-------------------------------------------------------------------------------- Domain name : PF00672.17_HAMP Domain size : 79 Domain Description : HAMP domain Domain gathering score : 19.8000 Domain trusted cutoff : 19.8000 Domain architecture : TM/SP [1 23], non-TM/SP [24 106] -------------------------------------------------------------------------------- Example 1 gi|169185846|ref|ZP_02846008.1| transcriptional regulator, AraC family [Paenibacillus sp. JDR-2]gi|169007267|gb|EDS54116.1| transcriptional regulator, AraC family [Paenibacillus sp. JDR-2] 755 (length) 297 360 .. (wrt seq) 1 79 [] (wrt HMM) No.of residues in non-TM/SP region : 40 [48%(over non-TM/SP length)] Scores for sequence family classification: Model Description Score E-value N -------- ----------- ----- ------- --- HTH_AraC Bacterial regulatory helix-turn-helix p 59.0 1.8e-14 2 HAMP HAMP domain 37.8 4.4e-08 1 Cache_1 Cache domain -5.8 0.064 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- HTH_AraC 1/2 653 699 .. 1 49 [] 20.0 0.0097 HTH_AraC 2/2 705 749 .. 1 49 [] 38.9 2e-08 HAMP 1/1 297 360 .. 1 79 [] 37.8 4.4e-08 Cache_1 1/1 157 238 .. 1 92 [] -5.8 0.064 Alignments of top-scoring domains: HTH_AraC: domain 1 of 2, from 653 to 699: score 20.0, E = 0.0097 CS HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey + r+Lee++ ++++ +++A e+G+ S sy ++ + tG + +y gi|1691858 653 RIIRYLEEHF-RKEIVFEEMAKEIGI-SYSYMRKIVYELTGKSLIDY 697 CS HH rr<-* ++ gi|1691858 698 MN 699 HTH_AraC: domain 2 of 2, from 705 to 749: score 38.9, E = 2e-08 CS HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey kA++lL e s+ ++i++iA+evGy + + f r F+ky G+ Ps y gi|1691858 705 KAKQLLVE---SK-MTITQIASEVGYYNVQSFNRFFRKYEGMPPSSY 747 CS HH rr<-* + gi|1691858 748 KT 749 HAMP: domain 1 of 1, from 297 to 360: score 37.8, E = 4.4e-08 CS HHHHHHHHHHHHHHHHHH-XXXXXXXXXXXXXXXXXXXXX.XXXXXX *->lllvllialllalllalllarrilrPlrrLaeaarriasGtdLdvri ++++++i+++++ +la+lla ++++P+rrL++++r+ + +L gi|1691858 297 IIFITGIIIIAGTILAVLLATWLSQPVRRLVRTMRERS---NL---- 336 CS XXXXX.........XXXXXXXXXXXXXXXXXX esgrdrvlpvsgpDEigeLarafNqMaerLre<-* + ++E+ L af +M+e+ + gi|1691858 337 --------GGTNKNELVFLESAFRRMQEEEEG 360 Cache_1: domain 1 of 1, from 157 to 238: score -5.8, E = 0.064 *->wTePYvdaalktgdlViTiaqPvydtseqrnktnddgdll....GVi + + ++l++g +V+++ +P+ +l+++++G i gi|1691858 157 IGGVWYPRQLQSGMQVVSYVLPLN-------------RLStttrGTI 190 giDvsledLlkltksiklGktGYaFivdnnGkvlaHPnlqpvtkllgdw< +++ + + +++ s+ +G +G+ +++ +G+++ H+++ + ++++ gi|1691858 191 VVNLKESQIASYLRSFEPGSEGF-MLLKSDGTIISHNDKSLLLTDGNKQ 238 -* gi|1691858 - - Example 2 gi|118725971|ref|ZP_01574605.1| transcriptional regulator, AraC family [Clostridium cellulolyticum H10]gi|118664670|gb|EAV71298.1| transcriptional regulator, AraC family [Clostridium cellulolyticum H10] 760 (length) 300 364 .. (wrt seq) 1 79 [] (wrt HMM) No.of residues in non-TM/SP region : 41 [49%(over non-TM/SP length)] Scores for sequence family classification: Model Description Score E-value N -------- ----------- ----- ------- --- HTH_AraC Bacterial regulatory helix-turn-helix 84.0 5.2e-22 2 HAMP HAMP domain 30.8 5.7e-06 1 Cache_1 Cache domain -5.7 0.063 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- HTH_AraC 1/2 660 706 .. 1 49 [] 34.1 5.6e-07 HTH_AraC 2/2 712 756 .. 1 49 [] 49.9 9.7e-12 HAMP 1/1 300 364 .. 1 79 [] 30.8 5.7e-06 Cache_1 1/1 161 241 .. 1 92 [] -5.7 0.063 Alignments of top-scoring domains: HTH_AraC: domain 1 of 2, from 660 to 706: score 34.1, E = 5.6e-07 CS HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey k + ++++n+ +++ i+ +Ae+vG+ S s+ ++ F +tG ++ y gi|1187259 660 KILDYIHKNY-KKDIAINMLAEHVGL-SYSHVRKIFNDETGENIVNY 704 CS HH rr<-* ++ gi|1187259 705 IN 706 HTH_AraC: domain 2 of 2, from 712 to 756: score 49.9, E = 9.7e-12 CS HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey +A rlL++ +n ++i+diA+++Gy +++ f r Fkky+G++P+ey gi|1187259 712 EAQRLLRQ---TN-MNINDIALSLGYNNKQSFNRFFKKYVGINPGEY 754 CS HH rr<-* r+ gi|1187259 755 RN 756 HAMP: domain 1 of 1, from 300 to 364: score 30.8, E = 5.7e-06 CS HHHHHHHHHHHHHHHHHH-XXXXXXXXXXXXXXXXXXXXX.XXXXXX *->lllvllialllalllalllarrilrPlrrLaeaarriasGtdLdvri ++++++++l+l +ll+++++rr+ +P+++L++ ++ ++G gi|1187259 300 IIYISIFLLVLFVLLSYVISRRLFNPVKKLVQEIKS-RKG------- 338 CS XXXXX...... ...XXXXXXXXXXXXXXXXXX esgrdrvlpvs.gpDEigeLarafNqMaerLre<-* ++ + ++E+ L+++f+ M+ + + gi|1187259 339 ----I---DIIgNGNEFTLLSKTFDVMIKQEDQ 364 Cache_1: domain 1 of 1, from 161 to 241: score -5.7, E = 0.063 *->wTePYvdaalktgdlViTiaqPvydtseqrnktnddgdllGVigiDv wT+P ++ + +++ Vi++ P+ +l+G i i++ gi|1187259 161 WTDPRPSDT-NGNSSVISYIFPLTY----------TTNLKGSITINI 196 sledLlkltksiklGktGYaFivdnnGkvlaHPnlqpvtkllgdw<-* + L +l++s + ++ i++ nG+v+ ++++ +k+l d+ gi|1187259 197 YESRLSNLINSNNYDISDFISIINANGEVISSVDKTILNKNLTDV 241 Example 4 gi|169187094|ref|ZP_02847254.1| transcriptional regulator, AraC family [Paenibacillus sp. JDR-2]gi|169005926|gb|EDS52777.1| transcriptional regulator, AraC family [Paenibacillus sp. JDR-2] 788 (length) 304 371 .. (wrt seq) 1 79 [] (wrt HMM) No.of residues in non-TM/SP region : 44 [53%(over non-TM/SP length)] Scores for sequence family classification: Model Description Score E-value N -------- ----------- ----- ------- --- HTH_AraC Bacterial regulatory helix-turn-helix 85.6 1.8e-22 2 HAMP HAMP domain 28.2 3.4e-05 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- HTH_AraC 1/2 679 725 .. 1 49 [] 36.0 1.5e-07 HTH_AraC 2/2 731 775 .. 1 49 [] 49.5 1.3e-11 HAMP 1/1 304 371 .. 