RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17809
(294 letters)
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 108 bits (272), Expect = 2e-27
Identities = 37/267 (13%), Positives = 77/267 (28%), Gaps = 79/267 (29%)
Query: 11 HILQVEMTGSSVFDYIHQADHTELAEQLGLGL---SQGHGLASPGSANSEEGSGMNTGTA 67
+ Q ++ G S+FDY+H D ++ EQL + A G + + +
Sbjct: 121 NYSQNDLIGQSLFDYLHPKDIAKVKEQLSSSDTAPRERLIDAKTGLPVKTDITPGPSRLC 180
Query: 68 NPDVSS----LMSLSSSSSYKGCDRSFCIRMKSTLTKRGCHFKSSGY--------RSLDG 115
+ S + S + D + K K C S+GY LD
Sbjct: 181 SGARRSFFCRMKCNRPSVKVEDKDFASTCSKKKADRKSFCTIHSTGYLKSWPPTKMGLDE 240
Query: 116 ---------------------------------------FAFALGSDGRFLYISETVSIY 136
+ DG+F+++ + +
Sbjct: 241 DNEPDNEGCNLSCLVAIGRLHSHMVPQPANGEIRVKSMEYVSRHAIDGKFVFVDQRATAI 300
Query: 137 LGLSQWQVIN-------------------------KGQVLTHYYRLMNKNGGYTWVQSCA 171
L +++ + ++ T+ Y+ K+G + ++S
Sbjct: 301 LAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKITTNCYKFKIKDGSFITLRSRW 360
Query: 172 TVVCSSKNADEQNIICVNYVISGREYE 198
+ + + I+ N V+ E
Sbjct: 361 FSFMNPWTKEVEYIVSTNTVVLANVLE 387
Score = 43.1 bits (101), Expect = 6e-05
Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 3/84 (3%)
Query: 66 TANPDVSSLMSLSSSS--SYKGCDRSFCIRMKSTLTKRGCHFKSSGYRSLDGFAFALGSD 123
+ D +++ ++ + +G + K R+ DGF F +G D
Sbjct: 46 SRKLDKLTVLRMAVQHMKTLRGATNPYTEANYKPTFLSDDELKHLILRAADGFLFVVGCD 105
Query: 124 -GRFLYISETVSIYLGLSQWQVIN 146
G+ L++SE+V L SQ +I
Sbjct: 106 RGKILFVSESVFKILNYSQNDLIG 129
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS,
circadian rhythm proteins, transcription-activato; 2.27A
{Mus musculus}
Length = 361
Score = 105 bits (263), Expect = 2e-26
Identities = 28/245 (11%), Positives = 70/245 (28%), Gaps = 62/245 (25%)
Query: 11 HILQVEMTGSSVFDYIHQADHTELAEQLGLGLSQGHGLASPGSANSEEGSGMNTGTANPD 70
L ++ S+F++I + +H+E+ + L L + L + +
Sbjct: 120 EHLPSDLVDQSIFNFIPEGEHSEVYKILSTHLLESDSLTPEYLKSKNQLE-FCCHMLRGT 178
Query: 71 VSSLMSLSSSSSYKGCDRSFCIRMKSTLTKRGCHFKSSGYRSLDG--------------- 115
+ S+Y+ + ++++ + +
Sbjct: 179 IDPK----EPSTYEYVRFIGNFKSLTSVSTSTHNGFEGTIQRTHRPSYEDRVCFVATVRL 234
Query: 116 ------------------FAFALGSDGRFLYISETVSIYLGL------------------ 139
F + +FL++ +G
Sbjct: 235 ATPQFIKEMCTVEEPNEEFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHVDD 294
Query: 140 ------SQWQVINKGQVLTHYYRLMNKNGGYTWVQSCATVVCSSKNADEQNIICVNYVIS 193
++ G+ + YYR + K + W+Q+ + N+ + I+C + V+S
Sbjct: 295 LENLAKCHEHLMQYGKGKSCYYRFLTKGQQWIWLQTHYYITYHQWNSRPEFIVCTHTVVS 354
Query: 194 GREYE 198
E
Sbjct: 355 YAEVR 359
Score = 45.7 bits (108), Expect = 7e-06
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 111 RSLDGFAFALGSDGRFLYISETVSIYLGLSQWQVIN 146
+LDGF A+ +DG +Y+SE+V+ L +++
Sbjct: 93 EALDGFFLAIMTDGSIIYVSESVTSLLEHLPSDLVD 128
>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock
