RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9185
(248 letters)
>2ql2_B Neurod1, neurogenic differentiation factor 1;
basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}
Length = 60
Score = 89.6 bits (223), Expect = 8e-24
Identities = 27/59 (45%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 144 KKTACDRERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQCLLEYG 202
+ A RER RM +N A D LR +P C +KLSKIE+LR+A YI L +L G
Sbjct: 3 RMKANARERNRMHGLNAALDNLRKVVP-CYSKTQKLSKIETLRLAKNYIWALSEILRSG 60
>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 = 86.7 bits (215), Expect = 1e-22
Identities = 26/62 (41%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 139 SERDYKKTACDRERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQCL 198
+ D +K A RER R+ +N AF+ L+ P ++L K+E LR AIRYI LQ L
Sbjct: 8 TNADRRKAATMRERRRLSKVNEAFETLKRSTSS--NPNQRLPKVEILRNAIRYIEGLQAL 65
Query: 199 LE 200
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 = 61.1 bits (148), Expect = 1e-12
Identities = 16/58 (27%), Positives = 25/58 (43%)
Query: 142 DYKKTACDRERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQCLL 199
D + ER R RD+N AF L K +K+ L+ A++ I L+ +
Sbjct: 4 DKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQV 61
>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 = 64.1 bits (155), Expect = 7e-12
Identities = 55/314 (17%), Positives = 91/314 (28%), Gaps = 111/314 (35%)
Query: 23 ILV---DSSDTEKL--KTNPHLEILHNADLNFVKDESSSPSSSTL-ISSQCLPSSMTSG- 75
IL+ T+ L T H+ + H++ DE S L Q LP + +
Sbjct: 268 ILLTTRFKQVTDFLSAATTTHISLDHHSM-TLTPDEVKSLLLKYLDCRPQDLPREVLTTN 326
Query: 76 ------------------------------QISSSTLTVLHPMEY--CY----------- 92
I S+L VL P EY +
Sbjct: 327 PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAH 386
Query: 93 -PPPPLSL---------PVLVEQSLVKY----ETPNTVTSTAPTPY-----SGANTTRCH 133
P LSL ++V L KY + P T + P+ Y N H
Sbjct: 387 IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALH 446
Query: 134 RKISDS---ERDYKKTAC-----DR-------------ERTRMRDMNRA--FDL------ 164
R I D + + D+ E + R D
Sbjct: 447 RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK 506
Query: 165 LRNRLPPCKPPGKKLSKIESLRMAIRYI--------RHLQCLLEYGPEYETILYSSR--S 214
+R+ G L+ ++ L+ YI R + +L++ P+ E L S+
Sbjct: 507 IRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTD 566
Query: 215 VVPSS--TNTSYVY 226
++ + ++
Sbjct: 567 LLRIALMAEDEAIF 580
Score = 31.4 bits (70), Expect = 0.29
Identities = 33/242 (13%), Positives = 61/242 (25%), Gaps = 78/242 (32%)
Query: 4 SDEQRQRGSGVIKENTSSMILVDSSDTEK-------LKTNPH------LEILHNADLNF- 49
D + ++ + I++ L + +E + + F
Sbjct: 39 QDMPKS----ILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFL 94
Query: 50 ---VKDESSSPSSSTLISSQCLPSSMTSGQISSSTLTVLHPMEYCYPPPPLSLPVLVEQS 106
+K E PS T + + Q V P L L Q+
Sbjct: 95 MSPIKTEQRQPSMMTRMYIEQRDRLYNDNQ-------VFAKYNVSRLQPYLKL----RQA 143
Query: 107 LVKYETPNTVTSTAPTPY--------SGANTTRCHRK---ISDSERDYKKTA-------- 147
L++ P SG K D YK
Sbjct: 144 LLELR---------PAKNVLIDGVLGSG--------KTWVALDVCLSYKVQCKMDFKIFW 186
Query: 148 -----CDRERTRMRDMNR-AFDLLRNRLPPCKPPGKKLSKIESLRMAIRYI----RHLQC 197
C+ T + + + + + N +I S++ +R + + C
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246
Query: 198 LL 199
LL
Sbjct: 247 LL 248
>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 = 47.7 bits (114), Expect = 8e-08
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 151 ERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQ 196
ER R + +F LR+ +P + G+K S+ + L A YI++++
Sbjct: 20 ERKRRDHIKDSFHSLRDSVPSLQ--GEKASRAQILDKATEYIQYMR 63
>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 = 46.9 bits (112), Expect = 2e-07
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 151 ERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQ 196
ER R ++ R+F LR+++P +K K+ L+ A YI +Q
