RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8988
(133 letters)
>2ql2_B Neurod1, neurogenic differentiation factor 1;
basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}
Length = 60
Score = 94.6 bits (236), Expect = 3e-27
Identities = 30/58 (51%), Positives = 40/58 (68%)
Query: 42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLH 99
++R AN RER RM LN A D LR+ VP ++ ++LS+IETLRLA YI +SE+L
Sbjct: 1 SRRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR 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 = 89.7 bits (223), Expect = 4e-25
Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 33 KTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYIS 92
+ +R+ +R+AA +RERRR+ +NEAF+ L+R + +RL ++E LR AI YI
Sbjct: 2 ELKRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNP-NQRLPKVEILRNAIRYIE 60
Query: 93 FMSELLH 99
+ LL
Sbjct: 61 GLQALLR 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 = 15/58 (25%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 43 QRRAANIRERRRMFNLNEAFDKLRRK-VPTFAYEKRLSRIETLRLAITYISFMSELLH 99
+R N ER+R ++NEAF +L R +K +++ L+ A+ I + + +
Sbjct: 5 KRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVR 62
>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 = 49.3 bits (118), Expect = 4e-09
Identities = 15/51 (29%), Positives = 26/51 (50%)
Query: 44 RRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFM 94
RR N+ ER+R L +F LR ++P ++ ++ L+ A YI +
Sbjct: 7 RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSV 57
>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 = 45.8 bits (109), Expect = 7e-08
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 44 RRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFM 94
R N ER+R ++ ++F LR VP+ EK SR + L A YI +M
Sbjct: 13 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEK-ASRAQILDKATEYIQYM 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 = 44.7 bits (106), Expect = 2e-07
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFM 94
+R N ER+R ++ ++F LR VP+ EK SR + L A YI +M
Sbjct: 2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKA-SRAQILDKATEYIQYM 52
>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 = 44.0 bits (104), Expect = 3e-07
Identities = 13/53 (24%), Positives = 23/53 (43%)
Query: 44 RRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSE 96
R N E+ R +L + +KL+ VP R + + L A +I + +
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 = 42.4 bits (100), Expect = 1e-06
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 42 AQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFM 94
+R A N E+R ++N+ +L+ V E +L++ LR AI YI F+
Sbjct: 5 EKRTAHNAIEKRYRSSINDKIIELKDLVV--GTEAKLNKSAVLRKAIDYIRFL 55
>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 = 39.3 bits (91), Expect = 2e-05
Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 36 RRVATLAQRRAANIRERRRM-FNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYI 91
+ + + E + ++N + +LR VP +LS++E L+ I YI
Sbjct: 6 HHHSHMGGGKGPAAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYI 62
>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 = 38.9 bits (91), Expect = 3e-05
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 4/56 (7%)
Query: 43 QRRAA-NIRERRRMFNLNEAFDKLRRKVPTFAYE---KRLSRIETLRLAITYISFM 94
+RRA N ERRR +N +L + +P + E S+ L A YI +
Sbjct: 4 KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59
>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 = 38.5 bits (89), Expect = 3e-04
Identities = 23/148 (15%), Positives = 46/148 (31%), Gaps = 42/148 (28%)
Query: 3 KSKAILECLFNGRLSGHGGSSTGTNGGHTKKTRRRVATLAQRRAANIRERRRM--F---- 56
K+K +++ R+ K+ + + A RA + + F
