RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5916
(190 letters)
>2ql2_B Neurod1, neurogenic differentiation factor 1;
basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}
Length = 60
Score = 86.2 bits (214), Expect = 4e-23
Identities = 32/58 (55%), Positives = 36/58 (62%), Gaps = 2/58 (3%)
Query: 86 RLNINARERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYILMQANALE 143
R+ NARER RMH LN ALD LR V+P +KLSKI TL LAKNYI + L
Sbjct: 3 RMKANARERNRMHGLNAALDNLRKVVP--CYSKTQKLSKIETLRLAKNYIWALSEILR 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 = 69.7 bits (171), Expect = 2e-16
Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 3/68 (4%)
Query: 77 KKNRQGKTVRLNINARERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYIL 136
K+ R RERRR+ +N+A + L+ + ++L K+ L A YI
Sbjct: 4 KRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPN---QRLPKVEILRNAIRYIE 60
Query: 137 MQANALEE 144
L +
Sbjct: 61 GLQALLRD 68
>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic
helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB:
2ql2_A*
Length = 76
Score = 57.2 bits (138), Expect = 9e-12
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 86 RLNINARERRRMHDLNDALDEL-RAVIPYAHSPSVRKLSKIATLLLAKNYILMQANALEE 144
R + NA ER+R D+N+A EL R H S + +K+ L A I LE+
Sbjct: 6 RAHHNALERKRRRDINEAFRELGRMCQM--HLKSDKAQTKLLILQQAVQVI----LGLEQ 59
Query: 145 LRR 147
R
Sbjct: 60 QVR 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 = 48.5 bits (116), Expect = 3e-08
Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 2/70 (2%)
Query: 86 RLNINARERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYILMQANALEEL 145
R N ER+R ++L + LR IP + K K+ L A YIL ++L
Sbjct: 7 RRTHNVLERQRRNELKRSFFALRDQIP--ELENNEKAPKVVILKKATAYILSVQAEEQKL 64
Query: 146 RRIITYIQAQ 155
++ +
Sbjct: 65 ISEEDLLRKR 74
>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 = 46.7 bits (111), Expect = 9e-08
Identities = 14/66 (21%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 90 NARERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYILMQANALEELRRII 149
N E+ R L +L++L+ ++P P + + ++ L AK +I ++ + I
Sbjct: 6 NEMEKNRRAHLRLSLEKLKGLVPL--GPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQI 63
Query: 150 TYIQAQ 155
+Q +
Sbjct: 64 DQLQRE 69
>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 = 44.3 bits (105), Expect = 7e-07
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 10/77 (12%)
Query: 86 RLNINARERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYI--LMQANA-- 141
R + NA ER+R + D+ LR +P S K S+ L A YI + + N
Sbjct: 3 RAHHNALERKRRDHIKDSFHSLRDSVP---SLQGEKASRAQILDKATEYIQYMRRKNHTH 59
Query: 142 ---LEELRRIITYIQAQ 155
+++L+R ++ Q
Sbjct: 60 QQDIDDLKRQNALLEQQ 76
>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 = 43.5 bits (103), Expect = 1e-06
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 10/69 (14%)
Query: 86 RLNINARERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYI--LMQANA-- 141
R + NA ER+R + D+ LR +P S K S+ L A YI + + N
Sbjct: 13 RAHHNALERKRRDHIKDSFHSLRDSVP---SLQGEKASRAQILDKATEYIQYMRRKNHTH 69
Query: 142 ---LEELRR 147
+++L+R
Sbjct: 70 QQDIDDLKR 78
