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= psy14584
(563 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 226 bits (576), Expect = 2e-59, Method: Compositional matrix adjust.
Identities = 151/437 (34%), Positives = 208/437 (47%), Gaps = 158/437 (36%)
Query: 218 SRQNHSEIEKRRRDKMNTYITELSAMVPMCHAMSRKLDKLTVLRMAVQHLKTIRGAVHSY 277
+R+ HS+IEKRRRDKMN++I EL+++VP C+AMSRKLDKLTVLRMAVQH+KT+RGA + Y
Sbjct: 13 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPY 72
Query: 278 TEGHYKPAFLTDQELKHLILQAAEGFL--------------------QNHSEIE------ 311
TE +YKP FL+D ELKHLIL+AA+GFL N+S+ +
Sbjct: 73 TEANYKPTFLSDDELKHLILRAADGFLFVVGCDRGKILFVSESVFKILNYSQNDLIGQSL 132
Query: 312 ------------KRRRDKMNTYITELSAMVPTLLPVKTADIPAEVSRLCPGARRSFFCRM 359
K + +T E T LPVKT DI SRLC GARRSFFCRM
Sbjct: 133 FDYLHPKDIAKVKEQLSSSDTAPRERLIDAKTGLPVKT-DITPGPSRLCSGARRSFFCRM 191
Query: 360 KCKHTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCVKEEPDTTTGAAASCHRKKKQQQSD 419
KC E+ D A++C +KK ++S
Sbjct: 192 KCNRPSVKV----------------------------EDKD----FASTCSKKKADRKS- 218
Query: 420 RKYSVIQCTGYLKSWAPAKMGLEESE--DRKYSVIQCTGYLKSWAPAKMXXXXXXXXXXX 477
+ I TGYLKSW P KMGL+E D + + C
Sbjct: 219 --FCTIHSTGYLKSWPPTKMGLDEDNEPDNEGCNLSC----------------------- 253
Query: 478 XXXXXXXXLVAVGRVLADKT-RILNKQVNLRPIQFLSRHALDGKFLFV------------ 524
LVA+GR+ + + N ++ ++ ++++SRHA+DGKF+FV
Sbjct: 254 --------LVAIGRLHSHMVPQPANGEIRVKSMEYVSRHAIDGKFVFVDQRATAILAYLP 305
Query: 525 --------------------------------------YQFKNKGGTYVQLQSEWKNFRN 546
Y+FK K G+++ L+S W +F N
Sbjct: 306 QELLGTSCYEYFHQDDIGHLAECHRQVLQTREKITTNCYKFKIKDGSFITLRSRWFSFMN 365
Query: 547 PWTKDIEYLISKNTLIL 563
PWTK++EY++S NT++L
Sbjct: 366 PWTKEVEYIVSTNTVVL 382
Score = 69.3 bits (168), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 34/51 (66%), Positives = 40/51 (78%), Gaps = 5/51 (9%)
Query: 167 AQGELLGQSWFDILHPKDVAKVKEQLFSSDLSPRERLIDVKSKQVIVGLPV 217
+Q +L+GQS FD LHPKD+AKVKEQL SSD +PRERLID K+ GLPV
Sbjct: 123 SQNDLIGQSLFDYLHPKDIAKVKEQLSSSDTAPRERLIDAKT-----GLPV 168
>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 = 92.4 bits (228), Expect = 6e-19, Method: Composition-based stats.
