RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3607
(95 letters)
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH,
PAS, circadian rhythm proteins, transcription-activato;
2.27A {Mus musculus}
Length = 361
Score = 75.0 bits (184), Expect = 9e-18
Identities = 37/54 (68%), Positives = 44/54 (81%)
Query: 22 DDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLK 75
DDKD +KR SRN SEKKRRDQFN+LI EL +M+ N RKMDKSTVL+ +I FL+
Sbjct: 6 DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 59
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 65.0 bits (158), Expect = 3e-14
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 5/68 (7%)
Query: 18 MDDT--DDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVST---NNRKMDKSTVLKSTIA 72
M+ + + R++ + EK+RRD+ N I+EL ++V T +RK+DK TVL+ +
Sbjct: 1 MEYAEHQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQ 60
Query: 73 FLKNYNGT 80
+K G
Sbjct: 61 HMKTLRGA 68
>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 = 46.2 bits (110), Expect = 2e-08
Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 19 DDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMV-STNNRKMDKSTVLKSTIAFLK 75
D + D KR N E+KRRD + L V S K ++ +L +++
Sbjct: 3 DIEVESDADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQ 60
>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 = 45.4 bits (108), Expect = 3e-08
Identities = 17/52 (32%), Positives = 26/52 (50%)
Query: 24 KDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLK 75
KR + N EK+ R N I EL +V K++KS VL+ I +++
Sbjct: 2 SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIR 53
>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 = 43.9 bits (104), Expect = 1e-07
Identities = 12/56 (21%), Positives = 25/56 (44%), Gaps = 5/56 (8%)
Query: 25 DDSKRKSRNLSEKKRRDQFNMLINELCTMV-----STNNRKMDKSTVLKSTIAFLK 75
D+ +R N E++RRD+ N I +L ++ + K +L +++
Sbjct: 2 DEKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQ 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 = 43.9 bits (104), Expect = 1e-07
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 25 DDSKRKSRNLSEKKRRDQFNMLINELCTMVST--NNRKMDKSTVLKSTIAFLK 75
+ KR++ N+ E++RR++ L + NN K K +LK A++
Sbjct: 3 MNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYIL 55
>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 = 43.1 bits (102), Expect = 3e-07
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 28 KRKSRNLSEKKRRDQFNMLINELCTMV-STNNRKMDKSTVLKSTIAFLK 75
KR N E+KRRD + L V S K ++ +L +++
Sbjct: 2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQ 50
>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 = 34.0 bits (78), Expect = 8e-04
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 2/50 (4%)
Query: 29 RKSRNLSEKKRRDQFNMLINELCTMV--STNNRKMDKSTVLKSTIAFLKN 76
R + N EK RR + + +L +V ++ + ++L +K
Sbjct: 2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKK 51
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 34.7 bits (79), Expect = 0.002
Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 11/57 (19%)
Query: 23 DKDD-SKRKSRNLSEKKRR--DQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKN 76
+ D SK + EK ++ +++N +E NNR DK AF +
Sbjct: 100 ELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADK--------AFYQQ 148
>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 = 32.5 bits (74), Expect = 0.002
Identities = 10/55 (18%), Positives = 30/55 (54%), Gaps = 6/55 (10%)
Query: 28 KRKSRNLSEKKRRDQFNMLINELCTMV------STNNRKMDKSTVLKSTIAFLKN 76
KR+S +E+ RR++ + ++EL +++ + K+T +++ ++++
Sbjct: 2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRH 56
>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 = 33.7 bits (76), Expect = 0.005
Identities = 15/108 (13%), Positives = 39/108 (36%), Gaps = 22/108 (20%)
Query: 4 HQLEQSFNRNSDDTMDDTDDKDDSKRKSRNLSEKKRR----------------DQFNMLI 47
+Q++ ++ SD + + + + R L + K + FN +
Sbjct: 207 YQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN--L 264
Query: 48 NELC-TMVSTNNRK-MDKSTVLKSTIAFLKNYNGTYYFGCSLNFFLSA 93
+ C +++T ++ D + +T L +++ T + L
Sbjct: 265 S--CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKY 310
>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic
helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB:
2ql2_A*
Length = 76
