RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7682
(383 letters)
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS,
circadian rhythm proteins, transcription-activato; 2.27A
{Mus musculus}
Length = 361
Score = 155 bits (393), Expect = 4e-44
Identities = 59/285 (20%), Positives = 114/285 (40%), Gaps = 27/285 (9%)
Query: 50 VNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ 109
V++ +EK+RR+Q N I+EL ++ + K DK +LQ++++ +R K+
Sbjct: 14 VSRNKSEKKRRDQFNVLIKELGSMLPG------NAR---KMDKSTVLQKSIDFLRKHKET 64
Query: 110 ETSSDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYS 169
SDA + + KPT ++NE L+LEAL+GF + DG + + +E++ S + +
Sbjct: 65 TAQSDASEIRQ--DWKPTFLSNEEFTQLMLEALDGFFLAIMTDGSIIYVSESVTSLLEHL 122
Query: 170 RQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTA--------- 220
+++ +S++N I G+H+ + L + ++ T + +
Sbjct: 123 PSDLVDQSIFNFIPEGEHSEVYKILSTHLLESDSLTPEYLKSKNQLEFCCHMLRGTIDPK 182
Query: 221 -STPNRTFNIRLLISSTHLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPP----T 275
+ S + + G E + S E C + R P
Sbjct: 183 EPSTYEYVRFIGNFKSLTSVSTSTHNGFEGTIQRTHRPSYEDRVCFVATVRLATPQFIKE 242
Query: 276 DKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKT 320
+ P E+FT + + +D YL V +
Sbjct: 243 MCTVEEPNEEFTSRHSLEWKFLFLDHRAPP--IIGYLPFEVLGTS 285
Score = 42.6 bits (100), Expect = 1e-04
Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH---ARFHNCLV 195
F + + F I Y EVLG S Y+ H D A+ H L+
Sbjct: 253 FTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHVDDLENLAKCHEHLM 306
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 133 bits (336), Expect = 9e-36
Identities = 57/291 (19%), Positives = 121/291 (41%), Gaps = 53/291 (18%)
Query: 56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSSDA 115
EKRRR++ N++I+ELA L+ + +++ K DK +L+ V ++ ++ +++
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCN------AMSRKLDKLTVLRMAVQHMKTLRG---ATNP 71
Query: 116 VQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPD-GYVNFCTENIKSFIRYSRQEVL 174
+ ++ KPT ++++ L L+L A +GFLFVV D G + F +E++ + YS+ +++
Sbjct: 72 YTE---ANYKPTFLSDDELKHLILRAADGFLFVVGCDRGKILFVSESVFKILNYSQNDLI 128
Query: 175 GKSVYNLIHHGDHARFHNCLVPS--SHQVNAWTSDSGGQAGK----RPSLTASTPNRTFN 228
G+S+++ +H D A+ L S + + + +G PS S R+F
Sbjct: 129 GQSLFDYLHPKDIAKVKEQLSSSDTAPRERLIDAKTGLPVKTDITPGPSRLCSGARRSFF 188
Query: 229 IRLLISSTHLTAGLSRAGGENGQ-----------------------------DDSGDVSS 259
R+ + + + D+ D
Sbjct: 189 CRMKCNRPSVKVEDKDFASTCSKKKADRKSFCTIHSTGYLKSWPPTKMGLDEDNEPDNEG 248
Query: 260 EGGPCLMCVAR-----RIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGVS 305
CL+ + R P + ++ ++ + G + +D +
Sbjct: 249 CNLSCLVAIGRLHSHMVPQPANGEIRVKSMEYVSRHAIDGKFVFVDQRATA 299
Score = 42.3 bits (99), Expect = 2e-04
Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 3/60 (5%)
Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH---ARFHNCLVPSSHQV 201
++ DG F + + + Y QE+LG S Y H D A H ++ + ++
Sbjct: 280 YVSRHAIDGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKI 339
>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological
rhythms, cytoplasm, nucleus, phosphoprotein,
transcription; 2.40A {Mus musculus}
Length = 309
Score = 93.1 bits (231), Expect = 1e-21
Identities = 26/212 (12%), Positives = 65/212 (30%), Gaps = 33/212 (15%)
Query: 126 PTVITNE----VLGPLLLEALEGFLFVVN-PDGYVNFCTENIKSFIRYSRQEVLGKSVYN 180
+ + E + +++ + F V+ G + + + + S +
Sbjct: 4 GSSYSMEQVEGITSEYIVKNADMFAVAVSLVSGKILYISNQVASIFHCKKDAFSDAKFVE 63
Query: 181 LIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRLLISST---- 236
+ D + FH+ + +++ W+ SG + + ++F R+ +
Sbjct: 64 FLAPHDVSVFHSYT--TPYKLPPWSVCSGLDSFTQE----CMEEKSFFCRVSVGKHHENE 117
Query: 237 ------HLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDKQLSAPI--EQFTM 288
+T L + + G + C + +A R+ + P FT
Sbjct: 118 IRYQPFRMTPYLVKVQEQQGAESQ--------LCCLLLAERVHSGYEAPRIPPEKRIFTT 169
Query: 289 KLDRSGTIIGMDTSGVSQTHTQYLNKAVACKT 320
+ +D V YL + +
Sbjct: 170 THTPNCLFQAVDERAVP--LLGYLPQDLIETP 199
Score = 39.6 bits (92), Expect = 0.001
Identities = 8/42 (19%), Positives = 14/42 (33%)
Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGD 186
F P+ E + Y Q+++ V +H D
Sbjct: 167 FTTTHTPNCLFQAVDERAVPLLGYLPQDLIETPVLVQLHPSD 208
>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock
protein, protein binding; 2.75A {Mus musculus}
Length = 320
Score = 88.1 bits (218), Expect = 9e-20