Identities = 42/56 (75%), Positives = 53/56 (94%)
Query: 218 SRQNHSEIEKRRRDKMNTYITELSAMVPMCHAMSRKLDKLTVLRMAVQHLKTIRGA 273
+R+ HS+IEKRRRDKMN++I EL+++VP C+AMSRKLDKLTVLRMAVQH+KT+RGA
Sbjct: 9 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA 64
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 18/27 (66%), Positives = 25/27 (92%)
Query: 305 QNHSEIEKRRRDKMNTYITELSAMVPT 331
+ HS+IEKRRRDKMN++I EL+++VPT
Sbjct: 11 EAHSQIEKRRRDKMNSFIDELASLVPT 37
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 32/90 (35%), Positives = 54/90 (60%), Gaps = 7/90 (7%)
Query: 219 RQNHSEIEKRRRDKMNTYITELSAMVPMCHAMSRKLDKLTVLRMAV----QHLKTIRGAV 274
R + ++ EK+RRD+ N I EL +M+P +RK+DK TVL+ ++ +H +T +
Sbjct: 13 RVSRNKSEKKRRDQFNVLIKELGSMLP---GNARKMDKSTVLQKSIDFLRKHKETTAQSD 69
Query: 275 HSYTEGHYKPAFLTDQELKHLILQAAEGFL 304
S +KP FL+++E L+L+A +GF
Sbjct: 70 ASEIRQDWKPTFLSNEEFTQLMLEALDGFF 99
>pdb|2KDK|A Chain A, Structure Of Human Circadian Clock Protein Bmal2
C-Terminal Pas Domain
Length = 121
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 52/111 (46%), Gaps = 50/111 (45%)
Query: 503 QVNLRPIQFLSRHALDGKFLFV-------------------------------------- 524
++N++P +F++R A++GKF++V
Sbjct: 7 EINVKPTEFITRFAVNGKFVYVDQRATAILGYLPQELLGTSCYEYFHQDDHNNLTDKHKA 66
Query: 525 ------------YQFKNKGGTYVQLQSEWKNFRNPWTKDIEYLISKNTLIL 563
Y+F+ K G++V L+S+W +F NP TK++EY++S NTL+L
Sbjct: 67 VLQSKEKILTDSYKFRAKDGSFVTLKSQWFSFTNPDTKELEYIVSVNTLVL 117
>pdb|1WA9|A Chain A, Crystal Structure Of The Pas Repeat Region Of The
Drosophila Clock Protein Period
pdb|1WA9|B Chain B, Crystal Structure Of The Pas Repeat Region Of The
Drosophila Clock Protein Period
Length = 368
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 24/33 (72%)
Query: 525 YQFKNKGGTYVQLQSEWKNFRNPWTKDIEYLIS 557
Y+F + G YV L++EW +F NPW++ +E+++
Sbjct: 228 YRFLIQNGCYVLLETEWTSFVNPWSRKLEFVVG 260
>pdb|3RTY|A Chain A, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
pdb|3RTY|B Chain B, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
pdb|3RTY|C Chain C, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
pdb|3RTY|D Chain D, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
pdb|3RTY|E Chain E, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
pdb|3RTY|F Chain F, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
pdb|3RTY|G Chain G, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
pdb|3RTY|H Chain H, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
Length = 339
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 24/33 (72%)
Query: 525 YQFKNKGGTYVQLQSEWKNFRNPWTKDIEYLIS 557
Y+F + G YV L++EW +F NPW++ +E+++
Sbjct: 224 YRFLIQNGCYVLLETEWTSFVNPWSRKLEFVVG 256
>pdb|3GEC|A Chain A, Crystal Structure Of A Tandem Pas Domain Fragment Of
Drosophila Period
Length = 312
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 24/33 (72%)
Query: 525 YQFKNKGGTYVQLQSEWKNFRNPWTKDIEYLIS 557
Y+F + G YV L++EW +F NPW++ +E+++
Sbjct: 233 YRFLIQNGCYVLLETEWTSFVNPWSRKLEFVVG 265
>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 = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 219 RQNHSEIEKRRRDKMNTYITELSAMVPMCHAMSRK--LDKLTVLRMAVQHLKTIRGAVH 275
R H+E+E+RRRDK+N +I +LS ++P S K K +L A +++ +R + H
Sbjct: 6 RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH 64
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 21/24 (87%)
Query: 307 HSEIEKRRRDKMNTYITELSAMVP 330
H+E+E+RRRDK+N +I +LS ++P
Sbjct: 9 HNEVERRRRDKINNWIVQLSKIIP 32
>pdb|3GDI|A Chain A, Mammalian Clock Protein Mper2 - Crystal Struture Of A Pas
Domain Fragment
pdb|3GDI|B Chain B, Mammalian Clock Protein Mper2 - Crystal Struture Of A Pas
Domain Fragment
Length = 309
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 24/36 (66%)
Query: 526 QFKNKGGTYVQLQSEWKNFRNPWTKDIEYLISKNTL 561
+F+ + G Y+ L + W +F NPW++ I ++I ++ +
Sbjct: 233 RFRTRNGEYITLDTSWSSFINPWSRKISFIIGRHKV 268
>pdb|4H10|B Chain B, Intermolecular Recognition Revealed By The Complex
Structure Of Human Clock-bmal1 Basic Helix-loop-helix
Domains With E-box Dna
Length = 71
Score = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 20/50 (40%), Positives = 33/50 (66%), Gaps = 3/50 (6%)
Query: 219 RQNHSEIEKRRRDKMNTYITELSAMVPMCHAMSRKLDKLTVLRMAVQHLK 268
R + ++ EK+RRD+ N I EL +M+P +RK+DK TVL+ ++ L+
Sbjct: 9 RVSRNKSEKKRRDQFNVLIKELGSMLP---GNARKMDKSTVLQKSIDFLR 55
>pdb|4DJ3|A Chain A, Unwinding The Differences Of The Mammalian Period Clock
Proteins From Crystal Structure To Cellular Function
pdb|4DJ3|B Chain B, Unwinding The Differences Of The Mammalian Period Clock
Proteins From Crystal Structure To Cellular Function
Length = 317
Score = 38.1 bits (87), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 526 QFKNKGGTYVQLQSEWKNFRNPWTKDIEYLISKN 559
+F + G YV L S W +F NPW++ + ++I ++
Sbjct: 243 RFCTQNGEYVILDSSWSSFVNPWSRKVSFIIGRH 276
>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 = 37.0 bits (84), Expect = 0.032, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 33/53 (62%)
Query: 219 RQNHSEIEKRRRDKMNTYITELSAMVPMCHAMSRKLDKLTVLRMAVQHLKTIR 271
+ NH+ IE+RRR +N I EL ++P + + +K T+L+ +V +++ ++
Sbjct: 28 KDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQ 80
Score = 28.9 bits (63), Expect = 8.7, Method: Composition-based stats.