1 79 [] 28.2 3.4e-05 Alignments of top-scoring domains: HTH_AraC: domain 1 of 2, from 679 to 725: score 36.0, E = 1.5e-07 CS HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey + + ++++n+ ++++s++ iA+++ + +psy srlFk++ vt+++y gi|1691870 679 QILAYIQNNF-DKEISLGGIADQLQL-DPSYASRLFKQEISVTFMDY 723 CS HH rr<-* gi|1691870 724 VI 725 HTH_AraC: domain 2 of 2, from 731 to 775: score 49.5, E = 1.3e-11 CS HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey k+++lL++ s+ l+++di ++vGy +++ f r Fkky G+tP+ey gi|1691870 731 KTKELLKT---SE-LTVKDIGASVGYANQRSFNRIFKKYEGMTPGEY 773 CS HH rr<-* r gi|1691870 774 RD 775 HAMP: domain 1 of 1, from 304 to 371: score 28.2, E = 3.4e-05 CS HHHHHHHHHHHHHHHHHH-XXXXXXXXXXXXXXXXXXXXX.XXXXXX *->lllvllialllalllalllarrilrPlrrLaeaarriasGtdLdvri +l+++++++l+a+l+a++l+ ri P++ L++ +++ d + gi|1691870 304 MLILMAFSILAAVLAAFYLTLRIYSPIHSLVQMVNNKK---DWR--- 344 CS XXXXX.........XXXXXXXXXXXXXXXXXX esgrdrvlpvsgpDEigeLarafNqMaerLre<-* + v p + + E+++L af M e+ e gi|1691870 345 ----SAV-PLHEQSEMAMLFSAFITMKEQGAE 371 Example 5 gi|192810581|ref|ZP_03039254.1| helix-turn-helix- domain containing protein AraC type [Geobacillus sp. Y412MC10]gi|192800873|gb|EDV77380.1| helix-turn-helix- domain containing protein AraC type [Geobacillus sp. Y412MC10] 756 (length) 297 360 .. (wrt seq) 1 79 [] (wrt HMM) No.of residues in non-TM/SP region : 40 [48%(over non-TM/SP length)] Scores for sequence family classification: Model Description Score E-value N -------- ----------- ----- ------- --- HTH_AraC Bacterial regulatory helix-turn-helix 60.5 6.3e-15 2 HAMP HAMP domain 26.7 9.7e-05 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- HTH_AraC 1/2 654 700 .. 1 49 [] 19.6 0.013 HTH_AraC 2/2 706 750 .. 1 49 [] 40.9 5e-09 HAMP 1/1 297 360 .. 1 79 [] 26.7 9.7e-05 Alignments of top-scoring domains: HTH_AraC: domain 1 of 2, from 654 to 700: score 19.6, E = 0.013 CS HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey + ++L e + ++++ +++A +G+ S sy ++ ++tG ++s+y gi|1928105 654 RIIHYLNERY-REEIVFEEMAKDIGI-SYSYMRKIVYEQTGKSISDY 698 CS HH rr<-* ++ gi|1928105 699 LN 700 HTH_AraC: domain 2 of 2, from 706 to 750: score 40.9, E = 5e-09 CS HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey kA++lL++ sn lsi++iA+evG+ + + f rlF+k G+ Ps y gi|1928105 706 KAKELLLN---SN-LSIGQIASEVGCMNVRSFNRLFRKFEGMPPSSY 748 CS HH rr<-* gi|1928105 749 KM 750 HAMP: domain 1 of 1, from 297 to 360: score 26.7, E = 9.7e-05 CS HHHHHHHHHHHHHHHHHH-XXXXXXXXXXXXXXXXXXXXX.XXXXXX *->lllvllialllalllalllarrilrPlrrLaeaarriasGtdLdvri +++++++++ ++ +l +++a ++++P r+L++++r G + gi|1928105 297 IIFLTIVIIFAGSILTVFMATWLSKPARELVRTIR----G-RV---- 334 CS XXXXX...... ...XXXXXXXXXXXXXXXXXX esgrdrvlpvs.gpDEigeLarafNqMaerLre<-* + p ++ ++E+ L +af +M+e+ + gi|1928105 335 ----N---PGVqDKNELVFLEAAFRRMQEEEEG 360