RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4627
(270 letters)
>2ql2_B Neurod1, neurogenic differentiation factor 1;
basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}
Length = 60
Score = 93.5 bits (233), Expect = 4e-25
Identities = 30/58 (51%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 157 SQRILANVRERQRTQSLNEAFTSLRKLIPALPSD-KLSKIQTLKLASRYIHFLCEILH 213
S+R+ AN RER R LN A +LRK++P KLSKI+TL+LA YI L EIL
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 = 91.7 bits (228), Expect = 2e-24
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 142 MKIRRKYPQTYGELHSQRILANVRERQRTQSLNEAFTSLRKLIPALPSDKLSKIQTLKLA 201
M+++RK +R A +RER+R +NEAF +L++ + P+ +L K++ L+ A
Sbjct: 1 MELKRKTTNAD-----RRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNA 55
Query: 202 SRYIHFLCEILH 213
RYI L +L
Sbjct: 56 IRYIEGLQALLR 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 = 52.2 bits (125), Expect = 2e-09
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 158 QRILANVRERQRTQSLNEAFTSL-RKLIPALPSD-KLSKIQTLKLASRYIHFLCEILH 213
+R N ER+R + +NEAF L R L SD +K+ L+ A + I L + +
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 = 52.0 bits (125), Expect = 3e-09
Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 153 GELHSQRILANVRERQRTQSLNEAFTSLRKLIPALPS-DKLSKIQTLKLASRYIHFL 208
G ++ +R NV ERQR L +F +LR IP L + +K K+ LK A+ YI +
Sbjct: 1 GHMNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSV 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 = 48.5 bits (116), Expect = 5e-08
Identities = 18/50 (36%), Positives = 29/50 (58%)
Query: 159 RILANVRERQRTQSLNEAFTSLRKLIPALPSDKLSKIQTLKLASRYIHFL 208
R N ER+R + ++F SLR +P+L +K S+ Q L A+ YI ++
Sbjct: 13 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYM 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 = 47.8 bits (114), Expect = 8e-08
Identities = 18/53 (33%), Positives = 30/53 (56%)
Query: 158 QRILANVRERQRTQSLNEAFTSLRKLIPALPSDKLSKIQTLKLASRYIHFLCE 210
+R N ER+R + ++F SLR +P+L +K S+ Q L A+ YI ++
Sbjct: 2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRR 54
>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 = 42.1 bits (99), Expect = 1e-05
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 1/53 (1%)
Query: 159 RILANVRERQRTQSLNEAFTSLRKLIPALPSD-KLSKIQTLKLASRYIHFLCE 210
R N E+ R L + L+ L+P P + + + L A +I L +
Sbjct: 2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLED 54
>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 = 44.8 bits (105), Expect = 2e-05
Identities = 48/298 (16%), Positives = 84/298 (28%), Gaps = 97/298 (32%)
Query: 10 TEVDENKSETIYRSENMDMYGVKNENPEISVNV----EKDIPEDNLDHN---LNSKNLLI 62
T+ + T ++ M +E + + +D+P + L N L+ +I
Sbjct: 278 TDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS----II 333
Query: 63 LEQMKSETAHPYLTDYFYTEVDQNKSENIYRS--ENLD------MYGTLV---KTEK-PE 110
E ++ A D + V+ +K I S L+ M+ L + P
Sbjct: 334 AESIRDGLATW---DN-WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPT 389
Query: 111 E-------ENYYMDEGDIMNNKRRKRSISSSSKSS-----SGDMKIRRKYPQTYGELHSQ 158
+ D ++N + + K S S ++++ K Y LH
Sbjct: 390 ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEY-ALHRS 448