Identities = 35/224 (15%), Positives = 61/224 (27%), Gaps = 33/224 (14%)
Query: 114 DAVQQGEVSSSKPTVITNE----VLGPLLLEALEGFLFVVN-PDGYVNFCTENIKSFIRY 168
+ E + + T E + L + F V+ G + + +E +R
Sbjct: 3 LGSPEFEPCAMDMSTYTLEELEHITSEYTLRNQDTFSVAVSFLTGRIVYISEQAGVLLRC 62
Query: 169 SRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFN 228
R G L+ D F+ PS G L T ++
Sbjct: 63 KRDVFRGARFSELLAPQDVGVFYGSTTPS------RLPTWGTGTSAGSGLKDFTQEKSVF 116
Query: 229 IRLLISST----------HLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDKQ 278
R+ LT +++ +G PC + +A RI +
Sbjct: 117 CRIRGGPDRDPGPRYQPFRLTPYVTKIRVSDGAPAQ--------PCCLLIAERIHSGYEA 168
Query: 279 LSAPI--EQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKT 320
P FT + S +D YL + +
Sbjct: 169 PRIPPDKRIFTTRHTPSCLFQDVDERAA--PLLGYLPQDLLGAP 210
Score = 41.5 bits (97), Expect = 3e-04
Identities = 12/60 (20%), Positives = 19/60 (31%), Gaps = 3/60 (5%)
Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH---ARFHNCLVPSSHQV 201
F P E + Y Q++LG V +H D H ++ + Q
Sbjct: 178 FTTRHTPSCLFQDVDERAAPLLGYLPQDLLGAPVLLFLHPEDRPLMLAIHKKILQLAGQP 237
>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm,
protein binding; 2.50A {Mus musculus}
Length = 317
Score = 79.7 bits (196), Expect = 6e-17
Identities = 29/197 (14%), Positives = 50/197 (25%), Gaps = 15/197 (7%)
Query: 117 QQGEVSSSKPTVITNEVLGPL----LLEALEGFLFVVN-PDGYVNFCTENIKSFIRYSRQ 171
+ TV + E L L + + F V + G + +E + R
Sbjct: 6 PEFPGRLEDVTVYSLEDLTALASEHTSKNTDTFAAVFSFLSGRLVHISEQAALILNSKRG 65
Query: 172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRL 231
+ +L+ D F+ P+ +R S P + F R+
Sbjct: 66 FLKSVHFVDLLAPQDVRAFYAHTAPTQLPFWN-------NWTQRASQYECAPAKPFFCRI 118
Query: 232 LISSTHLTAGLS--RAGGENGQDDSGDVSSEGGPCLMCVARRIPP-TDKQLSAPIEQFTM 288
S R S CL V + ++ FT
Sbjct: 119 CGGGDREKRHYSPFRILPYLVHVHSSAQPEPEPCCLTLVEKIHSGYEAPRIPVDKRIFTT 178
Query: 289 KLDRSGTIIGMDTSGVS 305
+ +D V
Sbjct: 179 THTPGCVFLEVDERAVP 195
Score = 42.3 bits (99), Expect = 1e-04
Identities = 10/54 (18%), Positives = 18/54 (33%), Gaps = 3/54 (5%)
Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH---ARFHNCLV 195
F P E + Y Q+++G S+ +H D H ++
Sbjct: 176 FTTTHTPGCVFLEVDERAVPLLGYLPQDLIGTSILTYLHPEDRPLMVAIHQKVL 229
>3rty_A Period circadian protein; PAS domain, signalling, timeless,
circadian clock protein; 2.85A {Drosophila melanogaster}
PDB: 1wa9_A 3gec_A
Length = 339
Score = 75.1 bits (184), Expect = 3e-15
Identities = 38/188 (20%), Positives = 69/188 (36%), Gaps = 12/188 (6%)
Query: 143 EGFLFVVN-PDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQV 201
+ F V++ DG V + T +I + Y R LG+S + +H D A F + +
Sbjct: 3 DSFCCVISMHDGIVLYTTPSITDVLGYPRDMWLGRSFIDFVHLKDRATFASQITTGIPIA 62
Query: 202 NAWTSDSGGQA-----GKRPSLTASTPNRTFNIRLLISSTHLTAGLSRAGGENGQDDSGD 256
+ S R + R + R E + D+
Sbjct: 63 ESRGSVPKDAKSTFCVMLRRYRGLKSGGFGVIGRPVSYEPFRLGLTFREAPEEARPDNYM 122
Query: 257 VSSEGGPCLMCVARRIPPT----DKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYL 312
VS+ L+ A I + D+ LS +F ++ +G I +D++ VS YL
Sbjct: 123 VSNGTNMLLVICATPIKSSYKVPDEILSQKSPKFAIRHTATGIISHVDSAAVS--ALGYL 180
Query: 313 NKAVACKT 320
+ + ++
Sbjct: 181 PQDLIGRS 188
Score = 42.7 bits (100), Expect = 1e-04
Identities = 10/56 (17%), Positives = 22/56 (39%), Gaps = 3/56 (5%)
Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH---ARFHNCLVPS 197
F G ++ S + Y Q+++G+S+ + HH D + ++
Sbjct: 156 FAIRHTATGIISHVDSAAVSALGYLPQDLIGRSIMDFYHHEDLSVMKETYETVMKK 211
>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory
system, two-component signal transduction, transferase,
phosphorylation, SCOD; 1.7A {Bacillus subtilis}
Length = 111
Score = 48.2 bits (115), Expect = 2e-07
Identities = 12/68 (17%), Positives = 26/68 (38%)
Query: 135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL 194
G L+ V+ +G + + + N K + Y + E++G + +H D +
Sbjct: 1 GEFPLQTKTDIHAVLASNGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYF 60
Query: 195 VPSSHQVN 202
H +
Sbjct: 61 YNEHHLMP 68
>3f1p_B ARYL hydrocarbon receptor nuclear translocator; PAS domain,
heterodimer, internal cavity, activator, angiogenesis,
congenital erythrocytosis; 1.17A {Homo sapiens} PDB:
3f1o_B* 3f1n_B 3h7w_B* 3h82_B* 1x0o_A 2hv1_A 2b02_A*
2k7s_A 2a24_B
Length = 121
Score = 46.9 bits (112), Expect = 7e-07
Identities = 13/58 (22%), Positives = 22/58 (37%)
Query: 137 LLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL 194
L + F+ N +G F + + Y QE+LGK++ H D +
