR------PEWWVYSIFWQ-------PLKDVNGRLVLSWGD 61
C E+ P R+ +VQ+ P W+ +S FW+ P +V+G L W D
Sbjct: 24 CSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDD 81
>pdb|4AV1|A Chain A, Crystal Structure Of The Human Parp-1 Dna Binding Domain
In Complex With Dna
pdb|4AV1|B Chain B, Crystal Structure Of The Human Parp-1 Dna Binding Domain
In Complex With Dna
pdb|4AV1|C Chain C, Crystal Structure Of The Human Parp-1 Dna Binding Domain
In Complex With Dna
pdb|4AV1|D Chain D, Crystal Structure Of The Human Parp-1 Dna Binding Domain
In Complex With Dna
Length = 223
Score = 29.3 bits (64), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 13/58 (22%)
Query: 17 CQETSPTLQQRLQFIVQNR------PEWWVYSIFWQ-------PLKDVNGRLVLSWGD 61
C E+ P R+ +VQ+ P W+ +S FW+ P +V+G L W D
Sbjct: 45 CSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDD 102
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
0.319 0.134 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,425,099
Number of Sequences: 62578
Number of extensions: 512748
Number of successful extensions: 1210
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1209
Number of HSP's gapped (non-prelim): 13
length of query: 519
length of database: 14,973,337
effective HSP length: 103
effective length of query: 416
effective length of database: 8,527,803
effective search space: 3547566048
effective search space used: 3547566048
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)