RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2365
(285 letters)
>2ql2_B Neurod1, neurogenic differentiation factor 1;
basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}
Length = 60
Score = 102 bits (256), Expect = 2e-28
Identities = 27/58 (46%), Positives = 36/58 (62%)
Query: 174 RRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMKILET 231
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 = 88.6 bits (220), Expect = 5e-23
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 169 IRVVKRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMKI 228
RR A +ERRR +N AF L+ + P+ +L K++ LR A YI L +
Sbjct: 7 TTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQ-RLPKVEILRNAIRYIEGLQAL 65
Query: 229 LE 230
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 = 68.8 bits (168), Expect = 2e-15
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 172 VKRRNTANKKERRRTQSINNAFSDL-RECIPNVPSDTKLSKIKTLRLATSYISYL 225
+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 = 61.2 bits (149), Expect = 2e-12
Identities = 18/54 (33%), Positives = 30/54 (55%)
Query: 174 RRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMK 227
+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 = 54.3 bits (131), Expect = 4e-10
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 174 RRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMK 227
+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 = 53.9 bits (130), Expect = 6e-10
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 165 DLPIIRVVKRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISY 224
D+ + +R N ER+R I ++F LR+ +P++ K S+ + L AT YI Y
Sbjct: 3 DIEVESDADKRAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQY 61
Query: 225 LMK 227
+ +
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 = 53.3 bits (128), Expect = 1e-09
Identities = 12/53 (22%), Positives = 24/53 (45%)
Query: 175 RNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMK 227
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 = 51.2 bits (123), Expect = 6e-09
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 173 KRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYL 225
++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 = 49.6 bits (119), Expect = 1e-08
Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 173 KRRNTANKKERRRTQSINNAFSDLRECIPNV---PSDTKLSKIKTLRLATSYISYL 225
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 = 37.8 bits (87), Expect = 2e-04
Identities = 16/56 (28%), Positives = 29/56 (51%)
Query: 170 RVVKRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYL 225
+ + A ++ +N+ +S LRE +P VP T+LS+++ L+ YI L
Sbjct: 10 HMGGGKGPAAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDL 65
>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 = 35.9 bits (83), Expect = 8e-04
Identities = 15/62 (24%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 174 RRNTANKKERRRTQSINNAFSDLRECIPNVPSD----TKLSKIKTLRLATSYISYLMKIL 229
+R + E+ R + A +L IP SK T+ A YI +L +
Sbjct: 2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG 61
Query: 230 ET 231
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 = 38.7 bits (89), Expect = 0.002
Identities = 39/254 (15%), Positives = 66/254 (25%), Gaps = 76/254 (29%)
Query: 54 TLSNITT---GATDCIYWSEDMQSPDSRYVTRSMSTSSDGFDEDEDQSERFCPSNDYTKY 110
L +TT TD + + S+ S DE + KY
Sbjct: 268 IL--LTTRFKQVTDFL--------SAATTTHISLDHHSMTLTPDE--VKSLL-----LKY 310
Query: 111 YYQDGVGPGAYPNVKHIVEPSYVNLDTATKTLRTVSKAGSIKSSLGNHKNRRIPDLPIIR 170
P P P +++ I S+ +
Sbjct: 311 L---DCRPQDLPREVLTTNPRRLSI---------------IAESIRDGLAT-------WD 345
Query: 171 VVKRRNTANKKERRRTQSINN-AFSDLREC------IP---NVPSDT------KLSKIKT 214
K N +K S+N ++ R+ P ++P+ + K