protein, protein binding; 2.75A {Mus musculus}
Length = 320
Score = 96.6 bits (240), Expect = 2e-23
Identities = 25/261 (9%), Positives = 52/261 (19%), Gaps = 88/261 (33%)
Query: 11 HILQVEMTGSSVFDYIHQADHTELAEQLGLGLSQGHGLASPGSANSEEGSGMNTGTANPD 70
+ G+ + + D T + P
Sbjct: 61 RCKRDVFRGARFSELLAPQDVGVFYGST-------------------------TPSRLPT 95
Query: 71 VSSLMSLSSSSSYKGCDRSFCIRMKSTLTKRG----CHFKSSGY-------------RSL 113
+ S S ++S R++ + F+ + Y
Sbjct: 96 WGTGTSAGSGLKDFTQEKSVFCRIRGGPDRDPGPRYQPFRLTPYVTKIRVSDGAPAQPCC 155
Query: 114 DGFAFALGS--------------------DGRFLYISETVSIYLGLSQWQVIN------- 146
A + S F + E + LG ++
Sbjct: 156 LLIAERIHSGYEAPRIPPDKRIFTTRHTPSCLFQDVDERAAPLLGYLPQDLLGAPVLLFL 215
Query: 147 ------------------KGQVLTH-YYRLMNKNGGYTWVQSCATVVCSSKNADEQNIIC 187
GQ H R +NG Y + + + ++
Sbjct: 216 HPEDRPLMLAIHKKILQLAGQPFDHSPIRFCARNGEYVTMDTSWAGFVHPWSRKVAFVLG 275
Query: 188 VNYVISGREYENFIMDCCQLE 208
+ V + E+
Sbjct: 276 RHKVRTAPLNEDVFTPPAPSP 296
Score = 44.2 bits (104), Expect = 2e-05
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 111 RSLDGFAFALG-SDGRFLYISETVSIYLGLSQWQVINK 147
R+ D F+ A+ GR +YISE + L +
Sbjct: 33 RNQDTFSVAVSFLTGRIVYISEQAGVLLRCKRDVFRGA 70
>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological
rhythms, cytoplasm, nucleus, phosphoprotein,
transcription; 2.40A {Mus musculus}
Length = 309
Score = 95.0 bits (236), Expect = 6e-23
Identities = 29/262 (11%), Positives = 56/262 (21%), Gaps = 88/262 (33%)
Query: 11 HILQVEMTGSSVFDYIHQADHTELAEQLGLGLSQGHGLASPGSANSEEGSGMNTGTANPD 70
H + + + +++ D + P S S
Sbjct: 50 HCKKDAFSDAKFVEFLAPHDVSVFHSYTT------PYKLPPWSVCS-------------- 89
Query: 71 VSSLMSLSSSSSYKGCDRSFCIRMKSTLTKRG----------CHFKS------------- 107
L S + ++SF R+ +
Sbjct: 90 -----GLDSFTQECMEEKSFFCRVSVGKHHENEIRYQPFRMTPYLVKVQEQQGAESQLCC 144
Query: 108 --------SGYRSLD------GFAFALGSDGRFLYISETVSIYLGLSQ------------ 141
SGY + F + F + E LG
Sbjct: 145 LLLAERVHSGYEAPRIPPEKRIFTTTHTPNCLFQAVDERAVPLLGYLPQDLIETPVLVQL 204
Query: 142 ------------WQVINKGQVL--THYYRLMNKNGGYTWVQSCATVVCSSKNADEQNIIC 187
+++ G R +NG Y + + + + + II
Sbjct: 205 HPSDRPLMLAIHKKILQAGGQPFDYSPIRFRTRNGEYITLDTSWSSFINPWSRKISFIIG 264
Query: 188 VNYVISGREYENFIMDCCQLED 209
+ V G E+ E+
Sbjct: 265 RHKVRVGPLNEDVFAAPPCPEE 286
Score = 44.6 bits (105), Expect = 2e-05
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 111 RSLDGFAFALG-SDGRFLYISETVSIYLGLSQWQVIN 146
++ D FA A+ G+ LYIS V+ + +
Sbjct: 22 KNADMFAVAVSLVSGKILYISNQVASIFHCKKDAFSD 58
>3rty_A Period circadian protein; PAS domain, signalling, timeless,
circadian clock protein; 2.85A {Drosophila melanogaster}
PDB: 1wa9_A 3gec_A
Length = 339
Score = 93.2 bits (231), Expect = 4e-22
Identities = 33/241 (13%), Positives = 61/241 (25%), Gaps = 52/241 (21%)
Query: 11 HILQVEMTGSSVFDYIHQADHTELAEQLGLGLSQGHGLASPGSANSEEGSGMNTGTANPD 70