Query: 159 RI------------------------------LANVRERQRTQSLNEAFTSLR----KLI 184
+ L N+ +R F R K+
Sbjct: 449 IVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIR 508
Query: 185 PA-----LPSDKLSKIQTLKLASRYI---------------HFL--CE-ILHGSEDGD 219
L+ +Q LK YI FL E L S+ D
Sbjct: 509 HDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTD 566
Score = 42.1 bits (98), Expect = 1e-04
Identities = 41/253 (16%), Positives = 81/253 (32%), Gaps = 59/253 (23%)
Query: 44 KDIPEDNLD---HNLNSKNLLILEQMKSETAHPYLTDYFYTEVDQ-----NKSENIYRSE 95
KDI D N + K+ + + K L+ E+D + R
Sbjct: 19 KDILSVFEDAFVDNFDCKD--VQDMPK-----SILSK---EEIDHIIMSKDAVSGTLR-- 66
Query: 96 NLDMYGTLVKTEKPEEE-NYYMDEGDIMNNKRRKRSISSSSKSSSGDMKIRRKYPQTYGE 154
++ TL+ K EE +++E +N K I + + S + Y +
Sbjct: 67 ---LFWTLL--SKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTR---MYIEQRDR 118
Query: 155 LHSQ-RILA--NVRERQRTQSLNEAFTSLRKLIPALPSDKLS--------K----IQTLK 199
L++ ++ A NV Q L +A LR P+ + K +
Sbjct: 119 LYNDNQVFAKYNVSRLQPYLKLRQALLELR------PAKNVLIDGVLGSGKTWVALDVCL 172
Query: 200 LASRYIHFLCEI--LH-GSEDGDGNNTEIVDQDRELFNGISPGGPNFESNNSNMKLTINN 256
+I L+ + + +++ ++L I P N+ S + +
Sbjct: 173 SYKVQCKMDFKIFWLNLKNCNSPE---TVLEMLQKLLYQIDP---NWTSRSDHSSNIKLR 226
Query: 257 YNMAHEKLSYAFS 269
+ +L
Sbjct: 227 IHSIQAELRRLLK 239
Score = 33.3 bits (75), Expect = 0.090
Identities = 29/192 (15%), Positives = 60/192 (31%), Gaps = 49/192 (25%)
Query: 29 YGVKNENPEISVN-------VEKDIPE----------DNLDHNLNSKNL--LILEQMKSE 69
+ V + + VN VEK E + N L I++
Sbjct: 397 FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIP 456
Query: 70 TAH-------PYLTDYFYTEVDQNKSENIYRSENLDMYGTLVKTEKPEE-ENYYMDEGDI 121
PYL YFY+ + + +N++ E+ ++D
Sbjct: 457 KTFDSDDLIPPYLDQYFYSHIG-------HHLKNIEHP------ERMTLFRMVFLDF-RF 502
Query: 122 MNNKRRKRSISSSSKSSS----GDMKIRRKYPQTYGELHSQRI--LANVRERQRTQSLNE 175
+ K R S + ++ S +K + Y + + + + + + +
Sbjct: 503 LEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICS 562
Query: 176 AFTSLRKLIPAL 187
+T L ++ AL
Sbjct: 563 KYTDLLRI--AL 572
Score = 30.6 bits (68), Expect = 0.58
Identities = 31/237 (13%), Positives = 69/237 (29%), Gaps = 71/237 (29%)
Query: 9 YTEVDENKSETIYRSENMDMYGVKNENPEISVNVEKDIPEDNLDHNLNSKNLLILEQMKS 68
++D N + RS++ N ++ ++ + L LL+L
Sbjct: 206 LYQIDPNWTS---RSDHS-------SNIKLRIHSIQAELRRLLKSKPYENCLLVL----- 250
Query: 69 ETAHPYLTDYFYTEVDQNKSENIYRSENLDMYG----TLVKTEKPEEENYYMDEGDIMNN 124
N+ ++ + + L+ T
Sbjct: 251 --------L------------NVQNAKAWNAFNLSCKILLTT------------------ 272
Query: 125 KRRKRSISSSSKSSSGDMKIRRKYPQTYGELHSQRILANVRERQRTQSL-NEAFTS---L 180
R + ++ +++ + T + +L + R Q L E T+
Sbjct: 273 --RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLD-CRPQDLPREVLTTNPRR 329
Query: 181 RKLIPALPSDKLSKIQTLKLASRYIHFLCEILHGSEDGDGNNTEIVDQDRELFNGIS 237
+I D L+ + H C+ L + N E + R++F+ +S
Sbjct: 330 LSIIAESIRDGLATWD------NWKHVNCDKLTTIIESSLNVLEPAEY-RKMFDRLS 379
>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 = 40.4 bits (95), Expect = 3e-05
Identities = 17/50 (34%), Positives = 20/50 (40%), Gaps = 4/50 (8%)
Query: 163 NVRERQRTQSLNEAFTSLRKLIPAL----PSDKLSKIQTLKLASRYIHFL 208