Sbjct: 346 NWKHVNC-DKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDV 404
Query: 215 LRLATSYISYLMKILETDD---IISIDDFKADLSNHSS-----HRKNKSQYDSPSEISSN 266
+ + Y + +E ISI +L HR Y+ P S+
Sbjct: 405 MVVVNKLHKYSL--VEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD 462
Query: 267 QSSQYVMDPSCQQY 280
+D QY
Sbjct: 463 DLIPPYLD----QY 472
Score = 37.1 bits (85), Expect = 0.007
Identities = 23/170 (13%), Positives = 59/170 (34%), Gaps = 20/170 (11%)
Query: 123 NVKHIVEPSYVNLDTATKTLRTVSKAGSIKSSLGNH-KNRRIPD-LPIIRVVKRRNTANK 180
+ + ++P++ + + ++ + SI++ L K++ + L ++ V+ N
Sbjct: 204 KLLYQIDPNWTSRSDHSSNIK--LRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNA 261
Query: 181 KERR-------RTQSINNAFSDLREC-IPNVPSDTKLSKIKTLRLATSYISYLMKIL--E 230
R + + + S I L+ + L Y+ + L E
Sbjct: 262 FNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPRE 321
Query: 231 TDDI----ISIDDFKADLSNHSSHRKNKSQYDSPSEISSNQSSQYVMDPS 276
+SI + + + N + + +SS V++P+
Sbjct: 322 VLTTNPRRLSI--IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPA 369
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS,
circadian rhythm proteins, transcription-activato; 2.27A
{Mus musculus}
Length = 361
Score = 38.0 bits (88), Expect = 0.003
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 173 KRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYI 222
KR + +++RR Q N +L +P K+ K L+ + ++
Sbjct: 12 KRVSRNKSEKKRRDQ-FNVLIKELGSMLPGNAR--KMDKSTVLQKSIDFL 58
>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 = 0.009
Identities = 36/149 (24%), Positives = 45/149 (30%), Gaps = 55/149 (36%)
Query: 22 YNTPNNNVMSYNSGYHPPPLYTAGPPEDKHG--ATLSNITTGATDCIYWSEDMQS--PDS 77
N N V+S GPP+ +G TL + D QS P S
Sbjct: 371 VNGAKNLVVS-------------GPPQSLYGLNLTLRKAKAPSG------LD-QSRIPFS 410
Query: 78 -RYVTRSMSTSSDGFDEDEDQSERFCP------S---NDYTKYYYQDGVGPGAYPNVKHI 127
R + S RF P S + +D V N K I
Sbjct: 411 ERKLKFSN---------------RFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDI 455
Query: 128 VEPSYVNLDTAT-KTLRTVSKAGSIKSSL 155
P Y DT LR +S GSI +
Sbjct: 456 QIPVY---DTFDGSDLRVLS--GSISERI 479
Score = 28.9 bits (64), Expect = 2.9
Identities = 23/151 (15%), Positives = 45/151 (29%), Gaps = 46/151 (30%)
Query: 81 TRSMSTSSDGFDEDEDQS---E---RFCPSNDYTKYYYQDGVGPGAYPNVKHIV----EP 130
+ + ++GF D++ + E +F Y + G + V ++ E
Sbjct: 38 NKILPEPTEGFAADDEPTTPAELVGKFL---GYVSSLVEPS-KVGQFDQVLNLCLTEFEN 93
Query: 131 SY----------VNLDTATKTLRTVSKAGS-IKS-----SLGNHKNRRIPDLPIIRVVKR 174
Y L T T+ K IK+ + + + + R V
Sbjct: 94 CYLEGNDIHALAAKLLQENDT--TLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGE 151
Query: 175 RNTANKKERRRT------QSINNA-FSDLRE 198
N + Q + F +LR+
Sbjct: 152 GNA-------QLVAIFGGQGNTDDYFEELRD 175
Score = 28.1 bits (62), Expect = 4.4
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 16/52 (30%)
Query: 195 DLR--ECIPNVPSDTKLSKIKTLRLATSYISYLMKILETDDIISIDDFKADL 244
DLR + + NV + KL KI + L S +S+++ + L
Sbjct: 1858 DLRALDTVTNVLNFIKLQKIDIIELQKS--------------LSLEEVEGHL 1895
Score = 27.7 bits (61), Expect = 5.6
Identities = 12/78 (15%), Positives = 28/78 (35%), Gaps = 24/78 (30%)
Query: 192 AFSDLREC-IPNVPSDTK--------LSKIKTLRLATSYISYLMKILE------TDDII- 235
S L+E +P T+ + + L ++ Y+ ++E D ++
Sbjct: 29 IASQLQEQFNKILPEPTEGFAADDEPTTPAE---LVGKFLGYVSSLVEPSKVGQFDQVLN 85
Query: 236 -SIDDFKAD-LSN---HS 248
+ +F+ L H+
Sbjct: 86 LCLTEFENCYLEGNDIHA 103
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 35.4 bits (81), Expect = 0.015
Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 173 KRRNTANKKERRRTQSINNAFSDLRECIPNVPSDT-KLSKIKTLRLATSYI 222
R ++ E+RR +N+ +L +P + + KL K+ LR+A ++
Sbjct: 12 NAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHM 62
>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 = 30.2 bits (68), Expect = 0.53
