RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10347
(67 letters)
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 62.7 bits (152), Expect = 9e-14
Identities = 26/57 (45%), Positives = 36/57 (63%)
Query: 1 MTAYITELSDMVPTCSALARKPDKLTILRMAVAHMKALRVTAVNTFRHHSQPWLFVH 57
M ++I EL+ +VPTC+A++RK DKLT+LRMAV HMK LR + +P
Sbjct: 28 MNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTEANYKPTFLSD 84
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH,
PAS, circadian rhythm proteins, transcription-activato;
2.27A {Mus musculus}
Length = 361
Score = 55.7 bits (134), Expect = 3e-11
Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 3/63 (4%)
Query: 1 MTAYITELSDMVPTCSALARKPDKLTILRMAVAHMKALRVTAVNTFRHHSQPWLFVHFGQ 60
I EL M+P + RK DK T+L+ ++ ++ + T + + F
Sbjct: 27 FNVLIKELGSMLPGNA---RKMDKSTVLQKSIDFLRKHKETTAQSDASEIRQDWKPTFLS 83
Query: 61 NID 63
N +
Sbjct: 84 NEE 86
>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 = 47.3 bits (113), Expect = 2e-09
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 1 MTAYITELSDMVPTCSALAR--KPDKLTILRMAVAHMKALR 39
+ +I +LS ++P S + K IL A +++ LR
Sbjct: 20 INNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60
>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 = 36.5 bits (85), Expect = 4e-05
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 2/35 (5%)
Query: 5 ITELSDMVPTCSALARKPDKLTILRMAVAHMKALR 39
L D VP+ K + IL A +++ +R
Sbjct: 31 FHSLRDSVPSLQ--GEKASRAQILDKATEYIQYMR 63
>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 = 35.8 bits (83), Expect = 9e-05
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 5 ITELSDMVPTCSALARKPDKLTILRMAVAHMKALR 39
I EL D+V A K +K +LR A+ +++ L+
Sbjct: 25 IIELKDLVVGTEA---KLNKSAVLRKAIDYIRFLQ 56
>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 = 35.0 bits (81), Expect = 2e-04
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 2/35 (5%)
Query: 5 ITELSDMVPTCSALARKPDKLTILRMAVAHMKALR 39
L D VP+ K + IL A +++ +R
Sbjct: 21 FHSLRDSVPSLQ--GEKASRAQILDKATEYIQYMR 53
>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 = 33.2 bits (76), Expect = 6e-04
Identities = 8/42 (19%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 1 MTAYITELSDMVPTC---SALARKPDKLTILRMAVAHMKALR 39
+ + EL+ ++P ++ P K T + A +++ L+
Sbjct: 17 LAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQ 58
>2ql2_B Neurod1, neurogenic differentiation factor 1;
basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}
Length = 60
Score = 25.7 bits (57), Expect = 0.45
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 7 ELSDMVPTCSALARKPDKLTILRMAVAHMKAL 38
L +VP S +K K+ LR+A ++ AL
Sbjct: 23 NLRKVVPCYSK-TQKLSKIETLRLAKNYIWAL 53
>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic
helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB:
2ql2_A*
Length = 76
Score = 26.0 bits (57), Expect = 0.48
Identities = 14/49 (28%), Positives = 18/49 (36%), Gaps = 4/49 (8%)
Query: 7 ELSDMVPTCSALARKPDKLTILRMAVAHMKAL----RVTAVNTFRHHSQ 51
EL M + KL IL+ AV + L R +N HH
Sbjct: 26 ELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNLNPLNHHHH 74
>3cnx_A Uncharacterized protein; putative dehydratase, NTF2-like protein,
structural genomics center for structural genomics,
JCSG; HET: MSE PGE PG6; 2.10A {Streptomyces avermitilis}
SCOP: d.17.4.17
Length = 170