N ER+R +N L K+IP SK L AS YI L
Sbjct: 10 NEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59
>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 = 39.7 bits (93), Expect = 7e-05
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 157 SQRILANVRERQRTQSLNEAFTSLRKLIPALPSDKLSKIQTLKLASRYIHFL 208
+R N E++ S+N+ L+ L+ + KL+K L+ A YI FL
Sbjct: 5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTEA-KLNKSAVLRKAIDYIRFL 55
>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 = 35.8 bits (82), Expect = 0.013
Identities = 15/107 (14%), Positives = 38/107 (35%), Gaps = 35/107 (32%)
Query: 151 TYGEL-------HSQRILANVRERQRTQSLNEAFTSLRKLIPALPSDKLSK----IQTLK 199
++G L + +A +Q L E F K++P P++ + +
Sbjct: 12 SHGSLEHVLLVPTASFFIA-------SQ-LQEQFN---KILPE-PTEGFAADDEPTTPAE 59
Query: 200 LASRYIHFLCEILHGSEDGDGNNTEIVDQDRELFNGISPGGPNFESN 246
L +++ ++ ++ S+ G +++ FE+
Sbjct: 60 LVGKFLGYVSSLVEPSKVGQ--FDQVL---NLCLT-------EFENC 94
Score = 31.9 bits (72), Expect = 0.23
Identities = 30/202 (14%), Positives = 67/202 (33%), Gaps = 55/202 (27%)
Query: 50 NLDHNLN-SKNLLIL-EQMKSE--TAHPYLTDYFYTEVDQNKSE------------NIYR 93
+L+H L + Q++ + P T+ F + D+ + ++
Sbjct: 15 SLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAAD-DEPTTPAELVGKFLGYVSSLVE 73
Query: 94 SENLDMYGTLVKTEKPEEENYYMDEGDIMNNKRRKRSISSSSKSSSGDMKIRRKYP-QTY 152
+ + ++ E EN Y++ DI ++++ + ++ K + Y
Sbjct: 74 PSKVGQFDQVLNLCLTEFENCYLEGNDI-------HALAAKLLQENDTTLVKTKELIKNY 126
Query: 153 GELHSQRILANVRERQRTQSLNEAFTSLRKLIPALPSDKLSKIQTLKLASRYIHFLCEIL 212
+ RI+A +++ S L A+ A F
Sbjct: 127 ---ITARIMAKRPFDKKSNS---------ALFRAVGEGN---------AQLVAIF----- 160
Query: 213 HGSEDGDGNNTEIVDQDRELFN 234
G G GN + ++ R+L+
Sbjct: 161 -G---GQGNTDDYFEELRDLYQ 178
Score = 30.0 bits (67), Expect = 0.98
Identities = 40/231 (17%), Positives = 67/231 (29%), Gaps = 85/231 (36%)
Query: 97 LDMYGT--LVKT-----EKPEEENYYMDEGDIMNNKRRKRSISSSSKSSSGDMKIRRKYP 149
+D+Y T + + ++ Y DI+ N +I + +IR Y
Sbjct: 1633 MDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGK---RIRENYS 1689
Query: 150 Q-TY-----GELHSQRILANVRER----------------QRTQ------SLNEAFTSLR 181
+ G+L +++I + E Q TQ AF L+
Sbjct: 1690 AMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEK-AAFEDLK 1748
Query: 182 K--LIP--------------AL--PSDKLSKIQTLKLAS---RYIHFLCEILHGSEDGDG 220
LIP AL +D +S +++ + E G
Sbjct: 1749 SKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVP---RDELGRS 1805
Query: 221 NNTEIVDQDRELFNGISPG--GPNFE-----------SNNSNMKLTINNYN 258
N I I+PG +F + + I NYN
Sbjct: 1806 NYGMI---------AINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYN 1847
>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 = 32.1 bits (73), Expect = 0.019
Identities = 17/48 (35%), Positives = 21/48 (43%), Gaps = 5/48 (10%)
Query: 166 ERQRTQSLNEAFTSLRKLIPALPSDK-----LSKIQTLKLASRYIHFL 208
E+ R L A L LIPA + SK T++ A RYI L
Sbjct: 10 EQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHL 57
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 34.2 bits (78), Expect = 0.032
Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 166 ERQRTQSLNEAFTSLRKLIPALPSD--KLSKIQTLKLASRYIHFLCEILHGSEDGDGNNT 223