Sbjct: 6 LNVCQPTRFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSF 63
>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 = 44.6 bits (106), Expect = 1e-06
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE 110
E+RRR++ NN+I +L+++I SM S K IL + + I+ ++Q
Sbjct: 13 ERRRRDKINNWIVQLSKIIP----DSSMESTKSGQSKGGILSKASDYIQELRQSN 63
Score = 38.9 bits (91), Expect = 1e-04
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 6 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETV 50
E+RRR++ NN+I +L+++I SM S K IL +
Sbjct: 13 ERRRRDKINNWIVQLSKIIP----DSSMESTKSGQSKGGILSKAS 53
>3f1p_A Endothelial PAS domain-containing protein 1; PAS domain,
heterodimer, internal cavity, activator, angiogenesis,
congenital erythrocytosis; 1.17A {Homo sapiens} PDB:
3f1o_A* 3f1n_A 3h7w_A* 3h82_A* 1p97_A 2a24_A
Length = 117
Score = 46.1 bits (110), Expect = 1e-06
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGD 186
FL + D +C + I I Y +E+LG+S Y H D
Sbjct: 11 FLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALD 52
>2kdk_A ARYL hydrocarbon receptor nuclear translocator-LI 2; circadian
clock, PAS domain, transcription, activator, biolo
rhythms, DNA-binding, nucleus; NMR {Homo sapiens}
Length = 121
Score = 45.0 bits (107), Expect = 3e-06
Identities = 11/42 (26%), Positives = 18/42 (42%)
Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGD 186
F+ +G + + + + Y QE+LG S Y H D
Sbjct: 15 FITRFAVNGKFVYVDQRATAILGYLPQELLGTSCYEYFHQDD 56
>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 = 47.4 bits (112), Expect = 8e-06
Identities = 66/458 (14%), Positives = 120/458 (26%), Gaps = 187/458 (40%)
Query: 12 QENN--YIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEE 69
Q N Y EEL + L +T Y
Sbjct: 163 QGNTDDYFEELRD-----------------------LYQT----------------YHVL 183
Query: 70 LAELISAASFAESMSSLAVKPDKCAILQETVNQIRN-IKQQETSSDAVQQGEVSSSKPTV 128
+ +LI + AE++S L + I ++ + D + S P
Sbjct: 184 VGDLIKFS--AETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDK----DYLLSIP-- 235
Query: 129 ITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHA 188
+ PL+ G + + + YV ++LG + L + A
Sbjct: 236 ----ISCPLI-----GVIQLAH---YVVTA-------------KLLGFTPGELRSYLKGA 270
Query: 189 RFHNCLVPSSH---QVNAWTS--DSGGQA-------GKRPSLTASTPNRTFNIRLLISST 236
H+ + ++ + ++W S S +A G R PN + +L S
Sbjct: 271 TGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAY--PNTSLPPSILEDSL 328
Query: 237 HLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDKQLSAPIEQFTMKLDRSGTI 296
EN EG P M + +Q+ + + L +
Sbjct: 329 -----------ENN---------EGVPSPMLSISNLT--QEQVQDYVNKTNSHLPAGKQV 366
Query: 297 --------------------IGMDT--------SGVSQT--------------------- 307
G++ SG+ Q+
Sbjct: 367 EISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASP 426
Query: 308 -HTQYLNKAVA-----CKTSATVWTCPNS---PLTST----------KLLLKALLLSICT 348
H+ L A + + P+ T + + ++ I
Sbjct: 427 FHSHLLVPASDLINKDLVKNNVSFN-AKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIR 485
Query: 349 DYALVQTDTCMYRSSPS---CFGLQGASR-TSLWQRIR 382
V+ +T + + FG GAS L R +
Sbjct: 486 LP--VKWETTT-QFKATHILDFGPGGASGLGVLTHRNK 520
Score = 36.6 bits (84), Expect = 0.016
Identities = 36/211 (17%), Positives = 62/211 (29%), Gaps = 79/211 (37%)
Query: 201 VNAWTSDSGGQAGKRPSLTASTPNRTFNIRLLIS-STHLTAGLSRAGGENGQDDSGDVSS 259
++A+++ RP LT S + LL+ ++ A S+ Q+
Sbjct: 1 MDAYST--------RP-LTLSHGS--LEHVLLVPTASFFIA--SQL-----QEQ------ 36
Query: 260 EGGPCLMCVARRIPPT-----DKQLSAPIE------QFTMKLDRSGTIIGMD---TSGVS 305
PT D + + P E + L + D ++
Sbjct: 37 -------FNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLT 89
Query: 306 QTHTQYLNK----AVACKTSATVWTCPNSPLTSTKLLLKALLLSICTDY--ALVQTDTCM 359
+ YL A+A A + ++ L TK L+K Y A +
Sbjct: 90 EFENCYLEGNDIHALA----AKLLQENDTTLVKTKELIKN--------YITARIMAKRPF 137
Query: 360 YRSSPS---------------CFGLQGASRT 375
+ S S FG QG +
Sbjct: 138 DKKSNSALFRAVGEGNAQLVAIFGGQGNTDD 168
>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 = 6e-05
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 9/57 (15%)
Query: 54 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE 110
EKR R N+ I EL +L+ K +K A+L++ ++ IR ++
Sbjct: 12 AIEKRYRSSINDKIIELKDLVVG---------TEAKLNKSAVLRKAIDYIRFLQHSN 59
Score = 37.4 bits (87), Expect = 5e-04
Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 12/72 (16%)
Query: 4 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVN--QCLNEKRRR- 60