Score = 27.5 bits (61), Expect = 0.26
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 3/52 (5%)
Query: 28 KRKSRNLSEKKRRDQFNMLINEL---CTMVSTNNRKMDKSTVLKSTIAFLKN 76
KR N E+KRR N EL C M +++ K +L+ + +
Sbjct: 5 KRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILG 56
>1uax_A Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid
ribonucleotidohydrolase, hydrolase; 2.00A {Pyrococcus
horikoshii} SCOP: c.55.3.1
Length = 220
Score = 26.4 bits (59), Expect = 1.1
Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 4/25 (16%)
Query: 25 DDSKRKSRNLSEKKRRDQFNMLINE 49
DSK+ L+ +R F+ LI+
Sbjct: 39 KDSKQ----LTPGQREKLFSKLIDI 59
>1io2_A Ribonuclease HII; endonuclease, hydrolase; 2.00A {Thermococcus
kodakarensis} SCOP: c.55.3.1 PDB: 2dfh_A 2dff_A 2dfe_A
1x1p_A
Length = 213
Score = 26.0 bits (58), Expect = 1.9
Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 4/25 (16%)
Query: 25 DDSKRKSRNLSEKKRRDQFNMLINE 49
DSK+ L+ K+R FN ++
Sbjct: 39 RDSKK----LTPKRREKLFNEILGV 59
>3qir_A PIWI-like protein 2; structural genomics consortium, SGC, PAZ
domain, RNAI, RNA B RNA binding protein; 2.45A {Homo
sapiens} PDB: 3o7x_A
Length = 148
Score = 25.8 bits (56), Expect = 2.0
Identities = 6/49 (12%), Positives = 13/49 (26%)
Query: 27 SKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLK 75
+ R + +L+ EL M + +K +
Sbjct: 89 HRPSERQDNHGMLLKGEILLLPELSFMTGIPEKMKKDFRAMKDLAQQIN 137
>1eke_A Ribonuclease HII; endonuclease, structural genomics, BSGC
structure funded by NIH, protein structure initiative,
PSI; HET: MES; 2.00A {Methanocaldococcus jannaschii}
SCOP: c.55.3.1
Length = 230
Score = 25.0 bits (55), Expect = 3.7
Identities = 8/24 (33%), Positives = 11/24 (45%), Gaps = 4/24 (16%)
Query: 25 DDSKRKSRNLSEKKRRDQFNMLIN 48
DSK L++ KR +L N
Sbjct: 39 KDSKE----LTKNKRAYLKKLLEN 58
>2wdq_A Succinate dehydrogenase flavoprotein subunit; succinate
dehydrogenase activity, cell inner membrane, trica acid
cycle; HET: FAD HEM CBE; 2.40A {Escherichia coli} PDB:
1nen_A* 2acz_A* 1nek_A* 2wdr_A* 2wdv_A* 2wp9_A* 2ws3_A*
2wu2_A* 2wu5_A*
Length = 588
Score = 24.9 bits (55), Expect = 5.7
Identities = 6/17 (35%), Positives = 8/17 (47%)
Query: 44 NMLINELCTMVSTNNRK 60
N++ T VS N R
Sbjct: 518 NLMETAYATAVSANFRT 534
>3kio_A Ribonuclease H2 subunit A; aicardi-goutieres syndrome, RNAse H2,
protein complex, autoimmune disease, endonuclease,
hydrolase, metal-binding; 2.90A {Mus musculus} PDB:
3p5j_A 3puf_A 3p56_A
Length = 301
Score = 24.5 bits (53), Expect = 6.7
Identities = 7/25 (28%), Positives = 11/25 (44%), Gaps = 4/25 (16%)
Query: 25 DDSKRKSRNLSEKKRRDQFNMLINE 49
DSK L+E +R F + +
Sbjct: 66 ADSK----TLTENERERLFAKMEED 86
>2wt7_A Proto-oncogene protein C-FOS; transcription, transcription
regulation, nucleus, activator, repressor, DNA-binding,
phosphoprotein, differentiation; 2.30A {Mus musculus}
PDB: 1fos_E* 1a02_F* 1s9k_D
Length = 63
Score = 23.6 bits (51), Expect = 7.1
Identities = 8/48 (16%), Positives = 15/48 (31%), Gaps = 4/48 (8%)
Query: 29 RKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKN 76
K R +RR+ + L E + + + L L+
Sbjct: 15 AKCR----NRRRELTDTLQAETDQLEDEKSALQTEIANLLKEKEKLEF 58
>2h88_A Succinate dehydrogenase flavoprotein subunit; complex II, membrane
protein, heme protein, iron sulfur PROT cytochrome B,
oxidoreductase; HET: FAD BHG HEM UNL; 1.74A {Gallus
gallus} PDB: 1yq4_A* 1yq3_A* 2fbw_A* 2h89_A* 2wqy_A*
1zoy_A* 1zp0_A* 3abv_A* 3ae1_A* 3ae2_A* 3ae3_A* 3ae4_A*
3ae5_A* 3ae6_A* 3ae7_A* 3ae8_A* 3ae9_A* 3aea_A* 3aeb_A*
3aec_A* ...
Length = 621
Score = 24.6 bits (54), Expect = 7.4
Identities = 5/17 (29%), Positives = 9/17 (52%)
Query: 44 NMLINELCTMVSTNNRK 60
N+++ L T+ RK
Sbjct: 527 NLMLCALQTIYGAEARK 543
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
0.315 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: 1,203,363
Number of extensions: 50494
Number of successful extensions: 167
Number of sequences better than 10.0: 1
Number of HSP's gapped: 163
Number of HSP's successfully gapped: 31
Length of query: 95
Length of database: 6,701,793
Length adjustment: 62
Effective length of query: 33
Effective length of database: 4,970,691
Effective search space: 164032803
Effective search space used: 164032803
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (23.8 bits)