Sbjct: 14 ERQRRNELKRSFFALRDQIPEL-ENNEKAPKVVILKKATAYILSVQ 58
>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 = 46.2 bits (110), Expect = 3e-07
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 151 ERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQ 196
ER R + +F LR+ +P + G+K S+ + L A YI++++
Sbjct: 10 ERKRRDHIKDSFHSLRDSVPSLQ--GEKASRAQILDKATEYIQYMR 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 = 44.2 bits (105), Expect = 8e-07
Identities = 13/48 (27%), Positives = 18/48 (37%), Gaps = 2/48 (4%)
Query: 151 ERTRMRDMNRAFDLLRNRLPPC--KPPGKKLSKIESLRMAIRYIRHLQ 196
ER R +N L +P + SK L A YI+ L+
Sbjct: 13 ERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 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 = 43.9 bits (104), Expect = 2e-06
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 151 ERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQ 196
E+ +N L++ + + KL+K LR AI YIR LQ
Sbjct: 14 EKRYRSSINDKIIELKDLVVGTE---AKLNKSAVLRKAIDYIRFLQ 56
>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 = 40.1 bits (93), Expect = 3e-05
Identities = 22/65 (33%), Positives = 28/65 (43%), Gaps = 2/65 (3%)
Query: 133 HRKISDSERDYKKTACDRERTRMR-DMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRY 191
H S K E + DMN + LR L P P G +LS++E L+ I Y
Sbjct: 3 HHHHHHSHMGGGKGPAAEEPLSLLDDMNHCYSRLR-ELVPGVPRGTQLSQVEILQRVIDY 61
Query: 192 IRHLQ 196
I LQ
Sbjct: 62 ILDLQ 66
>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 = 39.8 bits (93), Expect = 4e-05
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 3/49 (6%)
Query: 151 ERTRMRDMNRAFDLLRNRLPPC---KPPGKKLSKIESLRMAIRYIRHLQ 196
E+ R + A L + +P + SK ++ A RYIRHLQ
Sbjct: 10 EQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQ 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 = 43.5 bits (102), Expect = 4e-05
Identities = 35/187 (18%), Positives = 56/187 (29%), Gaps = 83/187 (44%)
Query: 2 SNSDEQRQRGSGVIKENTSSMILVDSSDTEKL-----KTNPHL------EI-LHNADLNF 49
S ++ + GV S M+ + + E++ KTN HL EI L N N
Sbjct: 322 SILEDSLENNEGV----PSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNL 377
Query: 50 V-----------------------KDESSSPSSS--TLISSQCLPSSMTSGQIS----SS 80
V D+S P S S++ LP ++ S
Sbjct: 378 VVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLP-------VASPFHSH 430
Query: 81 TLT--------VLHPMEYCYPPPPLSLPVLVEQSLVKYETPNTVTSTAPTPYSGANTTRC 132
L L + + +PV Y+T + G++
Sbjct: 431 LLVPASDLINKDLVKNNVSFNAKDIQIPV--------YDT-----------FDGSDL--- 468
Query: 133 HRKISDS 139
R +S S
Sbjct: 469 -RVLSGS 474
Score = 38.5 bits (89), Expect = 0.002
Identities = 44/303 (14%), Positives = 88/303 (29%), Gaps = 120/303 (39%)
Query: 5 DEQR---QRGSGVIKE--NTSSMILVDSSDTEKLKTNPHLEILHNADL-NFVKDESSSPS 58
+E R Q ++ + S+ L + T L ++ ++++ S++P
Sbjct: 171 EELRDLYQTYHVLVGDLIKFSAETLSELIRTT-LDAEKVFT--QGLNILEWLENPSNTPD 227
Query: 59 SSTLISSQCLPSSMTSGQISSSTLTVLHPMEYCYPPPPLSLPVLVEQSLVKYE------- 111
L+S P+S P++ L Y
Sbjct: 228 KDYLLSI------------------------------PISCPLIGVIQLAHYVVTAKLLG 257
Query: 112 -TPNTVTSTAPTPYSGANTTRCHRKI--------SDSERDYKKTACDRERTRMRDMNRAF 162
TP + S GA T + + +DS + + +A
Sbjct: 258 FTPGELRSY----LKGA--TGHSQGLVTAVAIAETDSWESFFVSV-----------RKAI 300
Query: 163 DLL------------RNRLPP-----CKPPGKK-----LSKIESLRMAIRYIRHLQCLLE 200
+L LPP + LS I +L +Q +
Sbjct: 301 TVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLS-ISNLTQE-----QVQDYVN 354
Query: 201 ----YGPEYETI---LY-SSRSVV----PSSTNTSYVYPLDDSC--VDCGSAIGQW-TQY 245
+ P + + L ++++V P S +Y L+ + S + Q +
Sbjct: 355 KTNSHLPAGKQVEISLVNGAKNLVVSGPPQS-----LYGLNLTLRKAKAPSGLDQSRIPF 409
Query: 246 AQR 248
++R
Sbjct: 410 SER 412
>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 = 39.8 bits (93), Expect = 5e-05
Identities = 9/46 (19%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 151 ERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQ 196