EKR R N+ I EL +L+ K +K A+L++ ++ + L ++
Sbjct: 12 AIEKRYRSSINDKIIELKDLVVG---------TEAKLNKSAVLRKAIDYIRFLQHSNQKL 62
Query: 61 EQENNYIEELAE 72
+QEN +
Sbjct: 63 KQENLSLRTAVH 74
>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 = 37.7 bits (88), Expect = 4e-04
Identities = 8/58 (13%), Positives = 22/58 (37%), Gaps = 8/58 (13%)
Query: 54 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQET 111
E++RR+ + L + + + K + IL + I+ ++++
Sbjct: 18 ALERKRRDHIKDSFHSLRDSVPSLQ--------GEKASRAQILDKATEYIQYMRRKNH 67
Score = 34.6 bits (80), Expect = 0.006
Identities = 10/70 (14%), Positives = 27/70 (38%), Gaps = 11/70 (15%)
Query: 4 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQE 63
E++RR+ + L + + + K + IL + + + RR+
Sbjct: 18 ALERKRRDHIKDSFHSLRDSVPSLQ--------GEKASRAQILDKAT-EYIQYMRRKNHT 68
Query: 64 NNYIEELAEL 73
+ +++ +L
Sbjct: 69 --HQQDIDDL 76
>3fc7_A HTR-like protein, sensor protein; APC87712.1, HTR-like
protein,haloarcula marismortui ATCC 430 structural
genomics, PSI-2; 2.65A {Haloarcula marismortui}
Length = 125
Score = 38.8 bits (91), Expect = 4e-04
Identities = 3/57 (5%), Positives = 18/57 (31%)
Query: 138 LLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL 194
L+ + + +G + ++ + ++G+ + ++ +
Sbjct: 24 LVSDSPDGIVHLTTNGTILSVNPSMAGRLGADPDTLVGQQLSAVMDSEAANQRLEAG 80
>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural
genomics, PSI-2, protein structure initiative; 2.40A
{Shewanella oneidensis}
Length = 129
Score = 38.2 bits (89), Expect = 9e-04
Identities = 11/57 (19%), Positives = 25/57 (43%)
Query: 138 LLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL 194
++ L + +VN +G++ C + + + + G+ N + AR+ N L
Sbjct: 12 FIQHLTEAMILVNANGFIRSCNQRSAELLDCPQVSLKGQDWRNFLTEHHQARYDNLL 68
>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 = 36.5 bits (85), Expect = 0.001
Identities = 12/56 (21%), Positives = 22/56 (39%), Gaps = 7/56 (12%)
Query: 56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQET 111
E++RR + L + I E K K IL++ I +++ +E
Sbjct: 14 ERQRRNELKRSFFALRDQIPELENNE-------KAPKVVILKKATAYILSVQAEEQ 62
Score = 32.3 bits (74), Expect = 0.041
Identities = 14/68 (20%), Positives = 22/68 (32%), Gaps = 10/68 (14%)
Query: 6 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENN 65
E++RR + L + I E K K IL++ + +E
Sbjct: 14 ERQRRNELKRSFFALRDQIPELENNE-------KAPKVVILKKATAYI---LSVQAEEQK 63
Query: 66 YIEELAEL 73
I E L
Sbjct: 64 LISEEDLL 71
>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 = 36.2 bits (84), Expect = 0.002
Identities = 8/59 (13%), Positives = 23/59 (38%), Gaps = 8/59 (13%)
Query: 54 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETS 112
E++RR+ + L + + + K + IL + I+ ++++ +
Sbjct: 8 ALERKRRDHIKDSFHSLRDSVPSLQ--------GEKASRAQILDKATEYIQYMRRKNHT 58
Score = 33.5 bits (77), Expect = 0.014
Identities = 9/70 (12%), Positives = 26/70 (37%), Gaps = 11/70 (15%)
Query: 4 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQE 63
E++RR+ + L + + + K + IL + + R +
Sbjct: 8 ALERKRRDHIKDSFHSLRDSVPSLQ--------GEKASRAQILDKATEYI---QYMRRKN 56
Query: 64 NNYIEELAEL 73
+ + +++ +L
Sbjct: 57 HTHQQDIDDL 66
>3zq5_A Phytochrome-like protein CPH1; arginine finger, tandem GAF domain,
receptor, PAS domain, chromophore, sensory transduction;
HET: CYC; 1.95A {Synechocystis SP} PDB: 2vea_A*
Length = 520
Score = 37.7 bits (87), Expect = 0.005
Identities = 12/95 (12%), Positives = 31/95 (32%), Gaps = 1/95 (1%)
Query: 144 GFLFVV-NPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVN 202
G + V+ PD ++ + N + S +++LG+++ + + L
Sbjct: 30 GLVVVLQEPDLTISQISANCTGILGRSPEDLLGRTLGEVFDSFQIDPIQSRLTAGQISSL 89
Query: 203 AWTSDSGGQAGKRPSLTASTPNRTFNIRLLISSTH 237
+ G + +R + L+
Sbjct: 90 NPSKLWARVMGDDFVIFDGVFHRNSDGLLVCELEP 124
>3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein
structure initiati northeast structural genomics
consortium; 2.60A {Desulfitobacterium hafniense}
Length = 126
Score = 35.3 bits (82), Expect = 0.007
Identities = 12/63 (19%), Positives = 25/63 (39%), Gaps = 12/63 (19%)
Query: 138 LLEALEGFLFVVNPDG---YVNFCTENIKSFIR---YSRQEVLGKSVYNLIHHGDHARFH 191
LE +E + ++N +G Y N + + Y+ +E++ + + G A
Sbjct: 4 FLETIEDMILIINREGRLLYAN------TAVPKKLGYTHEELMSMHILTITSAGKMAEGE 57
Query: 192 NCL 194
L
Sbjct: 58 KIL 60
>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 = 34.0 bits (78), Expect = 0.008
Identities = 10/67 (14%), Positives = 23/67 (34%), Gaps = 7/67 (10%)