>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 = 40.0 bits (94), Expect = 2e-05
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 86 RLNINARERRRMHDLNDALDELRAVIPYAHSPSVR-KLSKIATLLLAKNYI 135
R N ERRR +N+ + +L +IP + S + SK L A +YI
Sbjct: 6 RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYI 56
>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 = 40.1 bits (94), Expect = 3e-05
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 90 NARERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYI 135
NA E+R +ND + EL+ ++ + KL+K A L A +YI
Sbjct: 11 NAIEKRYRSSINDKIIELKDLVVGTEA----KLNKSAVLRKAIDYI 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 = 36.7 bits (85), Expect = 3e-04
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 93 ERRRMHDLNDALDELRAVIP--YAHSPSVRKLSKIATLLLAKNYI--LMQANA 141
E+ R + L AL EL ++IP + SK T+ A YI L Q +
Sbjct: 10 EQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62
>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 = 37.5 bits (86), Expect = 0.002
Identities = 31/193 (16%), Positives = 52/193 (26%), Gaps = 55/193 (28%)
Query: 22 PLGNV---GLGGF-----------------YFPPSVSAVSAGPPSDENCPEHLSHNSRFQ 61
P NV G+ G + ++ + N PE +
Sbjct: 149 PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLK---NCNSPETV------- 198
Query: 62 DPTHSGAMGSLQPLAKKNRQGKTVRLNINARERRRMHDLNDALDELRAVIPYAHS----- 116
+ LQ L + T R + ++ + R+H + L L PY +
Sbjct: 199 -------LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL 251
Query: 117 ----PSVRKL----SKIATLLLAKNYILMQANALEELRRI-ITYIQAQGTMTMPPGFDLQ 167
KI LL + + + L I+ T+T L
Sbjct: 252 NVQNAKAWNAFNLSCKI--LLTTRFKQV--TDFLSAATTTHISLDHHSMTLTPDEVKSLL 307
Query: 168 ATMLPVQQPDTPP 180
L + D P
Sbjct: 308 LKYLDCRPQDLPR 320
Score = 34.4 bits (78), Expect = 0.017
Identities = 8/59 (13%), Positives = 23/59 (38%), Gaps = 16/59 (27%)
Query: 99 DLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYILMQANALEELRRIITYIQAQGT 157
D D D ++++ S ++ ++I+M +A+ R+ + ++
Sbjct: 34 DCKDVQDMPKSIL------SKEEI----------DHIIMSKDAVSGTLRLFWTLLSKQE 76
>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 = 36.6 bits (84), Expect = 0.004
Identities = 18/93 (19%), Positives = 27/93 (29%), Gaps = 25/93 (26%)
Query: 101 NDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYILMQANALEELRRIITYIQAQGTMTM 160
+D +ELR + Y L + I A L EL R
Sbjct: 167 DDYFEELRDL--YQTYHV-----------LVGDLIKFSAETLSELIR----TTLDAEKVF 209
Query: 161 PPGFDLQATMLPVQQPDTPPPS---TSDPSNVS 190
G ++ + + P P S P +S
Sbjct: 210 TQGLNILEWL---ENPSNTPDKDYLLSIP--IS 237
Score = 31.9 bits (72), Expect = 0.14
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 6/35 (17%)
Query: 62 DPTH-----SGAMGSLQPLAKKNRQGKTVRLNINA 91
TH G L L +N+ G VR+ I A
Sbjct: 497 KATHILDFGPGGASGLGVLTHRNKDGTGVRV-IVA 530
Score = 29.6 bits (66), Expect = 0.73
Identities = 25/140 (17%), Positives = 49/140 (35%), Gaps = 49/140 (35%)
Query: 65 HS-----------GAMGSLQPLAK--KNRQGKTVRLNI----NARERRRMHDLND----- 102
HS M S++ L + R G T+++ + R M +N
Sbjct: 1762 HSLGEYAALASLADVM-SIESLVEVVFYR-GMTMQVAVPRDELGRSNYGMIAINPGRVAA 1819
Query: 103 --ALDELRAVIPYAHSPSVRKLSKIATLLL--AKNYIL--MQ------ANALEELRRIIT 150
