RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5774
(201 letters)
>2ql2_B Neurod1, neurogenic differentiation factor 1;
basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}
Length = 60
Score = 81.9 bits (203), Expect = 3e-21
Identities = 22/57 (38%), Positives = 34/57 (59%)
Query: 18 RKIFTNTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLLNGVLE 74
R++ N RER R ++ A LR++VP + +KLSK E LR++ YI L+ +L
Sbjct: 2 RRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR 58
>1mdy_A Protein (MYOD BHLH domain); protein-DNA complex,
transcription/DNA complex; HET: DNA; 2.80A {Mus
musculus} SCOP: a.38.1.1 PDB: 1mdy_B*
Length = 68
Score = 72.0 bits (177), Expect = 2e-17
Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 7 MEVGKHPRVLVRKIFTNTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYI 66
ME+ + R+ RER R V+ AF L+R ++ P+++L K EILR +IRYI
Sbjct: 1 MELKRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSN-PNQRLPKVEILRNAIRYI 59
Query: 67 RLLNGVLE 74
L +L
Sbjct: 60 EGLQALLR 67
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 50.6 bits (120), Expect = 8e-08
Identities = 37/231 (16%), Positives = 76/231 (32%), Gaps = 63/231 (27%)
Query: 16 LVRKIFTNTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRM-SIRYIRLLNG--- 71
++ +++ R+R N + F + V P KL + +L + + + L++G
Sbjct: 107 MMTRMYIEQRDR--LYNDNQVFA--KYNVSRLQPYLKL-RQALLELRPAKNV-LIDGVLG 160
Query: 72 ----VL--------EWQKQNEN-----NYNNNNTTD--INANNNIITNNRDFVVNANKRG 112
+ + Q + + N N N+ + + ++ N R
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQ---IDPNWTSRS 217
Query: 113 DSKTSIK-ETNPFERKPNGNYFNSK----------DVSDTQV--------K-----RKTN 148
D ++IK + + + SK +V + + K R
Sbjct: 218 DHSSNIKLRIHSIQAELR-RLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQ 276
Query: 149 MTRQYNKISTTTITRTEIIQTFNKDELEEFDGKVANT------REAEKNNP 193
+T + +TT I+ T DE++ K + RE NP
Sbjct: 277 VTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNP 327
Score = 32.9 bits (74), Expect = 0.074
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 16 LVRKIFTNTRERWRQQ---NVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLLNGV 72
L R +F + R + +Q + S A+ ++ T K K I +Y RL+N +
Sbjct: 492 LFRMVFLDFR--FLEQKIRHDSTAWNASGSILNTLQ-QLKFYKPYICDNDPKYERLVNAI 548
Query: 73 LEWQKQNENNYNNNNTTDI 91
L++ + E N + TD+
Sbjct: 549 LDFLPKIEENLICSKYTDL 567
Score = 30.6 bits (68), Expect = 0.34
Identities = 17/123 (13%), Positives = 42/123 (34%), Gaps = 22/123 (17%)
Query: 79 NENNYNNNNTTDINANNNIITNNRDFVVNANKRGDSKTSIKETNPFERKPNGNYFNSKDV 138
E+ Y DI + FV N + K+ + + + +++
Sbjct: 12 GEHQYQYK---DI-----LSVFEDAFVDNFD--------CKDVQDMPK----SILSKEEI 51
Query: 139 SDTQVKRKTNMTRQYNKISTTTITRTEIIQTFNKDELEEFDGKVANTREAEKNNPNKRIT 198
+ K ++ T + E++Q F ++ L + + + E+ P+ +T
Sbjct: 52 DHI-IMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPS-MMT 109
Query: 199 NDF 201
+
Sbjct: 110 RMY 112
>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic
helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB:
2ql2_A*
Length = 76
Score = 46.8 bits (111), Expect = 1e-07
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 23 NTRERWRQQNVSGAFGEL-RRLVPTHPPDKKLSKNEILRMSIRYIRLLNGVLEWQKQNEN 81
N ER R+++++ AF EL R DK +K IL+ +++ I L + + N
Sbjct: 10 NALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNLNPL 69
Query: 82 NYNNNN 87
N+++++
Sbjct: 70 NHHHHH 75
>2lfh_A DNA-binding protein inhibitor ID-3; structural genomics,
northeast structural genomics consortiu PSI-biology,
protein structure initiative; NMR {Homo sapiens}
Length = 68