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 306 NHSEIEKRRRDKMNTYITELSAMVP 330
NH+ IE+RRR +N I EL ++P
Sbjct: 30 NHNLIERRRRFNINDRIKELGTLIP 54
>pdb|4DJ2|A Chain A, Unwinding The Differences Of The Mammalian Period Clock
Proteins From Crystal Structure To Cellular Function
pdb|4DJ2|B Chain B, Unwinding The Differences Of The Mammalian Period Clock
Proteins From Crystal Structure To Cellular Function
pdb|4DJ2|C Chain C, Unwinding The Differences Of The Mammalian Period Clock
Proteins From Crystal Structure To Cellular Function
pdb|4DJ2|D Chain D, Unwinding The Differences Of The Mammalian Period Clock
Proteins From Crystal Structure To Cellular Function
Length = 320
Score = 33.5 bits (75), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 8/34 (23%), Positives = 21/34 (61%)
Query: 526 QFKNKGGTYVQLQSEWKNFRNPWTKDIEYLISKN 559
+F + G YV + + W F +PW++ + +++ ++
Sbjct: 244 RFCARNGEYVTMDTSWAGFVHPWSRKVAFVLGRH 277
>pdb|2QUQ|A Chain A, Crystal Structure Of The Essential Inner Kinetochore
Protein Cep3p
Length = 562
Score = 32.7 bits (73), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 28/96 (29%), Positives = 40/96 (41%), Gaps = 19/96 (19%)
Query: 237 ITELSAMVPMCHAMSRKLDKLTVLRMAVQHLKTIRGAVHSYTEG--HYKPAFLTDQELKH 294
+TEL+A +P KLDKL L + LK + V G Y P F
Sbjct: 443 LTELTANLPTIFG--SKLDKLVYLTERLSKLKLLWDKVQLLDSGDSFYHPVF-------- 492
Query: 295 LILQAAEGFLQNHSEIEKRRRDKMNTYITELSAMVP 330
LQN +I + + D+M + I L ++VP
Sbjct: 493 -------KILQNDIKIIELKNDEMFSLIKGLGSLVP 521
>pdb|2VEQ|A Chain A, Insights Into Kinetochore-Dna Interactions From The
Structure Of Cep3p
Length = 565
Score = 32.7 bits (73), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 28/96 (29%), Positives = 40/96 (41%), Gaps = 19/96 (19%)
Query: 237 ITELSAMVPMCHAMSRKLDKLTVLRMAVQHLKTIRGAVHSYTEG--HYKPAFLTDQELKH 294
+TEL+A +P KLDKL L + LK + V G Y P F
Sbjct: 446 LTELTANLPTIFG--SKLDKLVYLTERLSKLKLLWDKVQLLDSGDSFYHPVF-------- 495
Query: 295 LILQAAEGFLQNHSEIEKRRRDKMNTYITELSAMVP 330
LQN +I + + D+M + I L ++VP
Sbjct: 496 -------KILQNDIKIIELKNDEMFSLIKGLGSLVP 524
>pdb|4H6J|B Chain B, Identification Of Cys 255 In Hif-1 As A Novel Site For
Development Of Covalent Inhibitors Of Hif-1 ARNT PASB
DOMAIN PROTEIN-Protein Interaction
Length = 116
Score = 32.7 bits (73), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 517 LDGKFLFV-YQFKNKGGTYVQLQSEWKNFRNPWTKDIEYLISKNT 560
L G+ L V ++F++K ++ +++ F+NP++ +IEY+I NT
Sbjct: 64 LKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNT 108
>pdb|2HV1|A Chain A, Haddock Structure Of Arnt Pas-B Homodimer
pdb|2HV1|B Chain B, Haddock Structure Of Arnt Pas-B Homodimer
pdb|1X0O|A Chain A, Human Arnt C-Terminal Pas Domain
Length = 119
Score = 32.3 bits (72), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 517 LDGKFLFV-YQFKNKGGTYVQLQSEWKNFRNPWTKDIEYLISKNT 560
L G+ L V ++F++K ++ +++ F+NP++ +IEY+I NT
Sbjct: 67 LKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNT 111
>pdb|2A24|B Chain B, Haddock Structure Of Hif-2aARNT PAS-B Heterodimer
Length = 108