E+ R + + + L+ + P P + + + L A +I+ L+
Sbjct: 9 EKNRRAHLRLSLEKLKGLV-PLGPDSSRHTTLSLLTKAKLHIKKLE 53
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 41.5 bits (97), Expect = 1e-04
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 133 HRKISDSERDYKKTACDRERTRMRD-MNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRY 191
+ + ++ ++ E+ R RD MN D L + +P C +KL K+ LRMA+++
Sbjct: 3 YAEHQGRIKNAREAHSQIEKRR-RDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQH 61
Query: 192 IRHLQCLLEYGPE 204
++ L+ E
Sbjct: 62 MKTLRGATNPYTE 74
>1ej0_A FTSJ; methyltransferase, adoMet, adenosyl methionine, heat shock
proteins, 23S ribosomal RNA; HET: SAM; 1.50A
{Escherichia coli} SCOP: c.66.1.2 PDB: 1eiz_A*
Length = 180
Score = 31.3 bits (72), Expect = 0.19
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 230 DSCVDCGSAIGQWTQYAQR 248
+ VD G+A G W+QY
Sbjct: 24 MTVVDLGAAPGGWSQYVVT 42
>3dou_A Ribosomal RNA large subunit methyltransferase J; cell division,
structural genomics, protein structure initiative, PSI;
HET: SAM; 1.45A {Thermoplasma volcanium}
Length = 191
Score = 30.9 bits (71), Expect = 0.23
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 230 DSCVDCGSAIGQWTQYAQR 248
D+ ++ GS+ G WTQ
Sbjct: 27 DAVIEIGSSPGGWTQVLNS 45
>2nyu_A Putative ribosomal RNA methyltransferase 2; SAM, structural
genomics, structural genomics consortium, SGC; HET: SAM;
1.76A {Homo sapiens}
Length = 196
Score = 31.0 bits (71), Expect = 0.24
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 230 DSCVDCGSAIGQWTQYAQR 248
+DCG+A G W+Q A +
Sbjct: 24 LRVLDCGAAPGAWSQVAVQ 42
>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 = 0.26
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 137 SDSERDYKKTACDRERTRMRD-MNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIR 193
D ++ + + E+ R RD N L + LP +K+ K L+ +I ++R
Sbjct: 6 DDKDKAKRVSRNKSEKKR-RDQFNVLIKELGSMLPGNA---RKMDKSTVLQKSIDFLR 59
>2plw_A Ribosomal RNA methyltransferase, putative; malaria, SAM, structural
genomics, structural genomics consortium, SGC; HET: SAM;
1.70A {Plasmodium falciparum}
Length = 201
Score = 30.7 bits (70), Expect = 0.34
Identities = 5/19 (26%), Positives = 6/19 (31%)
Query: 230 DSCVDCGSAIGQWTQYAQR 248
+D G G W Q
Sbjct: 24 KIILDIGCYPGSWCQVILE 42
>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 = 28.0 bits (61), Expect = 2.0
Identities = 10/43 (23%), Positives = 18/43 (41%), Gaps = 16/43 (37%)
Query: 7 QRQRGSGVIKENTSSMILV--DSSDTEKLKTNPHLEILHNADL 47
++Q +K+ +S+ L DS+ P L I A +
Sbjct: 18 EKQA----LKKLQASLKLYADDSA--------PALAI--KATM 46
>3eld_A Methyltransferase; flavivirus, RNA capping, guanylyltransfer viral
enzyme structure; HET: SFG; 1.90A {Wesselsbron virus}
PDB: 3elu_A* 3elw_A* 3ely_A* 3emb_A* 3emd_A*
Length = 300
Score = 26.8 bits (59), Expect = 6.0
Identities = 6/14 (42%), Positives = 8/14 (57%)
Query: 233 VDCGSAIGQWTQYA 246
+D G G W+ YA
Sbjct: 86 LDLGCGRGGWSYYA 99
>3ez1_A Aminotransferase MOCR family; YP_604413.1, struct genomics, joint
center for structural genomics, JCSG; 2.60A {Deinococcus
geothermalis dsm 11300}
Length = 423
Score = 26.5 bits (59), Expect = 8.4
Identities = 7/18 (38%), Positives = 8/18 (44%)
Query: 191 YIRHLQCLLEYGPEYETI 208
Y RH L G E T+
Sbjct: 134 YDRHFLLLQTLGFELLTV 151
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 0.127 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: 3,470,613
Number of extensions: 183837
Number of successful extensions: 298
Number of sequences better than 10.0: 1
Number of HSP's gapped: 287
Number of HSP's successfully gapped: 29
Length of query: 248
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 157
Effective length of database: 4,160,982
Effective search space: 653274174
Effective search space used: 653274174
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: 56 (25.7 bits)