RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5860
(138 letters)
>2ql2_B Neurod1, neurogenic differentiation factor 1;
basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}
Length = 60
Score = 96.6 bits (241), Expect = 6e-28
Identities = 27/58 (46%), Positives = 36/58 (62%)
Query: 25 RRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMKILET 82
RR AN +ER R +N A +LR+ +P KLSKI+TLRLA +YI L +IL +
Sbjct: 2 RRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILRS 59
>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 = 82.0 bits (203), Expect = 6e-22
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 20 IRVVKRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMKI 79
RR A +ERRR +N AF L+ + P+ +L K++ LR A YI L +
Sbjct: 7 TTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQ-RLPKVEILRNAIRYIEGLQAL 65
Query: 80 LE 81
L
Sbjct: 66 LR 67
>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic
helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB:
2ql2_A*
Length = 76
Score = 64.5 bits (157), Expect = 4e-15
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 23 VKRRNTANKKERRRTQSINNAFSDL-RECIPNVPSDTKLSKIKTLRLATSYISYL 76
+R N ER+R + IN AF +L R C ++ SD +K+ L+ A I L
Sbjct: 3 ADKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGL 57
>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 = 57.3 bits (139), Expect = 4e-12
Identities = 18/54 (33%), Positives = 30/54 (55%)
Query: 25 RRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMK 78
+R T N ER+R + +F LR+ IP + ++ K K+ L+ AT+YI +
Sbjct: 6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQA 59
>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 = 50.5 bits (121), Expect = 2e-09
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 25 RRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMK 78
+R N ER+R I ++F LR+ +P++ K S+ + L AT YI Y+ +
Sbjct: 2 KRAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYMRR 54
>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 = 50.0 bits (120), Expect = 2e-09
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 16 DLPIIRVVKRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISY 75
D+ + +R N ER+R I ++F LR+ +P++ K S+ + L AT YI Y
Sbjct: 3 DIEVESDADKRAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQY 61
Query: 76 LMK 78
+ +
Sbjct: 62 MRR 64
>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 = 49.1 bits (117), Expect = 5e-09
Identities = 12/53 (22%), Positives = 24/53 (45%)
Query: 26 RNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMK 78
R+T N+ E+ R + + L+ +P P ++ + + L A +I L
Sbjct: 2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLED 54
>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 = 47.0 bits (112), Expect = 3e-08
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 24 KRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYL 76
++R N E+R SIN+ +L++ + ++ KL+K LR A YI +L
Sbjct: 5 EKRTAHNAIEKRYRSSINDKIIELKDLVVG--TEAKLNKSAVLRKAIDYIRFL 55
>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 = 46.6 bits (111), Expect = 3e-08
Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 24 KRRNTANKKERRRTQSINNAFSDLRECIPNV---PSDTKLSKIKTLRLATSYISYL 76
KRR N+ ERRR INN L + IP+ + + SK L A+ YI L
Sbjct: 4 KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59
>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 = 37.0 bits (85), Expect = 1e-04
Identities = 16/56 (28%), Positives = 29/56 (51%)
Query: 21 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYL 76
+ + A ++ +N+ +S LRE +P VP T+LS+++ L+ YI L
Sbjct: 10 HMGGGKGPAAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDL 65
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH,
PAS, circadian rhythm proteins, transcription-activato;
2.27A {Mus musculus}
Length = 361
Score = 36.9 bits (85), Expect = 0.001
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 24 KRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYI 73
KR + +++RR Q N +L +P K+ K L+ + ++
Sbjct: 12 KRVSRNKSEKKRRDQ-FNVLIKELGSMLPGNAR--KMDKSTVLQKSIDFL 58
>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 = 34.0 bits (78), Expect = 0.002
Identities = 15/62 (24%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 25 RRNTANKKERRRTQSINNAFSDLRECIPNVPSD----TKLSKIKTLRLATSYISYLMKIL 80
+R + E+ R + A +L IP SK T+ A YI +L +
Sbjct: 2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG 61
Query: 81 ET 82
T
Sbjct: 62 ST 63
>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 = 34.8 bits (79), Expect = 0.006
Identities = 20/143 (13%), Positives = 44/143 (30%), Gaps = 18/143 (12%)
Query: 11 PLYTADLPIIRVVKRRNTANKKERR-------RTQSINNAFSDLREC-IPNVPSDTKLSK 62
Y L ++ V+ N R + + + S I L+