Score = 24.9 bits (53), Expect = 2.1
Identities = 8/44 (18%), Positives = 11/44 (25%)
Query: 14 TCSALARKPDKLTILRMAVAHMKALRVTAVNTFRHHSQPWLFVH 57
TC+ + + V A N FR W
Sbjct: 107 TCTENILSGGPPPDDSDELGPLVGQLVVATNVFRRTPDGWKLWS 150
>2r5u_A Replicative DNA helicase; DNAB, primase, replication, ATP-binding,
autocatal cleavage, DNA replication, DNA-binding,
endonuclease; 1.90A {Mycobacterium tuberculosis}
Length = 200
Score = 24.2 bits (53), Expect = 3.4
Identities = 5/12 (41%), Positives = 6/12 (50%)
Query: 3 AYITELSDMVPT 14
Y+ L VPT
Sbjct: 104 PYLHTLISTVPT 115
>3dip_A Enolase; structural genomics, isomerase, PSI-2, protein structure
initiative, NEW YORK SGX research center for structural
genomics, NYSGXRC, lyase; HET: SIC; 2.50A
{Unidentified}
Length = 410
Score = 24.2 bits (53), Expect = 3.7
Identities = 8/23 (34%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 35 MKALRVTAVNTFRHHSQP-WLFV 56
M R+TA+ T R +P ++V
Sbjct: 1 MSLPRITALRTIRLPERPKLIWV 23
>1b79_A DNAB helicase; hexamer, DNA replication, hydrolase; 2.30A
{Escherichia coli} SCOP: a.81.1.1 PDB: 1jwe_A
Length = 119
Score = 23.7 bits (52), Expect = 5.0
Identities = 6/12 (50%), Positives = 8/12 (66%)
Query: 3 AYITELSDMVPT 14
AY+ ELS P+
Sbjct: 94 AYLAELSKNTPS 105
>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A
{Bacillus phage SPP1}
Length = 444
Score = 23.6 bits (52), Expect = 6.1
Identities = 5/12 (41%), Positives = 8/12 (66%)
Query: 3 AYITELSDMVPT 14
Y+TEL+ V +
Sbjct: 84 GYLTELAASVAS 95
>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A
{Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A
2r6e_A 2vyf_A 2vye_A
Length = 454
Score = 23.7 bits (52), Expect = 6.3
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 3 AYITELSDMVPT 14
+Y++EL+D VPT
Sbjct: 87 SYLSELADAVPT 98
>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus
aquaticus}
Length = 444
Score = 23.6 bits (52), Expect = 6.4
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 3 AYITELSDMVPT 14
AY+ +LS+ PT
Sbjct: 84 AYLLQLSEATPT 95
>1sqg_A SUN protein, FMU protein; rossmann-fold, mixed beta sheet,
methyltransferase-fold, RNA-binding domain; 1.65A
{Escherichia coli} SCOP: a.79.1.3 c.66.1.38 PDB: 1sqf_A
Length = 429
Score = 23.3 bits (51), Expect = 8.5
Identities = 4/39 (10%), Positives = 13/39 (33%), Gaps = 9/39 (23%)
Query: 16 SALARKPDK------LTILRMAVAHMKALRV---TAVNT 45
+ L +P ++ + + + R+ A+
Sbjct: 63 NKLMARPMTGKQRTVHYLIMVGLYQLLYTRIPPHAALAE 101
>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 = 22.3 bits (48), Expect = 8.9
Identities = 8/26 (30%), Positives = 16/26 (61%)
Query: 14 TCSALARKPDKLTILRMAVAHMKALR 39
T S ++ K+ ILR A+ +++ L+
Sbjct: 38 TSSNPNQRLPKVEILRNAIRYIEGLQ 63
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
0.329 0.134 0.414
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: 1,044,032
Number of extensions: 47083
Number of successful extensions: 148
Number of sequences better than 10.0: 1
Number of HSP's gapped: 146
Number of HSP's successfully gapped: 18
Length of query: 67
Length of database: 6,701,793
Length adjustment: 38
Effective length of query: 29
Effective length of database: 5,640,795
Effective search space: 163583055
Effective search space used: 163583055
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 51 (23.8 bits)