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= 046178
(515 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 38.1 bits (87), Expect = 0.013, Method: Composition-based stats.
Identities = 28/74 (37%), Positives = 39/74 (52%), Gaps = 7/74 (9%)
Query: 344 HVEAERQRREKLNHRFYALRAVVPNVSRMDKAS---LLSDAVSYIRELKVKIDDL--ESQ 398
H ERQRR +L F+ALR +P + +KA +L A +YI ++ + L E
Sbjct: 10 HNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEED 69
Query: 399 LL--QRESKKVKLE 410
LL +RE K KLE
Sbjct: 70 LLRKRREQLKHKLE 83
>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 = 35.4 bits (80), Expect = 0.071, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 8/77 (10%)
Query: 343 NHVEAERQRREKLNHRFYALRAVVPNVS----RMDKASLLSDAVSYIRELKVKIDDLESQ 398
NH ER+RR +N R L ++P + R +K ++L +V YIR+L+ + + +
Sbjct: 30 NHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQRE----QQR 85
Query: 399 LLQRESKKVKLEISDNH 415
E+++ KLE ++ H
Sbjct: 86 AKDLENRQKKLEHANRH 102
>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 = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 9/65 (13%)
Query: 343 NHVEAERQRREKLNHRFYALRAVVPNV--SRMDKASLLSDAVSYIRELKVK-------ID 393
+H ER+RR+ + F++LR VP++ + +A +L A YI+ ++ K ID
Sbjct: 5 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDID 64
Query: 394 DLESQ 398
DL+ Q
Sbjct: 65 DLKRQ 69
>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 = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 344 HVEAERQRREKLNHRFYALRAVVPNVSR------MDKASLLSDAVSYIRELK 389
H E ER+RR+K+N+ L ++P+ S K +LS A YI+EL+
Sbjct: 9 HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60
>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 = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 9/65 (13%)
Query: 343 NHVEAERQRREKLNHRFYALRAVVPNV--SRMDKASLLSDAVSYIRELKVK-------ID 393
+H ER+RR+ + F++LR VP++ + +A +L A YI+ ++ K ID
Sbjct: 7 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTLQQDID 66
Query: 394 DLESQ 398
DL+ Q
Sbjct: 67 DLKRQ 71
>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 = 0.27, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 9/65 (13%)
Query: 343 NHVEAERQRREKLNHRFYALRAVVPNV--SRMDKASLLSDAVSYIRELKVK-------ID 393
+H ER+RR+ + F++LR VP++ + +A +L A YI+ ++ K ID
Sbjct: 15 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDID 74
Query: 394 DLESQ 398
DL+ Q
Sbjct: 75 DLKRQ 79
>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 = 21/65 (32%), Positives = 36/65 (55%), Gaps = 9/65 (13%)
Query: 343 NHVEAERQRREKLNHRFYALRAVVPNV--SRMDKASLLSDAVSYIRELKVK-------ID 393
+H ER+RR+ + F++LR VP++ + +A +L A YI+ ++ K ID
Sbjct: 4 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDID 63
Query: 394 DLESQ 398
DL+ Q
Sbjct: 64 DLKRQ 68
>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 = 0.36, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 9/65 (13%)
Query: 343 NHVEAERQRREKLNHRFYALRAVVPNV--SRMDKASLLSDAVSYIRELKVK-------ID 393
+H ER+RR+ + F++LR VP++ + +A +L A YI+ ++ K ID
Sbjct: 6 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDID 65
Query: 394 DLESQ 398
DL+ Q
Sbjct: 66 DLKRQ 70
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 31/50 (62%), Gaps = 4/50 (8%)
Query: 344 HVEAERQRREKLNHRFYALRAVVPNVS----RMDKASLLSDAVSYIRELK 389
H + E++RR+K+N L ++VP + ++DK ++L AV +++ L+
Sbjct: 17 HSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 66
>pdb|2JLP|A Chain A, Crystal Structure Of Human Extracellular Copper-Zinc
Superoxide Dismutase.
pdb|2JLP|B Chain B, Crystal Structure Of Human Extracellular Copper-Zinc
Superoxide Dismutase.
pdb|2JLP|C Chain C, Crystal Structure Of Human Extracellular Copper-Zinc
Superoxide Dismutase.
pdb|2JLP|D Chain D, Crystal Structure Of Human Extracellular Copper-Zinc
Superoxide Dismutase
Length = 222
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 29/58 (50%)
Query: 373 DKASLLSDAVSYIRELKVKIDDLESQLLQRESKKVKLEISDNHSTTTSVDQARPSSAG 430
D A SD+ +IR++ K+ ++ +++QR L + + ++D A+P G
Sbjct: 5 DSAEPNSDSAEWIRDMYAKVTEIWQEVMQRRDDDGTLHAACQVQPSATLDAAQPRVTG 62
>pdb|3GG9|A Chain A, Crystal Structure Of Putative D-3-Phosphoglycerate
Dehydrogenase Oxidoreductase From Ralstonia Solanacearum
pdb|3GG9|B Chain B, Crystal Structure Of Putative D-3-Phosphoglycerate
Dehydrogenase Oxidoreductase From Ralstonia Solanacearum
pdb|3GG9|C Chain C, Crystal Structure Of Putative D-3-Phosphoglycerate
Dehydrogenase Oxidoreductase From Ralstonia Solanacearum
pdb|3GG9|D Chain D, Crystal Structure Of Putative D-3-Phosphoglycerate
Dehydrogenase Oxidoreductase From Ralstonia Solanacearum
Length = 352
Score = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 8/81 (9%)
Query: 369 VSRMDKASLLSD--------AVSYIRELKVKIDDLESQLLQRESKKVKLEISDNHSTTTS 420
V ++D SLL D V + +L ++ D+E+ +L RE +V ++ D
Sbjct: 15 VRKLDCFSLLQDHEVKVFNNTVKGVGQLAARVADVEALVLIRERTRVTRQLLDRLPKLKI 74
Query: 421 VDQARPSSAGSGGGFNLEVET 441
+ Q S +GG +LE T
Sbjct: 75 ISQTGRVSRDAGGHIDLEACT 95
>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 = 28.9 bits (63), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 31/50 (62%), Gaps = 4/50 (8%)
Query: 344 HVEAERQRREKLNHRFYALRAVVPNVS----RMDKASLLSDAVSYIRELK 389
H + E++RR+K+N L ++VP + ++DK ++L AV +++ L+
Sbjct: 13 HSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 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
0.316 0.132 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,513,661
Number of Sequences: 62578
Number of extensions: 383948
Number of successful extensions: 1012
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1008
Number of HSP's gapped (non-prelim): 14
length of query: 515
length of database: 14,973,337
effective HSP length: 103
effective length of query: 412
effective length of database: 8,527,803
effective search space: 3513454836
effective search space used: 3513454836
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)