Query: 6 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENN 65
EK RR +E+L L+ + + ++L + + + +
Sbjct: 9 EKNRRAHLRLSLEKLKGLVPLGPDSS-------RHTTLSLLTKAKLHIKKLEDSDRKAVH 61
Query: 66 YIEELAE 72
I++L
Sbjct: 62 QIDQLQR 68
Score = 31.3 bits (71), Expect = 0.095
Identities = 9/55 (16%), Positives = 21/55 (38%), Gaps = 7/55 (12%)
Query: 56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE 110
EK RR +E+L L+ + + ++L + I+ ++ +
Sbjct: 9 EKNRRAHLRLSLEKLKGLVPLGPDSS-------RHTTLSLLTKAKLHIKKLEDSD 56
>4e04_A Bacteriophytochrome (light-regulated signal trans histidine
kinase), PHYB1; bacteriophytochrome chromophore binding
domain; HET: LBV; 1.79A {Rhodopseudomonas palustris}
Length = 327
Score = 36.1 bits (83), Expect = 0.013
Identities = 11/60 (18%), Positives = 22/60 (36%)
Query: 144 GFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNA 203
G L + D + ++N+ + ++G+S ++ H R L V A
Sbjct: 30 GLLLALAADMTIVAGSDNLPELTGLAIGALIGRSAADVFDSETHNRLTIALAEPGAAVGA 89
>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 = 33.2 bits (76), Expect = 0.013
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETS 112
E+ RR + + ELA LI A +++S+ P K ++ IR+++Q ++
Sbjct: 10 EQARRNRLAVALHELASLIPAEWKQQNVSA---APSKATTVEAACRYIRHLQQNGST 63
Score = 26.7 bits (59), Expect = 2.9
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 6 EKRRREQENNYIEELAELISAASFAESMSSLAVK 39
E+ RR + + ELA LI A +++S+ K
Sbjct: 10 EQARRNRLAVALHELASLIPAEWKQQNVSAAPSK 43
>1oj5_A Steroid receptor coactivator 1A; transcriptional coactivator,
complex, LXXLL motif, transcriptional regulation; 2.2A
{Mus musculus} SCOP: d.110.3.8
Length = 132
Score = 34.5 bits (79), Expect = 0.018
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 282 PIEQFTMKLDRSGTIIGMDTSGVSQT 307
+E F K D +G II +DTS +
Sbjct: 5 GVESFMTKQDTTGKIISIDTSSLRAA 30
Score = 28.4 bits (63), Expect = 1.8
Identities = 7/49 (14%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 139 LEALEGFLFVVNPDGYVNFC-TENIKSFIRYSRQEVLGKSVYNLIHHGD 186
+ +E F+ + G + T ++++ R ++++ K +Y
Sbjct: 3 MTGVESFMTKQDTTGKIISIDTSSLRAAGRTGWEDLVRKCIYAFFQPQG 51
>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase,
phosphoprotein, transfe two-component regulatory system;
3.80A {Thermotoga maritima}
Length = 349
Score = 35.3 bits (82), Expect = 0.025
Identities = 12/86 (13%), Positives = 28/86 (32%), Gaps = 11/86 (12%)
Query: 137 LLLEALEGFL-----------FVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHG 185
+L+E L F ++ DG + + + ++ VLG+ + +L
Sbjct: 1 MLVEHLRNFSESILESLETAIITLSKDGRITEWNKKAEQLFGLKKENVLGRRLKDLPDFE 60
Query: 186 DHARFHNCLVPSSHQVNAWTSDSGGQ 211
+ + + V G +
Sbjct: 61 EIGSVAESVFENKEPVFLNFYKFGER 86
>3bwl_A Sensor protein; structural genomics, APC87707.1, PAS domain,
HTR-like protei protein structure initiative; HET: MSE
I3A; 1.73A {Haloarcula marismortui atcc 43049}
Length = 126
Score = 32.9 bits (76), Expect = 0.043
Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 12/50 (24%)
Query: 147 FVVNPDG---YVNFCTENIKSFIR---YSRQEVLGKSVYNLIHHGDHARF 190
V++ DG VN + F Y EVLG+S++ D
Sbjct: 31 DVLDADGTICEVN------QRFCAELGYDESEVLGRSIWEFDLMFDAEDV 74
>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 = 35.2 bits (80), Expect = 0.043
Identities = 27/210 (12%), Positives = 65/210 (30%), Gaps = 63/210 (30%)
Query: 1 AKCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRR 60
K L+ + ++L + L P + +I+ E++ +
Sbjct: 308 LKYLDCR---------PQDLPREV-----------LTTNPRRLSIIAESIR---DGLATW 344
Query: 61 EQENNY-IEELAELISAASFAESMSSLAVKP--DKCAILQETVNQIRNIKQQETSSDAVQ 117
+ + ++L +I S + + D+ ++ + +I +
Sbjct: 345 DNWKHVNCDKLTTIIE--SSLNVLEPAEYRKMFDRLSVFPPSA----HIPTI------LL 392
Query: 118 Q---GEVSSSKPTVITNEVLGPLLLE--ALEGFLFVVNPDGYVNFCTENI------KSFI 166
+V S V+ N++ L+E E + + P Y+ + +S +
Sbjct: 393 SLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI--PSIYLELKVKLENEYALHRSIV 450
Query: 167 -RYSRQEVLGKS----------VYNLI-HH 184
Y+ + Y+ I HH
Sbjct: 451 DHYNIPKTFDSDDLIPPYLDQYFYSHIGHH 480
>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase,
phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A
{Methylococcus capsulatus}
Length = 227
Score = 33.5 bits (77), Expect = 0.068
Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 11/48 (22%)
Query: 147 FVVNPDG---YVN--FCTENIKSFIRYSRQEVLGKSVYNLIHHGDHAR 189
+ + G Y N FC + RY R+E++G+ + +++ G H +