Identities = 12/51 (23%), Positives = 19/51 (37%)
Query: 225 LMKILETDDIISIDDFKADLSNHSSHRKNKSQYDSPSEISSNQSSQYVMDP 275
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 = 30.0 bits (67), Expect = 0.71
Identities = 13/78 (16%), Positives = 35/78 (44%), Gaps = 4/78 (5%)
Query: 169 IRVVKRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMKI 228
IRV A+K+++ N + + + ++ ++++K++ L Y+S L+ +
Sbjct: 50 IRVSSILKEADKEKKLELFPYQNNSKYVAKKLDSLTQPSQMTKLQMLY----YLSLLLGV 105
Query: 229 LETDDIISIDDFKADLSN 246
E + + L++
Sbjct: 106 YENRRVNNKTKLLERLNS 123
>1sat_A Serratia protease; parallel beta helix, parallel beta roll,
hydrolase (serine protease); 1.75A {Serratia marcescens}
SCOP: b.80.7.1 d.92.1.6 PDB: 1af0_A* 1smp_A 1srp_A
Length = 471
Score = 28.7 bits (63), Expect = 2.8
Identities = 20/123 (16%), Positives = 35/123 (28%), Gaps = 10/123 (8%)
Query: 7 HAGSHYGGSNESF-----YHYNTPNNNVMSYNSGYHPPPLYTAGPPEDKHGATLSNITTG 61
H G + G + Y +T ++MSY S + T G + A
Sbjct: 186 HPGDYNAGEGDPTYADVTYAEDTRQFSLMSYWSETN-----TGGDNGGHYAAAPLLDDIA 240
Query: 62 ATDCIYWSEDMQSPDSRYVTRSMSTSSDGFDEDEDQSERFCPSNDYTKYYYQDGVGPGAY 121
A +Y + + +T D + + + D D G A
Sbjct: 241 AIQHLYGANLSTRTGDTVYGFNSNTGRDFLSTTSNSQKVIFAAWDAGGNDTFDFSGYTAN 300
Query: 122 PNV 124
+
Sbjct: 301 QRI 303
>3p8c_D Wiskott-aldrich syndrome protein family member 1; actin
polymerization, protein binding; 2.29A {Homo sapiens}
Length = 279
Score = 27.2 bits (59), Expect = 6.4
Identities = 16/108 (14%), Positives = 24/108 (22%), Gaps = 4/108 (3%)
Query: 2 SADILHAGSHYGGSNE---SFYHYNTPNNNVM-SYNSGYHPPPLYTAGPPEDKHGATLSN 57
S + + S + T + +Y+ PPPL P D L
Sbjct: 91 SLQDITMRKAFRSSTIQDQQLFDRKTLPIPLQETYDVCEQPPPLNILTPYRDDGKEGLKF 150
Query: 58 ITTGATDCIYWSEDMQSPDSRYVTRSMSTSSDGFDEDEDQSERFCPSN 105
T + W E M D +
Sbjct: 151 YTNPSYFFDLWKEKMLQDTEDKRKEKRKQKQKNLDRGGSGGSGGSGGS 198
>1ji6_A Pesticidial crystal protein CRY3BB; toxin; 2.40A {Bacillus
thuringiensis} SCOP: b.18.1.3 b.77.2.1 f.1.3.1
Length = 589
Score = 27.1 bits (59), Expect = 8.4
Identities = 10/52 (19%), Positives = 17/52 (32%)
Query: 9 GSHYGGSNESFYHYNTPNNNVMSYNSGYHPPPLYTAGPPEDKHGATLSNITT 60
++ Y N +V + +S PP T P E + L+
Sbjct: 367 DDQKNETSTQTYDSKRNNGHVSAQDSIDQLPPETTDEPLEKAYSHQLNYAEC 418
>3n9t_A PNPC; phospholipid binds, N-terminal helix tunnel, oxidoreductase;
HET: HGX FLC; 2.00A {Pseudomonas putida}
Length = 290
Score = 26.6 bits (58), Expect = 8.9
Identities = 13/76 (17%), Positives = 22/76 (28%), Gaps = 5/76 (6%)
Query: 19 FYHYNTPNNNVMSYNSGYHPPPLYTAGPPEDKHGATLSNITT----GATDCIYWSEDMQS 74
F+ P+ + P G D G + A + +Y +D
Sbjct: 108 FFIEGMPDRGYGENMALTDGVPALVYGRVLDVQGRPVVGAVLDVWQTADNGMYSGQDPDQ 167
Query: 75 PDSRYVTRSMSTSSDG 90
P R + +DG
Sbjct: 168 PFGNLRGR-YRSDNDG 182
>1kw3_B 2,3-dihydroxybiphenyl dioxygenase; four TIME repetitions of the
beta-alpha-beta-BETA-beta motif oxidoreductase; 1.45A
{Pseudomonas SP} SCOP: d.32.1.3 d.32.1.3 PDB: 1dhy_A
1eiq_A 1eir_A* 1eil_A 1kw6_B* 1kw8_B* 1kw9_B* 1kwb_B
1kwc_B*
Length = 292
Score = 26.9 bits (59), Expect = 9.0
Identities = 6/28 (21%), Positives = 8/28 (28%)
Query: 9 GSHYGGSNESFYHYNTPNNNVMSYNSGY 36
G H SFY + + G
Sbjct: 238 GRHTNDQTLSFYADTPSPMIEVEFGWGP 265
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
0.311 0.127 0.371
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: 4,219,954
Number of extensions: 235643
Number of successful extensions: 416
Number of sequences better than 10.0: 1
Number of HSP's gapped: 408
Number of HSP's successfully gapped: 31
Length of query: 285
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 192
Effective length of database: 4,105,140
Effective search space: 788186880
Effective search space used: 788186880
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 (21.8 bits)
S2: 57 (26.1 bits)