+ G S D++H D A Q+ G+ S M
Sbjct: 28 GYPRDMWLGRSFIDFVHLKDRATFASQITTGIPIAESRGSVPKDAKSTFCVMLRRYRGLK 87
Query: 71 VSSLMSLSSSSSYKGCDRSFCIRMKSTLTKRGCHFKSSG--------------------- 109
+ SY+ R + + S+G
Sbjct: 88 SGGFGVIGRPVSYEPFRLGLTFREAPEEARPDNYMVSNGTNMLLVICATPIKSSYKVPDE 147
Query: 110 --YRSLDGFAFALGSDGRFLYISETVSIYLGLSQ------------------------WQ 143
+ FA + G ++ LG
Sbjct: 148 ILSQKSPKFAIRHTATGIISHVDSAAVSALGYLPQDLIGRSIMDFYHHEDLSVMKETYET 207
Query: 144 VINKGQV-----LTHYYRLMNKNGGYTWVQSCATVVCSSKNADEQNIICVNYVISGREYE 198
V+ KGQ + YR + +NG Y +++ T + + + ++ + V G +
Sbjct: 208 VMKKGQTAGASFCSKPYRFLIQNGCYVLLETEWTSFVNPWSRKLEFVVGHHRVFQGPKQC 267
Query: 199 N 199
N
Sbjct: 268 N 268
Score = 41.2 bits (96), Expect = 2e-04
Identities = 8/34 (23%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 114 DGFAFALG-SDGRFLYISETVSIYLGLSQWQVIN 146
D F + DG LY + +++ LG + +
Sbjct: 3 DSFCCVISMHDGIVLYTTPSITDVLGYPRDMWLG 36
>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 = 83.1 bits (206), Expect = 3e-20
Identities = 27/98 (27%), Positives = 47/98 (47%), Gaps = 24/98 (24%)
Query: 123 DGRFLYISETVSIYLG-LSQ-----------------------WQVINKGQVLTHYYRLM 158
D +F Y + ++ +G + + KGQV++ YR++
Sbjct: 18 DMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRML 77
Query: 159 NKNGGYTWVQSCATVVCSSKNADEQNIICVNYVISGRE 196
K+GGY W+++ TV+ + +N Q I+CVNYV+S E
Sbjct: 78 AKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIE 115
Score = 27.2 bits (61), Expect = 3.0
Identities = 6/31 (19%), Positives = 14/31 (45%)
Query: 16 EMTGSSVFDYIHQADHTELAEQLGLGLSQGH 46
E+ G S +++ H D + + ++G
Sbjct: 38 ELLGRSAYEFYHALDSENMTKSHQNLCTKGQ 68
>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm,
protein binding; 2.50A {Mus musculus}
Length = 317
Score = 87.8 bits (217), Expect = 4e-20
Identities = 26/259 (10%), Positives = 50/259 (19%), Gaps = 89/259 (34%)
Query: 11 HILQVEMTGSSVFDYIHQADHTELAEQLGLGLSQGHGLASPGSANSEEGSGMNTGTANPD 70
+ + + D + D + P N
Sbjct: 61 NSKRGFLKSVHFVDLLAPQDVRAFY-------AHTAPTQLPFWNNW-------------- 99
Query: 71 VSSLMSLSSSSSYKGCDRSFCIRMKSTLTKRGCHF------------KSSGYRSLDGFAF 118
+ +S + F R+ + H+ SS +
Sbjct: 100 -----TQRASQYECAPAKPFFCRICGGGDREKRHYSPFRILPYLVHVHSSAQPEPEPCCL 154
Query: 119 AL------------------------GSDGRFLYISETVSIYLGL--------------- 139
L FL + E LG
Sbjct: 155 TLVEKIHSGYEAPRIPVDKRIFTTTHTPGCVFLEVDERAVPLLGYLPQDLIGTSILTYLH 214
Query: 140 ---------SQWQVINKGQ---VLTHYYRLMNKNGGYTWVQSCATVVCSSKNADEQNIIC 187
+V+ R +NG Y + S + + + II
Sbjct: 215 PEDRPLMVAIHQKVLKYAGHPPFEHSPVRFCTQNGEYVILDSSWSSFVNPWSRKVSFIIG 274
Query: 188 VNYVISGREYENFIMDCCQ 206
+ V + E+ +
Sbjct: 275 RHKVRTSPLNEDVFATRIK 293
Score = 43.5 bits (102), Expect = 4e-05
Identities = 10/53 (18%), Positives = 20/53 (37%), Gaps = 1/53 (1%)
Query: 96 STLTKRGCHFKSSGYRSLDGFAFALG-SDGRFLYISETVSIYLGLSQWQVINK 147