Sbjct: 3 SITDLQGRILYANDNFC-----AVSRYGREELVGQD-HRIVNSGYHGK 44
Score = 32.0 bits (73), Expect = 0.25
Identities = 6/43 (13%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 147 FVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHAR 189
+ + G + + + F + E+LG+S +++ +
Sbjct: 125 LLTDRAGRIIYANPALCRFSGMAEGELLGQS-PSILDSPLADQ 166
>2ool_A Sensor protein; bacteriophytochrome, photoconversion,
photoreceptor, biliver signaling protein; HET: LBV;
2.20A {Rhodopseudomonas palustris} SCOP: d.110.2.1
d.110.3.9
Length = 337
Score = 33.8 bits (77), Expect = 0.089
Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 2/75 (2%)
Query: 144 GFLFVVN-PDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSS-HQV 201
G+LFVV+ D + + N++ +R +L + + + AR + L +
Sbjct: 43 GYLFVVSETDLRIASVSANVEDLLRQPPASLLNVPIAHYLTAASAARLTHALHGGDPAAI 102
Query: 202 NAWTSDSGGQAGKRP 216
N D G+R
Sbjct: 103 NPIRLDVVTPDGERA 117
>2r78_A Sensor protein; sensory box sensor histidine kinase/response
regulator, structural genomics, PSI, MCSG; 1.60A
{Geobacter sulfurreducens pca}
Length = 117
Score = 32.1 bits (74), Expect = 0.089
Identities = 12/56 (21%), Positives = 20/56 (35%), Gaps = 13/56 (23%)
Query: 141 ALEGFLFVVNPDG---YVNFCTENIKSFIR---YSRQEVLGKSVYNLIHHGDHARF 190
A++G F+++ +G VN + Y+R E L L D
Sbjct: 20 AIDGI-FIMDAEGHYLDVN------PAICSAIGYTRDEFLALDWGVLSRGVDSGWA 68
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.4 bits (73), Expect = 0.15
Identities = 16/79 (20%), Positives = 25/79 (31%), Gaps = 25/79 (31%)
Query: 6 EKRR--REQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNE--KRRRE 61
E R RE++ ++EL A +E + L E +R+ E
Sbjct: 85 ESIRKWREEQRKRLQELDA-------ASK--------VMEQEWREKAKKDLEEWNQRQSE 129
Query: 62 Q-----ENNYIEELAELIS 75
Q NN I +
Sbjct: 130 QVEKNKINNRIAD-KAFYQ 147
Score = 32.4 bits (73), Expect = 0.16
Identities = 16/76 (21%), Positives = 27/76 (35%), Gaps = 16/76 (21%)
Query: 6 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAI------LQETVNQCLNEKRR 59
K R EQ + L EL A+ K K + E V + N+
Sbjct: 88 RKWREEQR----KRLQEL--DAASKVMEQEWREKAKK-DLEEWNQRQSEQVEK--NKINN 138
Query: 60 REQENNYIEEL-AELI 74
R + + ++ A++I
Sbjct: 139 RIADKAFYQQPDADII 154
>2e7s_A RAB guanine nucleotide exchange factor SEC2; coiled coil,
endocytosis/exocytosis complex; 3.00A {Saccharomyces
cerevisiae} SCOP: h.1.33.1
Length = 135
Score = 31.8 bits (71), Expect = 0.16
Identities = 17/128 (13%), Positives = 53/128 (41%), Gaps = 3/128 (2%)
Query: 4 LNEKRRR-EQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQ 62
LN+ + + IE +L + L+ + D+ L+E + + + + E+
Sbjct: 10 LNKSLKTIASQKAAIENYNQLK--EDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEE 67
Query: 63 ENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSSDAVQQGEVS 122
E + + + E ++A+ F E+ + +A + ++ ++ +++ ++
Sbjct: 68 EADKLNKEVEDLTASLFDEANNLVADARMEKYAIEILNKRLTEQLREKDMLLDTLTLQLK 127
Query: 123 SSKPTVIT 130
+ K + +
Sbjct: 128 NLKKVMHS 135
>1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET:
HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1
Length = 129
Score = 31.6 bits (71), Expect = 0.17
Identities = 7/51 (13%), Positives = 19/51 (37%)
Query: 132 EVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLI 182
+ +G +AL V+ G ++ + V+G++ + +
Sbjct: 21 DGMGTAEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRNFFTEV 71
>2ocy_A RAB guanine nucleotide exchange factor SEC2; RAB, GEF, guanine
exchange factor, coiled-coil, endocytosis/exocytosis
complex; 3.30A {Saccharomyces cerevisiae} SCOP: h.1.33.1
Length = 154
Score = 31.7 bits (71), Expect = 0.19
Identities = 15/132 (11%), Positives = 53/132 (40%), Gaps = 2/132 (1%)
Query: 6 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENN 65
+ + IE +L + L+ + D+ L+E + + + + E+E +
Sbjct: 25 SLKTIASQKAAIENYNQL--KEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEAD 82
Query: 66 YIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSSDAVQQGEVSSSK 125
+ + E ++A+ F E+ + +A + ++ ++ +++ + ++ + K
Sbjct: 83 KLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQLREKDTLLDTLTLQLKNLK 142
Query: 126 PTVITNEVLGPL 137
+ + + +
Sbjct: 143 KVMHSLDNESTV 154
>3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2,
protein structure initiative, northeast structural
genomics consortium; 2.00A {Colwellia psychrerythraea}
Length = 124
Score = 30.5 bits (70), Expect = 0.32
Identities = 10/49 (20%), Positives = 18/49 (36%), Gaps = 13/49 (26%)