Sbjct: 241 KPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTP 300
Query: 63 IKTLRLATSYISYLMKIL--ETDDI----ISIDDFKADLSNHSSHRKNKSQYDSPSEISS 116
+ L Y+ + L E +SI + + + N + +
Sbjct: 301 DEVKSLLLKYLDCRPQDLPREVLTTNPRRLSI--IAESIRDGLATWDNWKHVNCDKLTTI 358
Query: 117 NQSSQYVMDPSCQQ--YTSPALF 137
+SS V++P+ + + ++F
Sbjct: 359 IESSLNVLEPAEYRKMFDRLSVF 381
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 34.6 bits (79), Expect = 0.006
Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 24 KRRNTANKKERRRTQSINNAFSDLRECIPNVPSDT-KLSKIKTLRLATSYI 73
R ++ E+RR +N+ +L +P + + KL K+ LR+A ++
Sbjct: 12 NAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHM 62
>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 = 31.6 bits (71), Expect = 0.080
Identities = 22/128 (17%), Positives = 47/128 (36%), Gaps = 27/128 (21%)
Query: 12 LYTADLPIIRVVKRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKL--SKIKTLRLA 69
LY + V N A+ + FS + + + N P + + K R+
Sbjct: 1635 LYKTS-KAAQDV--WNRADNHFKD-----TYGFS-ILDIVINNPVNLTIHFGGEKGKRIR 1685
Query: 70 TSYISYLMKILETDDIISIDDFKADLSNHSSHRKNKSQYDSPSEISSNQSSQYVMDPSCQ 129
+Y + + + + + + FK +++ HS+ + S ++ +
Sbjct: 1686 ENYSAMIFETIVDGKLKTEKIFK-EINEHST----SYTFRSEKG---------LLSAT-- 1729
Query: 130 QYTSPALF 137
Q+T PAL
Sbjct: 1730 QFTQPALT 1737
Score = 31.2 bits (70), Expect = 0.100
Identities = 16/122 (13%), Positives = 43/122 (35%), Gaps = 29/122 (23%)
Query: 43 AFSDLREC-IPNVPSDTK--------LSKIKTLRLATSYISYLMKILE------TDDII- 86
S L+E +P T+ + + L ++ Y+ ++E D ++
Sbjct: 29 IASQLQEQFNKILPEPTEGFAADDEPTTPAE---LVGKFLGYVSSLVEPSKVGQFDQVLN 85
Query: 87 -SIDDFKAD-LSN---HS-----SHRKNKSQYDSPSEISSNQSSQYVMDPSCQQYTSPAL 136
+ +F+ L H+ + + + I + +++ + + ++ AL
Sbjct: 86 LCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSAL 145
Query: 137 FS 138
F
Sbjct: 146 FR 147
Score = 28.5 bits (63), Expect = 0.87
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 16/52 (30%)
Query: 46 DLR--ECIPNVPSDTKLSKIKTLRLATSYISYLMKILETDDIISIDDFKADL 95
DLR + + NV + KL KI + L S +S+++ + L
Sbjct: 1858 DLRALDTVTNVLNFIKLQKIDIIELQKS--------------LSLEEVEGHL 1895
>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1,
nicotinic acid riboside kinase activity, NAD
biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB:
2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*
Length = 207
Score = 29.4 bits (66), Expect = 0.25
Identities = 12/51 (23%), Positives = 19/51 (37%)
Query: 76 LMKILETDDIISIDDFKADLSNHSSHRKNKSQYDSPSEISSNQSSQYVMDP 126
L K L +IS DDF S + + QYD ++ + +
Sbjct: 41 LQKHLPNCSVISQDDFFKPESEIETDKNGFLQYDVLEALNMEKMMSAISCW 91
>3nfi_A DNA-directed RNA polymerase I subunit RPA49; winged helix,
transcription, DNA binding, DN protein; HET: MSE PE4;
1.90A {Saccharomyces cerevisiae} PDB: 3nfh_A
Length = 237
Score = 28.4 bits (63), Expect = 0.71
Identities = 14/89 (15%), Positives = 36/89 (40%), Gaps = 8/89 (8%)
Query: 9 PPPLYTADLPIIRVVKRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRL 68
P IRV A+K+++ N + + + ++ ++++K++ L
Sbjct: 43 PKKELQF----IRVSSILKEADKEKKLELFPYQNNSKYVAKKLDSLTQPSQMTKLQMLY- 97
Query: 69 ATSYISYLMKILETDDIISIDDFKADLSN 97
Y+S L+ + E + + L++
Sbjct: 98 ---YLSLLLGVYENRRVNNKTKLLERLNS 123
>1pyb_A Methionyl-tRNA synthetase beta subunit; oligonucleotide,
oligosaccharide-binding fold, OB-fold, beta-barrel, RNA
binding protein; 2.50A {Aquifex aeolicus} SCOP:
b.40.4.4
Length = 111
Score = 24.9 bits (55), Expect = 6.1
Identities = 8/17 (47%), Positives = 11/17 (64%), Gaps = 1/17 (5%)
Query: 80 LETDDIISIDDF-KADL 95
+E +I I+DF K DL
Sbjct: 1 MEEKALIGIEDFLKVDL 17
>2cvd_A Glutathione-requiring prostaglandin D synthase;
glutathione-S-transferase, isomerase; HET: GSH HQL;
1.45A {Homo sapiens} SCOP: a.45.1.1 c.47.1.5 PDB:
1iyi_A* 1v40_A* 1iyh_A* 3vi5_A* 3vi7_A* 2vcq_A* 2vcw_A*
2vcx_A* 2vcz_A* 2vd0_A* 2vd1_A* 3kxo_A* 3ee2_A* 1pd2_1*
Length = 198
Score = 25.4 bits (56), Expect = 6.4
Identities = 11/54 (20%), Positives = 20/54 (37%)
Query: 29 ANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMKILET 82
+ E+ +I + D C P + + L T +LM+ L+T
Sbjct: 79 NTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDT 132
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
0.313 0.127 0.355
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: 1,952,378
Number of extensions: 95664
Number of successful extensions: 204
Number of sequences better than 10.0: 1
Number of HSP's gapped: 198
Number of HSP's successfully gapped: 24
Length of query: 138
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 54
Effective length of database: 4,356,429
Effective search space: 235247166
Effective search space used: 235247166
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 (21.9 bits)
S2: 52 (24.2 bits)