Score = 32.3 bits (72), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 517 LDGKFLFV-YQFKNKGGTYVQLQSEWKNFRNPWTKDIEYLISKNT 560
L G+ L V ++F++K ++ +++ F+NP++ +IEY+I NT
Sbjct: 61 LKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNT 105
>pdb|3F1N|B Chain B, Crystal Structure Of A High Affinity Heterodimer Of Hif2
Alpha And Arnt C-Terminal Pas Domains, With Internally
Bound Ethylene Glycol.
pdb|3F1O|B Chain B, Crystal Structure Of The High Affinity Heterodimer Of Hif2
Alpha And Arnt C-Terminal Pas Domains, With An
Internally- Bound Artificial Ligand
pdb|3F1P|B Chain B, Crystal Structure Of A High Affinity Heterodimer Of Hif2
Alpha And Arnt C-Terminal Pas Domains
pdb|3H7W|B Chain B, Crystal Structure Of The High Affinity Heterodimer Of Hif2
Alpha And Arnt C-Terminal Pas Domains With The
Artificial Ligand Ths017
pdb|3H82|B Chain B, Crystal Structure Of The High Affinity Heterodimer Of Hif2
Alpha And Arnt C-Terminal Pas Domains With The
Artificial Ligand Ths020
pdb|4GHI|B Chain B, Crystal Structure Of The High Affinity Heterodimer Of Hif2
Alpha And Arnt C-terminal Pas Domains In Complex With A
Benzoxadiazole Antagonist
Length = 121
Score = 32.0 bits (71), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 517 LDGKFLFV-YQFKNKGGTYVQLQSEWKNFRNPWTKDIEYLISKNT 560
L G+ L V ++F++K ++ +++ F+NP++ +IEY+I NT
Sbjct: 69 LKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNT 113
>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 = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 218 SRQNHSEIEKRRRDKMNTYITELSAMVPMCHAMSRKLDKLTVLRMAVQHLKTI----RGA 273
SR H+E+EK RR + + +L +VP+ SR L++L A H+K + R A
Sbjct: 1 SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRH-TTLSLLTKAKLHIKKLEDSDRKA 59
Query: 274 VH 275
VH
Sbjct: 60 VH 61
>pdb|3U5V|A Chain A, Crystal Structure Of Max-E47
Length = 76
Score = 30.8 bits (68), Expect = 1.8, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 25/47 (53%)
Query: 219 RQNHSEIEKRRRDKMNTYITELSAMVPMCHAMSRKLDKLTVLRMAVQ 265
R +H+ +E++RR +N EL M M + KL +L+ AVQ
Sbjct: 6 RAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQ 52
>pdb|2B02|A Chain A, Crystal Structure Of Arnt Pas-B Domain
Length = 119
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 517 LDGKFLFV-YQFKNKGGTYVQLQSEWKNFRNPWTKDIEYLISKNTLI 562
L G+ L V ++F++K ++ ++ F+NP++ +IEY+I NT +
Sbjct: 67 LKGQVLSVXFRFRSKNQEWLWXRTSSFTFQNPYSDEIEYIICTNTNV 113
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
0.318 0.132 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,492,716
Number of Sequences: 62578
Number of extensions: 465926
Number of successful extensions: 1028
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 975
Number of HSP's gapped (non-prelim): 53
length of query: 563
length of database: 14,973,337
effective HSP length: 104
effective length of query: 459
effective length of database: 8,465,225
effective search space: 3885538275
effective search space used: 3885538275
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)