E++R +N L L+P + KL K+ L++A +++ L + + + T
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTEANYKPT 80
Query: 224 EIVDQD 229
+ D +
Sbjct: 81 FLSDDE 86
>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 = 0.081
Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 1/58 (1%)
Query: 166 ERQRTQSLNEAFTSLRKLIPALPSDKLSKIQTLKLASRYIHFLCEILHGSEDGDGNNT 223
E++R N L ++P + K+ K L+ + ++ E S+ +
Sbjct: 20 EKKRRDQFNVLIKELGSMLPG-NARKMDKSTVLQKSIDFLRKHKETTAQSDASEIRQD 76
>2nyy_A Botulinum neurotoxin type A; neurotoxin, FAB, protein antibody
complex, toxin- system complex; 2.61A {Clostridium
botulinum} PDB: 2nz9_A 3bta_A 3v0a_A* 3v0b_A 3v0c_A
3zus_A 3zur_A
Length = 1295
Score = 29.1 bits (64), Expect = 1.8
Identities = 18/140 (12%), Positives = 47/140 (33%), Gaps = 2/140 (1%)
Query: 73 PYLTDYFYTEVDQNKSENIYRSENLDMYGTLVKTEKPEEENYYMDEGDIMNNKRRKRSIS 132
T E + +LD+ T + E + ++ ++ + +
Sbjct: 473 DLNKGEEIT--SDTNIEAAEENISLDLIQQYYLTFNFDNEPENISIENLSSDIIGQLELM 530
Query: 133 SSSKSSSGDMKIRRKYPQTYGELHSQRILANVRERQRTQSLNEAFTSLRKLIPALPSDKL 192
+ + K + L +Q T S+NEA + ++ SD +
Sbjct: 531 PNIERFPNGKKYELDKYTMFHYLRAQEFEHGKSRIALTNSVNEALLNPSRVYTFFSSDYV 590
Query: 193 SKIQTLKLASRYIHFLCEIL 212
K+ A+ ++ ++ +++
Sbjct: 591 KKVNKATEAAMFLGWVEQLV 610
>1epw_A Bontoxilysin B, botulinum neurotoxin type B; zinc, metalloprotease,
transmembrane, hydrolase; 1.90A {Clostridium botulinum}
SCOP: b.29.1.6 b.42.4.2 d.92.1.7 h.4.2.1 PDB: 1f31_A*
1g9a_A* 1g9b_A* 1g9c_A* 1g9d_A* 1i1e_A* 1s0b_A 1s0c_A
1s0d_A 1s0e_A 1s0f_A 1s0g_A 2np0_A 3zuq_A 2etf_A 2xhl_A
1z0h_A 2nm1_A 3g94_A 1f82_A ...
Length = 1290
Score = 27.9 bits (61), Expect = 4.8
Identities = 20/169 (11%), Positives = 58/169 (34%), Gaps = 8/169 (4%)
Query: 44 KDIPEDNLDHNLNSKNLLILEQMKSETAHPYLTDYFYTEVDQNKSENIYRSENLDMYGTL 103
K + + ++++++L + S + D E + +++ Y + + +
Sbjct: 437 KSVKAPGICIDVDNEDLFFIADKNS-----FSDDLSKNERIEYNTQSNYIENDFPINELI 491
Query: 104 VKTEKPEEENYYMDEGDIMNNKRRKRSISSSSKSSSGDMKIRRKYPQTYGELHSQRILAN 163
+ T+ + + + + KI + L+SQ +
Sbjct: 492 LDTDLISKIE---LPSENTESLTDFNVDVPVYEKQPAIKKIFTDENTIFQYLYSQTFPLD 548
Query: 164 VRERQRTQSLNEAFTSLRKLIPALPSDKLSKIQTLKLASRYIHFLCEIL 212
+R+ T S ++A K+ D + + A + ++ +I+
Sbjct: 549 IRDISLTSSFDDALLFSNKVYSFFSMDYIKTANKVVEAGLFAGWVKQIV 597
>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 = 26.1 bits (56), Expect = 9.7
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 9/27 (33%)
Query: 166 ERQRTQSLNEAFTSLRKL-----IPAL 187
E+Q +L + SL KL PAL
Sbjct: 18 EKQ---ALKKLQASL-KLYADDSAPAL 40
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
0.309 0.128 0.351
Gapped
Lambda K H
0.267 0.0444 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,855,167
Number of extensions: 217967
Number of successful extensions: 372
Number of sequences better than 10.0: 1
Number of HSP's gapped: 362
Number of HSP's successfully gapped: 35
Length of query: 270
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 178
Effective length of database: 4,133,061
Effective search space: 735684858
Effective search space used: 735684858
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 56 (26.1 bits)