Score = 44.3 bits (104), Expect = 6e-07
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 30 QQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLL 69
+++ + LR LVP P +LS+ EIL+ I YI L
Sbjct: 26 LDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDL 65
>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ,
heterodimer, transcription/DNA complex; 1.80A {Homo
sapiens} SCOP: a.38.1.1
Length = 88
Score = 39.6 bits (93), Expect = 5e-05
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 17 VRKIFTNTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLL 69
V++ N ER R+ + +F LR +P ++K K IL+ + YI +
Sbjct: 5 VKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSV 57
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 41.5 bits (97), Expect = 8e-05
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 26 ERWRQQNVSGAFGELRRLVPTHPPDK-KLSKNEILRMSIRYIRLLNGVLEWQKQNENNYN 84
E+ R+ ++ EL LVPT KL K +LRM++++++ L G E NY
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYT--EANYK 78
Query: 85 NNNTTDINANNNIITNNRDFVV 106
+D + I+ F+
Sbjct: 79 PTFLSDDELKHLILRAADGFLF 100
>1an4_A Protein (upstream stimulatory factor); protein-DNA complex,
double helix, overhanging base, transcription/DNA
complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1
Length = 65
Score = 37.3 bits (87), Expect = 2e-04
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 18 RKIFTNTRERWRQQNVSGAFGELRRLVPTH---PPDKKLSKNEILRMSIRYIRLL 69
R+ N ER R+ ++ +L +++P SK IL + YI+ L
Sbjct: 5 RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS,
circadian rhythm proteins, transcription-activato; 2.27A
{Mus musculus}
Length = 361
Score = 37.2 bits (86), Expect = 0.002
Identities = 14/94 (14%), Positives = 34/94 (36%), Gaps = 4/94 (4%)
Query: 22 TNTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLLNGVLEWQK--QN 79
N E+ R+ + EL ++P +K+ K+ +L+ SI ++R +
Sbjct: 16 RNKSEKKRRDQFNVLIKELGSMLPG--NARKMDKSTVLQKSIDFLRKHKETTAQSDASEI 73
Query: 80 ENNYNNNNTTDINANNNIITNNRDFVVNANKRGD 113
++ ++ ++ F + G
Sbjct: 74 RQDWKPTFLSNEEFTQLMLEALDGFFLAIMTDGS 107
>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ,
transcription/DNA complex; 2.00A {Homo sapiens} SCOP:
a.38.1.1
Length = 80
Score = 34.8 bits (80), Expect = 0.002
Identities = 10/45 (22%), Positives = 23/45 (51%)
Query: 23 NTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIR 67
N E+ R+ ++ + +L+ LVP P + + +L + +I+
Sbjct: 6 NEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIK 50
>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A);
basic-helix-loop- helix-leucine zipper, transcription
factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1
PDB: 1ukl_C
Length = 82
Score = 33.9 bits (78), Expect = 0.005
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 23 NTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLL 69
N E+ + +++ EL+ LV + KL+K+ +LR +I YIR L
Sbjct: 11 NAIEKRYRSSINDKIIELKDLVVG--TEAKLNKSAVLRKAIDYIRFL 55
>1hlo_A Protein (transcription factor MAX); transcriptional regulation,
DNA binding, complex (transcription factor MAX/DNA),
transcription/DNA complex; HET: DNA; 2.80A {Homo
sapiens} SCOP: a.38.1.1
Length = 80
Score = 33.5 bits (77), Expect = 0.006
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 18 RKIFTNTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLL 69
++ N ER R+ ++ +F LR VP+ +K S+ +IL + YI+ +
Sbjct: 12 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQ-GEKASRAQILDKATEYIQYM 62
>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA,