+ + L+ V V ++ K L+ NY + Q AL+ + ++
Sbjct: 1820 SFSQEALQYV--------VERVGKRTGWLVEIV-NYNVENQQYVAAGDLRALDTVTNVLN 1870
Query: 151 YIQAQGTMTMPPGFDLQATM 170
+I+ Q + LQ ++
Sbjct: 1871 FIKLQKIDIIE----LQKSL 1886
Score = 29.6 bits (66), Expect = 0.79
Identities = 30/173 (17%), Positives = 47/173 (27%), Gaps = 62/173 (35%)
Query: 40 VSAGPPSDENCPEHLSH-NSRFQDPTHSGAMGSLQ---PLAKKNRQGKTVRLNINARERR 95
V +GPP L N + G Q P +++ + L + +
Sbjct: 378 VVSGPPQS------LYGLNLTLRK--AKAPSGLDQSRIPFSERKLKFSNRFLPVAS---- 425
Query: 96 RMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYILMQANALEELRRIITYIQAQ 155
P+ HS + S + L KN + A + +I Y
Sbjct: 426 ----------------PF-HSHLLVPASDLINKDLVKNNVSFNAKDI----QIPVY---- 460
Query: 156 GTMTMPPGFDLQA-------------TMLPVQQPDTPPPSTS-----DPSNVS 190
T G DL+ LPV+ T + P S
Sbjct: 461 DTFD---GSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGAS 510
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS,
circadian rhythm proteins, transcription-activato; 2.27A
{Mus musculus}
Length = 361
Score = 33.0 bits (75), Expect = 0.044
Identities = 13/70 (18%), Positives = 31/70 (44%), Gaps = 10/70 (14%)
Query: 70 GSLQPLAKKNRQGKTVRLNINARERRRMHD-LNDALDELRAVIPYAHSPSVRKLSKIATL 128
G+++ K + + + ++RR D N + EL +++P + RK+ K L
Sbjct: 1 GAVEEDDKDKAKRVSRN---KSEKKRR--DQFNVLIKELGSMLP----GNARKMDKSTVL 51
Query: 129 LLAKNYILMQ 138
+ +++
Sbjct: 52 QKSIDFLRKH 61
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 33.1 bits (75), Expect = 0.045
Identities = 17/60 (28%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 76 AKKNRQGKTVRLNINARERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYI 135
A+ + K R + E+RR +N +DEL +++P ++ RKL K+ L +A ++
Sbjct: 4 AEHQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNA-MSRKLDKLTVLRMAVQHM 62
>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding
protein; NMR {Erwinia amylovora} SCOP: a.4.6.2
Length = 99
Score = 26.9 bits (60), Expect = 2.0
Identities = 7/30 (23%), Positives = 11/30 (36%)
Query: 26 VGLGGFYFPPSVSAVSAGPPSDENCPEHLS 55
G Y P SV+ + + + LS
Sbjct: 7 HHHHGSYTPESVAKLLEKISAGGYGDKRLS 36
>3rac_A Histidine-tRNA ligase; structural genomics, PSI-biology, midwest
center for structu genomics, MCSG, PSI-BIO; 2.30A
{Alicyclobacillus acidocaldarius subsp}
Length = 373
Score = 27.7 bits (62), Expect = 2.1
Identities = 15/96 (15%), Positives = 29/96 (30%), Gaps = 7/96 (7%)
Query: 75 LAKKNRQG-KTVRLNINARER---RRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLL 130
L N + + A++ + + A + A + L + A
Sbjct: 213 LTSGNYVQFRELWQLHAAKDVDLLANLLTWSPAERDAAKRSREASDRELEALLRDAVDPR 272
Query: 131 AKNYILMQANALEELRRIITYIQAQGTMTMPPGFDL 166
A + +A L R+ + G + FDL
Sbjct: 273 AAADVR---DAWRYLCRLAEALHDSGLASDVVTFDL 305
>1sjj_A Actinin; 3-helix bundle, calponin homology domain, calmodulin-like
domain, actin binding protein, contractIle protein;
20.00A {Gallus gallus} SCOP: i.15.1.1
Length = 863
Score = 27.2 bits (59), Expect = 4.1
Identities = 10/73 (13%), Positives = 24/73 (32%), Gaps = 7/73 (9%)
Query: 90 NARERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYILMQANALEELRRII 149
N M + ++L I R ++++ +L ++ + + E R