+L ++ D FA GR ++ISE ++ L + + +
Sbjct: 18 YSLEDLTALASEHTSKNTDTFAAVFSFLSGRLVHISEQAALILNSKRGFLKSV 70
>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 = 79.2 bits (196), Expect = 8e-19
Identities = 17/101 (16%), Positives = 37/101 (36%), Gaps = 25/101 (24%)
Query: 123 DGRFLYISETVSIYLGLSQWQVINK-------------------------GQVLTHYYRL 157
+G F ++ +G +++ K GQVL+ +R
Sbjct: 21 EGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRF 80
Query: 158 MNKNGGYTWVQSCATVVCSSKNADEQNIICVNYVISGREYE 198
+KN + W+++ + + + + + IIC N + E
Sbjct: 81 RSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKNSSQE 121
Score = 26.8 bits (60), Expect = 3.9
Identities = 5/30 (16%), Positives = 12/30 (40%)
Query: 16 EMTGSSVFDYIHQADHTELAEQLGLGLSQG 45
E+ G ++ ++ H D L + +
Sbjct: 41 ELLGKNIVEFCHPEDQQLLRDSFQQVVKLK 70
>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 = 78.5 bits (194), Expect = 2e-18
Identities = 15/99 (15%), Positives = 37/99 (37%), Gaps = 25/99 (25%)
Query: 123 DGRFLYISETVSIYLGLSQWQVINK-------------------------GQVLTHYYRL 157
+G+F+Y+ + + LG +++ ++LT Y+
Sbjct: 22 NGKFVYVDQRATAILGYLPQELLGTSCYEYFHQDDHNNLTDKHKAVLQSKEKILTDSYKF 81
Query: 158 MNKNGGYTWVQSCATVVCSSKNADEQNIICVNYVISGRE 196
K+G + ++S + + + I+ VN ++ G
Sbjct: 82 RAKDGSFVTLKSQWFSFTNPDTKELEYIVSVNTLVLGHS 120
Score = 27.3 bits (61), Expect = 3.0
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 16 EMTGSSVFDYIHQADHTELAEQLGLGLSQG 45
E+ G+S ++Y HQ DH L ++ L
Sbjct: 42 ELLGTSCYEYFHQDDHNNLTDKHKAVLQSK 71
>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 = 46.9 bits (111), Expect = 5e-07
Identities = 6/54 (11%), Positives = 19/54 (35%)
Query: 143 QVINKGQVLTHYYRLMNKNGGYTWVQSCATVVCSSKNADEQNIICVNYVISGRE 196
+V+ +G + YR + +G + + + I+ ++ +
Sbjct: 63 EVMTRGTASSPSYRFILNDGTMLSAHTRCKLCYPQSPDMQPFIMGIHIIDREHS 116
>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 = 46.3 bits (110), Expect = 7e-07
Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 21/89 (23%)
Query: 120 LGSDGRFLYISETVSIYLGLSQWQVI---------------------NKGQVLTHYYRLM 158
L S+GR +YIS ++LG Q ++I N+ ++ +R +
Sbjct: 15 LASNGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYFYNEHHLMPCTFRFI 74
Query: 159 NKNGGYTWVQSCATVVCSSKNADEQNIIC 187
K+ WV++ +V + E+ II
Sbjct: 75 KKDHTIVWVEAAVEIVTTRAERTEREIIL 103
Score = 27.8 bits (62), Expect = 1.8
Identities = 6/24 (25%), Positives = 11/24 (45%)
Query: 16 EMTGSSVFDYIHQADHTELAEQLG 39
EM GS + ++H+ D +
Sbjct: 38 EMIGSFLKTFLHEEDQFLVESYFY 61
>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 = 43.9 bits (103), Expect = 4e-05
Identities = 42/268 (15%), Positives = 84/268 (31%), Gaps = 71/268 (26%)
Query: 8 QGTHILQVEMTG-----SS-----VFDYIHQAD-HTELAEQLGL---------------- 40
QG+ + M G +S V++ +AD H + + G
Sbjct: 1624 QGSQ--EQGM-GMDLYKTSKAAQDVWN---RADNHFK--DTYGFSILDIVINNPVNLTIH 1675