Query: 147 FVVNPDG---YVNFCTENIKSFIR---YSRQEVLGKSVYNLIHHGDHAR 189
V + G N K YS+++ +G+ V N++H
Sbjct: 21 VVTDLQGFIIDWN------KGSETLYGYSKEQAIGQPV-NMLHVPGDTE 62
>3s7o_A Bacteriophytochrome; biliverdin, PAS, GAF, photoreceptor,
fluorescent protein; HET: LBV GOL; 1.24A {Deinococcus
radiodurans} PDB: 3s7n_A* 3s7p_A* 3s7q_A* 2o9c_A*
2o9b_A* 1ztu_A*
Length = 343
Score = 31.1 bits (70), Expect = 0.56
Identities = 11/72 (15%), Positives = 22/72 (30%), Gaps = 1/72 (1%)
Query: 144 GFLFVVN-PDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVN 202
G L + G V + N +F+ + G+++ L+ A +
Sbjct: 53 GALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQ 112
Query: 203 AWTSDSGGQAGK 214
+ AG
Sbjct: 113 YRATLDWPAAGH 124
>2vv6_A FIXL, sensor protein FIXL; signaling protein, transferase,
phosphoprotein, nitrogen FIX PER-ARNT-SIM,
metal-binding, PAS, iron, heme; HET: HEM; 1.5A
{Bradyrhizobium japonicum} PDB: 1xj6_A* 1xj4_A* 2vv7_A*
2vv8_A* 1lsw_A* 1dp8_A* 1dp9_A* 1drm_A* 1lsv_A* 1dp6_A*
1lsx_A* 1lt0_A* 1y28_A* 2cmn_A* 1xj3_A* 1xj2_A* 2owh_A*
2owj_A*
Length = 119
Score = 29.8 bits (68), Expect = 0.58
Identities = 10/56 (17%), Positives = 22/56 (39%), Gaps = 10/56 (17%)
Query: 141 ALEGFLFVVNPDG---YVNFCTENIKSFIRYSRQEVLGKSVYNLI---HHGDHARF 190
+ + V++ G + E + F +S E +G++V L+ H +
Sbjct: 2 IPDAMI-VIDGHGIIQLFSTAAERL--F-GWSELEAIGQNVNILMPEPDRSRHDSY 53
>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural
genomics, midwest center for structural genomics; HET:
PGE; 2.49A {Geobacter sulfurreducens}
Length = 114
Score = 29.5 bits (67), Expect = 0.64
Identities = 8/55 (14%), Positives = 19/55 (34%), Gaps = 4/55 (7%)
Query: 137 LLLEALEGFLFVVNPDG-YVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARF 190
L E L + + + Y+ + + ++LG S Y++ +
Sbjct: 7 LFTEHAPAALAMFDREMRYL-AVSRRWREDYGLGDGDILGMSHYDI--FPEIGEE 58
>3nhq_A Bacteriophytochrome; photoreceptor, PAS, signaling, signaling
protei; HET: BLA; 2.55A {Pseudomonas aeruginosa} PDB:
3c2w_A* 3g6o_A* 3ibr_A*
Length = 505
Score = 31.2 bits (70), Expect = 0.67
Identities = 8/32 (25%), Positives = 14/32 (43%)
Query: 144 GFLFVVNPDGYVNFCTENIKSFIRYSRQEVLG 175
G L + DG V +ENI++ + +
Sbjct: 27 GALVTLRADGMVLAASENIQALLGFVASPGSY 58
>3olo_A Two-component sensor histidine kinase; structural genomics, PSI-2,
protein structure initiative, MI center for structural
genomics, MCSG, TRA; 2.09A {Nostoc SP}
Length = 118
Score = 29.5 bits (67), Expect = 0.79
Identities = 9/52 (17%), Positives = 20/52 (38%), Gaps = 12/52 (23%)
Query: 147 FVVNPDG---YVNFCTENIKSFIR---YSRQEVLGKSVYNLIHHGDHARFHN 192
F + + YVN + R YSR+++L ++ ++ +
Sbjct: 27 FCLGDNWQFLYVN------DATCRMTEYSREQLLSMNLQDIDVDFALHDWEE 72
>1d06_A Nitrogen fixation regulatory protein FIXL; oxygen sensor, histidine
kinase, PAS, high-resolution, two-C system, signaling
protein; HET: HEM; 1.40A {Sinorhizobium meliloti} SCOP:
d.110.3.2 PDB: 1ew0_A*
Length = 130
Score = 29.4 bits (67), Expect = 0.84
Identities = 12/60 (20%), Positives = 26/60 (43%), Gaps = 11/60 (18%)
Query: 138 LLE-ALEGFLFVVNPDG---YVNFCTENIKSFIRYSRQEVLGKSVYNLI---HHGDHARF 190
+L+ + + V DG N F Y+ +EV+G+++ L+ + +H +
Sbjct: 21 ILDTVPDATV-VSATDGTIVSFNAAAVRQ--F-GYAEEEVIGQNLRILMPEPYRHEHDGY 76
>1v9y_A Heme PAS sensor protein; signaling protein; HET: HEM; 1.32A
{Escherichia coli} SCOP: d.110.3.2 PDB: 1v9z_A* 1vb6_A*
1s67_L* 1s66_L*
Length = 167
Score = 29.2 bits (66), Expect = 1.2
Identities = 16/103 (15%), Positives = 39/103 (37%), Gaps = 21/103 (20%)
Query: 94 AILQETVNQIRNIKQQETSSDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDG 153
++ + ++ + +DA + + P L + + G + ++N +
Sbjct: 13 GLVPRGSHMRQDAEVIMKLTDADNAAD-----------GIFFPALEQNMMGAV-LINEND 60
Query: 154 ---YVNFCTENIKSFIRYSRQEVLGKSVYNLI---HHGDHARF 190
+ N E + + Y R+EV+G ++ LI H +
Sbjct: 61 EVMFFNPAAEKL--W-GYKREEVIGNNIDMLIPRDLRPAHPEY 100
>3fg8_A Uncharacterized protein RHA05790; PAS domain, structural genomics,
PS protein structure initiative, midwest center for
structural genomics, MCSG; HET: 3PB; 1.80A {Rhodococcus
SP}
Length = 118
Score = 28.5 bits (64), Expect = 1.5
Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 8/58 (13%)
Query: 138 LLEAL-EGFLFVVNPDG---YVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFH 191
L GF ++ D YVN +R SR E+LG+ V ++ + F
Sbjct: 17 LYFQGGLGF-MALDEDLRIIYVNSGCLRH---VRRSRDELLGRVVTEVLPETQGSYFD 70