Sbjct: 118 KTKELIKNYITARI-------------MAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQG 164
Query: 57 NLNEAFDKLRRKVPTFAYEKRLSRIETLRLAITYISFMSELLHGTPNGSTSGSPIYQ--- 113
N ++ F++LR Y+ + L I F +E L + ++
Sbjct: 165 NTDDYFEELRD-----LYQTYHVLVGDL------IKFSAETLSELIRTTLDAEKVFTQGL 213
Query: 114 -----MSQREYIP---YTALVP-TYPAI 132
+ P Y +P + P I
Sbjct: 214 NILEWLENPSNTPDKDYLLSIPISCPLI 241
Score = 27.7 bits (61), Expect = 1.6
Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 5/52 (9%)
Query: 58 LNEAFDK-LRRKVPTFAYEKRL-SRIETLRLAITYISFMSELLHGTPNGSTS 107
L E F+K L FA + + E L ++ ++S L+ + G
Sbjct: 33 LQEQFNKILPEPTEGFAADDEPTTPAE---LVGKFLGYVSSLVEPSKVGQFD 81
>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 = 37.1 bits (85), Expect = 8e-04
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 19/58 (32%)
Query: 49 IRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETLRLAI------TYISFMSELLHG 100
I +R R++N N+ F K V RL LR A+ + L+ G
Sbjct: 113 IEQRDRLYNDNQVFAK--YNVS------RLQPYLKLRQALLELRPAKNV-----LIDG 157
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS,
circadian rhythm proteins, transcription-activato; 2.27A
{Mus musculus}
Length = 361
Score = 31.5 bits (71), Expect = 0.066
Identities = 13/86 (15%), Positives = 28/86 (32%), Gaps = 9/86 (10%)
Query: 25 GTNGGHTKKTRRRVATLAQRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEKRLSRIETL 84
G K +RV+ N E++R N +L +P +++ + L
Sbjct: 1 GAVEEDDKDKAKRVSR-------NKSEKKRRDQFNVLIKELGSMLP--GNARKMDKSTVL 51
Query: 85 RLAITYISFMSELLHGTPNGSTSGSP 110
+ +I ++ E +
Sbjct: 52 QKSIDFLRKHKETTAQSDASEIRQDW 77
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 30.7 bits (69), Expect = 0.13
Identities = 15/71 (21%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 51 ERRRMFNLNEAFDKLRRKVPT-FAYEKRLSRIETLRLAITYISFMSELLHGTPNGSTSGS 109
E+RR +N D+L VPT A ++L ++ LR+A+ ++ + + + +
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTEANYKPT 80
Query: 110 PIYQMSQREYI 120
+ + I
Sbjct: 81 FLSDDELKHLI 91
>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 = 25.9 bits (57), Expect = 1.3
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 4/53 (7%)
Query: 43 QRRAANIRERRRMFNLNEAFDKLRRKVPTFAYEK----RLSRIETLRLAITYI 91
+R + E+ R L A +L +P ++ S+ T+ A YI
Sbjct: 2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYI 54
>3v5u_A Uncharacterized membrane protein MJ0091; lipid cubic phase, cation
protein complex, sodium,calcium EX membrane protein;
HET: OLC MYS 1PE; 1.90A {Methanocaldococcus jannaschii}
PDB: 3v5s_A*
Length = 320
Score = 26.8 bits (60), Expect = 2.5
Identities = 9/45 (20%), Positives = 18/45 (40%)
Query: 69 VPTFAYEKRLSRIETLRLAITYISFMSELLHGTPNGSTSGSPIYQ 113
+ FA ++ R + + YI ++ L G + GS +
Sbjct: 271 LYLFAKYSKIGRWQGILFLALYIIAIASLRMGGGSLVPRGSRSHH 315
>3czx_A Putative N-acetylmuramoyl-L-alanine amidase; structural genomics,
PSI, MCSG, protein structure initiative; 1.60A
{Neisseria meningitidis MC58}
Length = 182
Score = 25.3 bits (56), Expect = 7.0
Identities = 8/43 (18%), Positives = 13/43 (30%), Gaps = 7/43 (16%)
Query: 18 GHGGSSTGTNGGHTK------KTRRRVAT-LAQRRAANIRERR 53
GH + G G + R VA+ L ++
Sbjct: 11 GHSNTDPGAVNGSDREADLAQDMRNIVASILRNDYGLTVKTDG 53
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
0.319 0.133 0.380
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: 2,048,824
Number of extensions: 114530
Number of successful extensions: 245
Number of sequences better than 10.0: 1
Number of HSP's gapped: 240
Number of HSP's successfully gapped: 24
Length of query: 133
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 50
Effective length of database: 4,384,350
Effective search space: 219217500
Effective search space used: 219217500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.2 bits)