Query: 41 -GLSQGHGLASPGSANSEEGSGMNTGTANPDVSSLMSLSSSSSYKGCDRSFCIRMKST-- 97
G +G + SA E + S+S +++ ++ + T
Sbjct: 1676 FGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRS-EKGLLSATQFTQP 1734
Query: 98 ---LTKRGC--HFKSSGYRSLDGFAFA---LG------SDGRFLYISETVSI--YLGLSQ 141
L ++ KS G D FA LG S + I V + Y G++
Sbjct: 1735 ALTLMEKAAFEDLKSKGLIPADAT-FAGHSLGEYAALASLADVMSIESLVEVVFYRGMTM 1793
Query: 142 WQVINKGQVLTHYYRLMNKNGGYTWVQSCATVV--CSSKNADEQNIIC--VNY------- 190
+ + ++ Y ++ N G + + + VNY
Sbjct: 1794 QVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQY 1853
Query: 191 VISGREYENFIMDC-CQLEDYIQQRGVK 217
V +G + +D + ++I+ + +
Sbjct: 1854 VAAG-DLRA--LDTVTNVLNFIKLQKID 1878
>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 = 32.0 bits (73), Expect = 0.082
Identities = 8/37 (21%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 111 RSLDGFAFALGSDGRFLYISETVSIYLGLSQWQVINK 147
+ GF AL D R +Y++ ++ S+ +++ +
Sbjct: 20 QGGLGF-MALDEDLRIIYVNSGCLRHVRRSRDELLGR 55
>3icy_A Sensor protein; sensory box histidine kinase/response regulator
domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A
{Chlorobaculum tepidum}
Length = 118
Score = 29.6 bits (67), Expect = 0.45
Identities = 11/98 (11%), Positives = 21/98 (21%), Gaps = 30/98 (30%)
Query: 110 YRSL----DGFAFALGSDG--RFLYISETVSIYLGLSQW--------------------- 142
++L + L G + L
Sbjct: 6 LQALVDNIPAAIYHLDVSGQATIRFRPPAFLKTLVSEHAGTTRLNTLSMIHHDDRHMLSN 65
Query: 143 ---QVINKGQVLTHYYRLMNKNGGYTWVQSCATVVCSS 177
++ LT YR++ G W++ S
Sbjct: 66 AYSKLREAKHSLTLVYRIVTPEGKLHWIEDHMRSSFSD 103
>3mr0_A Sensory box histidine kinase/response regulator; PAS fold,
structural genomics, PSI-2; HET: PG5; 1.49A
{Burkholderia thailandensis}
Length = 142
Score = 29.8 bits (68), Expect = 0.59
Identities = 7/26 (26%), Positives = 13/26 (50%), Gaps = 3/26 (11%)
Query: 152 THY---YRLMNKNGGYTWVQSCATVV 174
Y YR+ ++G + W+QS +
Sbjct: 80 DTYDVEYRVRTRSGDFRWIQSRGQAL 105
>3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein.,
structural genomics, PSI-2, protein STR initiative;
1.90A {Marinobacter aquaeolei}
Length = 115
Score = 29.1 bits (66), Expect = 0.59
Identities = 15/77 (19%), Positives = 23/77 (29%), Gaps = 25/77 (32%)
Query: 123 DGRFLYISETVSIYLGLSQ--------W-----------------QVINKGQVLTHYYRL 157
F YI + LG Q W + G YR
Sbjct: 13 TMAFEYIGPQIEALLGWPQGSWKSVEDWATRMHPEDQEWVVNFCVKQSECGVDHEADYRA 72
Query: 158 MNKNGGYTWVQSCATVV 174
++++G Y W++ VV
Sbjct: 73 LHRDGHYVWIRDVVHVV 89
>3eeh_A Putative light and redox sensing histidine kinase; structural
genomic MCSG, protein structure initiative, midwest
center for STRU genomics; HET: PG5; 1.95A {Haloarcula
marismortui}
Length = 125
Score = 29.4 bits (67), Expect = 0.60
Identities = 9/76 (11%), Positives = 14/76 (18%), Gaps = 25/76 (32%)
Query: 124 GRFLYISETVSIYLGLS-------------------------QWQVINKGQVLTHYYRLM 158