BHLHZ, heterodimer, transcription/DNA complex; 1.80A
{Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A
1nlw_B
Length = 83
Score = 32.4 bits (74), Expect = 0.016
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 18 RKIFTNTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLL 69
++ N ER R+ ++ +F LR VP+ +K S+ +IL + YI+ +
Sbjct: 2 KRAHHNALERKRRDHIKDSFHSLRDSVPS-LQGEKASRAQILDKATEYIQYM 52
>1a0a_A BHLH, protein (phosphate system positive regulatory protein
PHO4); transcription factor, basic helix loop helix;
HET: DNA; 2.80A {Saccharomyces cerevisiae} SCOP:
a.38.1.1
Length = 63
Score = 29.0 bits (65), Expect = 0.17
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 26 ERWRQQNVSGAFGELRRLVPTHPPDKK----LSKNEILRMSIRYIRLL 69
E+ R+ ++ A EL L+P + SK + + RYIR L
Sbjct: 10 EQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHL 57
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 30.8 bits (69), Expect = 0.33
Identities = 20/110 (18%), Positives = 33/110 (30%), Gaps = 35/110 (31%)
Query: 30 QQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLLNGVLEWQKQNENNYNNNNTT 89
Q N F ELR L T+ L + I + L+ L+ +K
Sbjct: 163 QGNTDDYFEELRDLYQTYHV---LVGDLIKFSAETLSELIRTTLDAEKVFTQGL------ 213
Query: 90 DINANNNIITNNRDFVVNANKRGDSKTSIKETNPFERKPNGNYFNSKDVS 139
+I +++ NP P+ +Y S +S
Sbjct: 214 NI----------LEWL---------------ENP-SNTPDKDYLLSIPIS 237
>1leh_A Leucine dehydrogenase; oxidoreductase; 2.20A {Lysinibacillus
sphaericus} SCOP: c.2.1.7 c.58.1.1
Length = 364
Score = 28.3 bits (64), Expect = 1.7
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 51 KKLSKNEILRMSIRYIRLLNG 71
++ R R+I+ LNG
Sbjct: 88 FADKNEDMFRALGRFIQGLNG 108
>1ciy_A Cryia(A); toxin, ICP; 2.25A {Bacillus thuringiensis} SCOP: b.18.1.3
b.77.2.1 f.1.3.1
Length = 590
Score = 28.3 bits (62), Expect = 2.3
Identities = 21/156 (13%), Positives = 43/156 (27%), Gaps = 5/156 (3%)
Query: 16 LVRKIFTNTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLLNGVLEW 75
L R+I+TN + G + + + L+ I R +G
Sbjct: 235 LTREIYTNPVLENFDGSFRGMAQRIEQNIRQPHLMDILNSITIYTDVHRGFNYWSGH--- 291
Query: 76 QKQNENNYNNNNTTDINANNNIITNNRDFVVNANKRGDSKTSIKETNPFERKPNGNYFNS 135
Q + + + N V + G + + R G+ N+
Sbjct: 292 --QITASPVGFSGPEFAFPLFGNAGNAAPPVLVSLTGLGIFRTLSSPLYRRIILGSGPNN 349
Query: 136 KDVSDTQVKRKTNMTRQYNKISTTTITRTEIIQTFN 171
+++ + + N ST R +
Sbjct: 350 QELFVLDGTEFSFASLTTNLPSTIYRQRGTVDSLDV 385
>2gag_A Heterotetrameric sarcosine oxidase alpha-subunit; flavoenzyme,
electron transfer, folate-ME enzyme, oxidoreductase;
HET: NAD FAD FMN; 1.85A {Stenotrophomonas maltophilia}
PDB: 2gah_A* 1x31_A* 1vrq_A* 3ad7_A* 3ad8_A* 3ad9_A*
3ada_A*
Length = 965
Score = 27.2 bits (60), Expect = 4.3
Identities = 9/52 (17%), Positives = 19/52 (36%), Gaps = 2/52 (3%)
Query: 21 FTNTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLLNGV 72
T+ E+ V G R ++ +S M+ + + L +G+
Sbjct: 719 CTSVTEQLATVAVVGPRS--RDVIAKLASTVDVSNEGFKFMAFKDVVLDSGI 768
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.312 0.128 0.361
Gapped
Lambda K H
0.267 0.0557 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,938,292
Number of extensions: 159496
Number of successful extensions: 347
Number of sequences better than 10.0: 1
Number of HSP's gapped: 340
Number of HSP's successfully gapped: 32
Length of query: 201
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 112
Effective length of database: 4,216,824
Effective search space: 472284288
Effective search space used: 472284288
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (25.4 bits)