>3prt_A Carboxypeptidase T; hydrolase; 1.66A {Thermoactinomyces vulgaris}
PDB: 1obr_A 3qnv_A
Length = 323
Score = 29.6 bits (67), Expect = 1.6
Identities = 10/33 (30%), Positives = 14/33 (42%)
Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKS 177
+F +NPDG + R +RQ G S
Sbjct: 107 IVFNINPDGGEYDISSGSYKSWRKNRQPNSGSS 139
>1ll8_A PAS kinase; PAS domain, ligand binding, ligand screening, kinase
regulation, transferase; NMR {Homo sapiens} SCOP:
d.110.3.5
Length = 114
Score = 27.8 bits (62), Expect = 2.5
Identities = 7/46 (15%), Positives = 16/46 (34%), Gaps = 1/46 (2%)
Query: 147 FVVNPD-GYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFH 191
F V+ + + + YS Q+++G+ + D
Sbjct: 12 FTVDAKTTEILVANDKACGLLGYSSQDLIGQKLTQFFLRSDSDVVE 57
>3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase,
two-component regulatory system; HET: PG4 PGE; 1.47A
{Thermotoga maritima} PDB: 3a0v_A*
Length = 96
Score = 27.5 bits (61), Expect = 2.5
Identities = 6/44 (13%), Positives = 18/44 (40%)
Query: 146 LFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHAR 189
+ ++ DG + + + ++ VLG+ + +L +
Sbjct: 5 IITLSKDGRITEWNKKAEQLFGLKKENVLGRRLKDLPDFEEIGS 48
>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein,
feedback inhibition, deoxyribonucleoside kinase, salvage
pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP:
c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A*
2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A*
1zm7_A* 1zmx_A*
Length = 230
Score = 28.5 bits (63), Expect = 2.8
Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 6/50 (12%)
Query: 29 FAESMSSLAVKPDKCAILQETVNQCLN--EKRRREQENN----YIEELAE 72
+ S+ V+ D L+ + +R R +E+ Y++EL E
Sbjct: 136 YKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHE 185
>1nwz_A PYP, photoactive yellow protein; PAS, LOV, GAF, domains fold,
signaling protein; HET: HC4; 0.82A {Halorhodospira
halophila} SCOP: d.110.3.1 PDB: 1kou_A* 1ot9_A* 1otb_A*
1s4r_A* 1s4s_A* 1ts0_A* 1ts6_A* 1ts7_A* 1ts8_A* 1uwn_X*
1uwp_X* 2d01_A* 2phy_A* 2pyp_A* 2pyr_A* 2qj5_A* 2qj7_A*
2qws_A* 2zoh_A* 2zoi_A* ...
Length = 125
Score = 27.8 bits (61), Expect = 2.8
Identities = 7/51 (13%), Positives = 18/51 (35%)
Query: 132 EVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLI 182
+ L+ L ++ DG + ++V+GK+ + +
Sbjct: 16 AKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDV 66
>3aai_A Copper homeostasis operon regulatory protein; all alpha proteins,
4-helix bundle, transcription; 2.10A {Thermus
thermophilus}
Length = 94
Score = 26.3 bits (58), Expect = 5.5
Identities = 11/64 (17%), Positives = 23/64 (35%), Gaps = 7/64 (10%)
Query: 11 EQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEEL 70
E E Y ++ + + A A + + +L+ + + R +EEL
Sbjct: 35 EDEKVYCVDVLKQLKAVEGA--LDRVGEM-----VLRAHLKDHVATAHERGDVEEIVEEL 87
Query: 71 AELI 74
E +
Sbjct: 88 MEAL 91
>3o7b_A Ribosome biogenesis NEP1 RNA methyltransferase; spout, rRNA
processi transferase; HET: TYR SAH; 1.45A {Archaeoglobus
fulgidus}
Length = 244
Score = 27.6 bits (61), Expect = 5.6
Identities = 10/48 (20%), Positives = 17/48 (35%)
Query: 270 RRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVA 317
RRI D L + + R ++ G ++ L+ VA
Sbjct: 143 RRITAGDTTLIEFKDVGLRDIVRGRDVLLFREKGGRFEFSELLDGDVA 190
>3ono_A Ribose/galactose isomerase; structural genomics, PSI-2, protein
structure initiative, MI center for structural genomics,
MCSG; HET: MSE; 1.75A {Vibrio parahaemolyticus}
Length = 214
Score = 27.5 bits (61), Expect = 5.7
Identities = 11/70 (15%), Positives = 25/70 (35%), Gaps = 4/70 (5%)
Query: 5 NEKRRREQENNYIEELAEL--ISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQ 62
E+ +Q N L + A E + ++ + K A+ +C + +
Sbjct: 147 IERAAPQQAN--AAILNNVKAAVAKDVVEGLRAIDQELVKTAVGSTQFQECFFAHCQVPE 204
Query: 63 ENNYIEELAE 72
Y++ L +
Sbjct: 205 IAEYVKSLLD 214
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
0.315 0.128 0.369
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: 5,370,445
Number of extensions: 299166
Number of successful extensions: 728
Number of sequences better than 10.0: 1
Number of HSP's gapped: 701
Number of HSP's successfully gapped: 74
Length of query: 383
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 288
Effective length of database: 4,049,298
Effective search space: 1166197824
Effective search space used: 1166197824
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.5 bits)