L I+ G S Q + G+ R+
Sbjct: 32 SEVLVINSAYEDIWGRSVAKLRENPHDFLNGIHPEDRELMKDTMQSLMDGESADVECRVN 91
Query: 159 NKNGGYTWVQSCATVV 174
WV +
Sbjct: 92 ATEEYQRWVWIQGEPI 107
>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase,
phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A
{Methylococcus capsulatus}
Length = 227
Score = 28.5 bits (64), Expect = 2.0
Identities = 8/37 (21%), Positives = 16/37 (43%)
Query: 142 WQVINKGQVLTHYYRLMNKNGGYTWVQSCATVVCSSK 178
W+ I++G + + K+G WV S + +
Sbjct: 51 WRTISRGNIWQGEFCNRRKDGTRYWVDSTIVPLMDNA 87
>3zyl_A Phosphatidylinositol-binding clathrin assembly PR; endocytosis,
endobrevin, synaptobrevin, VAMP2, VAMP3, AP180,
membrane, adaptor protein; 1.70A {Rattus norvegicus}
PDB: 3zyk_A 1hf8_A 1hfa_A* 1hg2_A* 1hg5_A*
Length = 271
Score = 28.6 bits (63), Expect = 2.3
Identities = 13/111 (11%), Positives = 38/111 (34%)
Query: 122 SDGRFLYISETVSIYLGLSQWQVINKGQVLTHYYRLMNKNGGYTWVQSCATVVCSSKNAD 181
+ +++++ S W V+ K + TH+ + ++ S T+ S D
Sbjct: 59 MNVNIPQLADSLFERTTNSSWVVVFKSLITTHHLMVYGNERFIQYLASRNTLFNLSNFLD 118
Query: 182 EQNIICVNYVISGREYENFIMDCCQLEDYIQQRGVKREEPSNNDPENDSPD 232
+ + + R Y ++ + + K + ++ + +
Sbjct: 119 KSGLQGYDMSTFIRRYSRYLNEKAVSYRQVAFDFTKVKRGADGVMRTMNTE 169
>3zym_A Phosphatidylinositol-binding clathrin assembly PR
vesicle-associated membrane protein...; endocytosis,
synaptobrevin, VAMP2, VAMP3, AP180; HET: PO4; 2.03A
{Rattus norvegicus}
Length = 310
Score = 28.7 bits (63), Expect = 2.5
Identities = 13/111 (11%), Positives = 38/111 (34%)
Query: 122 SDGRFLYISETVSIYLGLSQWQVINKGQVLTHYYRLMNKNGGYTWVQSCATVVCSSKNAD 181
+ +++++ S W V+ K + TH+ + ++ S T+ S D
Sbjct: 59 MNVNIPQLADSLFERTTNSSWVVVFKSLITTHHLMVYGNERFIQYLASRNTLFNLSNFLD 118
Query: 182 EQNIICVNYVISGREYENFIMDCCQLEDYIQQRGVKREEPSNNDPENDSPD 232
+ + + R Y ++ + + K + ++ + +
Sbjct: 119 KSGLQGYDMSTFIRRYSRYLNEKAVSYRQVAFDFTKVKRGADGVMRTMNTE 169
>1wif_A RSGI RUH-020, riken cDNA 4930408O21; PDZ domain, structural
genomics, mouse cDNA, riken structural
genomics/proteomics initiative; NMR {Mus musculus} SCOP:
b.36.1.1
Length = 126
Score = 26.8 bits (59), Expect = 4.4
Identities = 10/53 (18%), Positives = 22/53 (41%)
Query: 78 SSSSSYKGCDRSFCIRMKSTLTKRGCHFKSSGYRSLDGFAFALGSDGRFLYIS 130
SS SS ++ + K++++ ++ G + +G +L IS
Sbjct: 2 SSGSSGSKNEKEQLSKAKASVSSLNKVIQTKLTVGNLGLGLVVIQNGPYLQIS 54
>1ji1_A Alpha-amylase I; beta/alpha barrel, hydrolase; 1.60A
{Thermoactinomyces vulgaris} SCOP: b.1.18.2 b.71.1.1
c.1.8.1 PDB: 1uh3_A* 2d0f_A* 1izj_A 1uh4_A* 1uh2_A*
2d0g_A* 2d0h_A* 1izk_A
Length = 637
Score = 27.5 bits (61), Expect = 6.0
Identities = 10/55 (18%), Positives = 13/55 (23%), Gaps = 1/55 (1%)
Query: 223 NNDPENDSPDADREDGRNSGDSRNHDHLSPPDIEDGTSEGDNSGDQRG-RNHLDH 276
N D ND + + D S GD G L +
Sbjct: 145 NGDSSNDVQTGSYTYNGTPTEKKAWGSSVYADPGYDNSLVFFGGDLAGIDQKLGY 199