Sbjct: 679 NKHTNYTMEHIRVGWEQLLTTI-------ARTINEVENQILTRDAKGISQEQMNEFRASF 731
Query: 150 TYIQAQGTMTMPP 162
+ + T M
Sbjct: 732 NHFDRKKTGMMDC 744
>1nh8_A ATP phosphoribosyltransferase; prtase, de novo His biosynthesis,
PRPP, structural genomics, PSI, protei structure
initiative; HET: AMP HIS; 1.80A {Mycobacterium
tuberculosis H37RV} SCOP: c.94.1.1 d.58.5.3 PDB: 1nh7_A*
Length = 304
Score = 26.9 bits (60), Expect = 4.2
Identities = 9/39 (23%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 89 INARERRRMHDLN---DALDELRAVIPYAHSPSVRKLSK 124
+ ++ M D + AL + A+ P SP++ L+
Sbjct: 227 VFGQQYL-MLDYDCPRSALKKATAITPGLESPTIAPLAD 264
>3jv7_A ADH-A; dehydrogenase, nucleotide binding, rossmann-fold,
oxidoreduc; HET: NAD; 2.00A {Rhodococcus ruber} PDB:
2xaa_A*
Length = 345
Score = 26.8 bits (60), Expect = 4.8
Identities = 7/39 (17%), Positives = 14/39 (35%), Gaps = 11/39 (28%)
Query: 80 RQGKTVRLNINARERRRMHDLNDALDEL-------RAVI 111
R G+ + ++ E + + A L R V+
Sbjct: 309 RAGR-LDIHT---ETFTLDEGPAAYRRLREGSIRGRGVV 343
>1h2b_A Alcohol dehydrogenase; oxidoreductase, archaea, hyperthermophIle,
zinc; HET: OCA NAJ; 1.62A {Aeropyrum pernix} SCOP:
b.35.1.2 c.2.1.1
Length = 359
Score = 26.5 bits (59), Expect = 6.5
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 11/39 (28%)
Query: 80 RQGKTVRLNINARERRRMHDLNDALDEL-------RAVI 111
QGK VR+ + + ++ ++ND L+ L RAV+
Sbjct: 323 LQGK-VRVEV---DIHKLDEINDVLERLEKGEVLGRAVL 357
>1h3d_A ATP-phosphoribosyltransferase; hisitidine biosynthesis,
glycosyltransferase; HET: AMP TLA; 2.7A {Escherichia
coli} SCOP: c.94.1.1 d.58.5.3 PDB: 1q1k_A*
Length = 299
Score = 26.5 bits (59), Expect = 6.8
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 89 INARERRRMHDLN---DALDELRAVIPYAHSPSVRKLSK 124
I ARE + ++ + LDE+ A++P A P++ L+
Sbjct: 221 IQARESK-YIMMHAPTERLDEVIALLPGAERPTILPLAG 258
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 25.7 bits (55), Expect = 7.7
Identities = 6/33 (18%), Positives = 15/33 (45%), Gaps = 11/33 (33%)
Query: 143 EELRRIITYIQAQGTMTM--P---PGFDLQATM 170
+ L+++ Q ++ + P ++ATM
Sbjct: 20 QALKKL------QASLKLYADDSAPALAIKATM 46
>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA
replication, MCM complex, AAA+ Pro ATP-binding,
DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}
Length = 595
Score = 26.1 bits (58), Expect = 8.3
Identities = 12/47 (25%), Positives = 20/47 (42%)
Query: 104 LDELRAVIPYAHSPSVRKLSKIATLLLAKNYILMQANALEELRRIIT 150
+D LR I YA K++ A L+ ++ M+ + E I
Sbjct: 504 IDTLRKYIAYARKYVTPKITSEAKNLITDFFVEMRKKSSETPDSPIL 550
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 0.130 0.376
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: 2,889,454
Number of extensions: 165769
Number of successful extensions: 354
Number of sequences better than 10.0: 1
Number of HSP's gapped: 348
Number of HSP's successfully gapped: 30
Length of query: 190
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 102
Effective length of database: 4,244,745
Effective search space: 432963990
Effective search space used: 432963990
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: 54 (25.0 bits)