>3p23_A Serine/threonine-protein kinase/endoribonuclease; kinase domain,
kinase and RNAse function, ATP binding ssRNA
dephosphorylated, hydrolase; HET: ADP; 2.70A {Homo
sapiens}
Length = 432
Score = 27.4 bits (61), Expect = 6.7
Identities = 7/40 (17%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 184 NIICVNYVISGREYENFIMDCCQ--LEDYIQQRGVKREEP 221
N+I R+++ ++ C L++Y++Q+
Sbjct: 79 NVIRYFCTEKDRQFQYIAIELCAATLQEYVEQKDFAHLGL 118
>1ti6_A Pyrogallol hydroxytransferase large subunit; molybdenum binding
enzyme, MGD-cofactors, DMSO-reductase family,
4Fe-4S-cluster; HET: MGD BTT; 2.00A {Pelobacter
acidigallici} SCOP: b.52.2.2 c.81.1.1 PDB: 1ti2_A*
1ti4_A* 1vld_M* 1vle_M* 1vlf_M*
Length = 875
Score = 27.3 bits (60), Expect = 8.5
Identities = 8/33 (24%), Positives = 12/33 (36%), Gaps = 1/33 (3%)
Query: 134 SIYLGLSQWQVINK-GQVLTHYYRLMNKNGGYT 165
+I S + G + Y+R MN G
Sbjct: 136 AILSTPSSHHMWGNVGYRHSTYFRFMNMMGFTY 168
>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG,
structural genomics, center for structural genomics;
1.65A {Burkholderia thailandensis} PDB: 3mqo_A
Length = 120
Score = 26.0 bits (58), Expect = 8.8
Identities = 8/55 (14%), Positives = 13/55 (23%)
Query: 120 LGSDGRFLYISETVSIYLGLSQWQVINKGQVLTHYYRLMNKNGGYTWVQSCATVV 174
+G LY S +G V+ + G W +
Sbjct: 43 IGRSFEVLYPSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 97
>1wte_A ECOO109IR; restriction endonuclease, DNA complex, hydrolase/DNA
complex; 1.90A {Escherichia coli} SCOP: c.52.1.29 PDB:
1wtd_A
Length = 272
Score = 26.6 bits (58), Expect = 8.9
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 104 HFKSSGYRSLDGFAFALGSDGRFLYISETVSIYLGLSQWQVINKGQVLTHYYRL 157
H + YR L G G++ + I + V +Y G W +N G+ T ++ L
Sbjct: 168 HGLTDKYRILRGIN--TGANHNVIDIRDKVHVYAGKEFWSWLNNGEAETQHWVL 219
>1tmo_A TMAO reductase, trimethylamine N-oxide reductase; oxidoreductase,
oxotransferase, molybdoenzyme, MO-cofactor, molybdenum;
HET: 2MD; 2.50A {Shewanella massilia} SCOP: b.52.2.2
c.81.1.1
Length = 829
Score = 27.1 bits (60), Expect = 9.7
Identities = 7/41 (17%), Positives = 16/41 (39%), Gaps = 3/41 (7%)
Query: 134 SIYLGLSQWQVINK-GQVLTHYYRLMNKNGGYTWVQSCATV 173
++ G + W+ + +H R + +G Y V+
Sbjct: 141 GLHAGQTGWRATGQLHSSTSHMQRAVGMHGNY--VKKIGDY 179
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 0.387
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: 4,426,577
Number of extensions: 255292
Number of successful extensions: 411
Number of sequences better than 10.0: 1
Number of HSP's gapped: 397
Number of HSP's successfully gapped: 47
Length of query: 294
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 201
Effective length of database: 4,105,140
Effective search space: 825133140
Effective search space used: 825133140
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: 57 (26.1 bits)