# hmmscan :: search sequence(s) against a profile database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query sequence file: AA/23726_FusoPortal_Gene_840.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_840 [L=559] Description: # 935032 # 936708 # -1 # ID=1_840;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.267 Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-43 148.0 12.4 3e-43 147.1 12.4 1.4 1 5TM-5TMR_LYT 5TMR of 5TMR-LYT 5e-28 97.1 1.9 5.6e-27 93.8 1.5 2.6 2 His_kinase Histidine kinase 9.1e-07 29.3 0.8 3.1e-06 27.6 0.8 1.9 1 HATPase_c Histidine kinase-, DNA gyrase B-, and HSP90-lik 0.00015 21.7 1.9 0.00015 21.7 1.9 2.5 3 SpoVT_C Stage V sporulation protein T C-terminal, trans 0.0036 17.6 0.0 0.006 16.8 0.0 1.3 1 GAF_3 GAF domain ------ inclusion threshold ------ 0.012 15.4 1.3 0.099 12.4 0.2 2.3 2 HATPase_c_3 Histidine kinase-, DNA gyrase B-, and HSP90-lik 0.089 13.3 0.0 0.17 12.4 0.0 1.4 1 GAF GAF domain 0.14 11.9 0.0 0.3 10.8 0.0 1.5 1 RD3 RD3 protein 0.24 11.3 9.3 0.18 11.8 7.0 1.9 2 MreD rod shape-determining protein MreD 0.29 11.1 20.0 0.17 11.9 18.1 1.6 1 ECF_trnsprt ECF transporter, substrate-specific component 0.3 11.1 12.5 0.44 10.6 11.7 1.7 2 ThiW Thiamine-precursor transporter protein (ThiW) Domain annotation for each model (and alignments): >> 5TM-5TMR_LYT 5TMR of 5TMR-LYT # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 147.1 12.4 2e-46 3e-43 7 168 .. 32 192 .. 27 193 .. 0.97 Alignments for each domain: == domain 1 score: 147.1 bits; conditional E-value: 2e-46 5TM-5TMR_LYT 7 llsekrktlksklllglifglfsilgtytgieiegaiantRaigvvvaGllgGplvGliagliaglhRyl..lgGftalacgis 88 ++++k kt+k+ ++l ++f+l+si gty g++++gai ntR +gv+ +G+lgGp v++i+gl+ag+hR + lg ta++c+is 23726_FusoPortal_Gene_840 32 IIKSKAKTKKDIVALSFFFSLLSISGTYIGLNFNGAILNTRNVGVIAGGILGGPYVSIITGLVAGIHRAFvnLGRETAIPCAIS 115 4778888***************************************************************99999********* PP 5TM-5TMR_LYT 89 tilagllaGlihrklkrrrkkltvlvalligllveilqmllilllakpfdqalalvktialPmilvnslgtalflsilrd 168 ti+ g+l++++hr++k +k +++ ++++++++e l m+lil+l+k+ +a ++v + ++Pm+l+ns+g++++++i++d 23726_FusoPortal_Gene_840 116 TIIGGFLTAYVHRFIK---NKDRIFFGFFLACTIENLSMGLILILLKDKILAQNIVTSFYIPMVLMNSIGASVLILIVED 192 ****************...699********************************************************98 PP >> His_kinase Histidine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 0.3 0.0 0.54 8.3e+02 42 69 .. 268 296 .. 243 299 .. 0.75 2 ! 93.8 1.5 3.7e-30 5.6e-27 2 78 .] 363 440 .. 362 440 .. 0.93 Alignments for each domain: == domain 1 score: 0.3 bits; conditional E-value: 0.54 His_kinase 42 kllrysleseee..vtLeeElellesYlel 69 + r++l ++ e ++++e+ e++e++l++ 23726_FusoPortal_Gene_840 268 NNTRKVL-KTGEvmLVIKEDDEIIEDFLDI 296 4556777.334465679**********998 PP == domain 2 score: 93.8 bits; conditional E-value: 3.7e-30 His_kinase 2 elkaLqaqinPHFlfNtLnsiqslaeedpeeaeemlekLskllrysl.eseeevtLeeElellesYlelqklrfgdrl 78 elkaLq+qinPHFlfN+Ln++ sl++++pe+a+e++ +Ls++lry+l ++ ++v L +El+ +++Y++++k+rfgd+l 23726_FusoPortal_Gene_840 363 ELKALQSQINPHFLFNVLNTMTSLIRTNPEKAREVTIDLSNYLRYNLdNNVKSVELIKELNQIDNYIKIEKARFGDKL 440 9************************99********************54335599********************986 PP >> HATPase_c Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 27.6 0.8 2.1e-09 3.1e-06 9 107 .. 459 551 .. 456 554 .. 0.86 Alignments for each domain: == domain 1 score: 27.6 bits; conditional E-value: 2.1e-09 HHHHHHHHHHHHT.....TTTEEEEEEEEETTEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCCTSTSSSHHHHHHHH.HHHH CS HATPase_c 9 iisnlvdNavkft.....kageievtisaakddlvvsveDnGiGippedlpklftkfsqdsstkrggggtGlGlsivkk.lvel 86 ii+ lv+N++k++ ++g ++v +++ ++d++v +eD+G Gi + ++ ++++ + ++ +Gl+ v++ l l 23726_FusoPortal_Gene_840 459 IIQPLVENSIKHGilkkrENGCVKVIVKKIDKDIEVIIEDDGVGIEQTVID----NLDK-------QIQENIGLKNVHQrLKLL 531 8999*******6666556999999999998999**************9999....7777.......78899********66669 PP TTTEEEEEEETTTEEEEEEEE CS HATPase_c 87 mgGeiwvesepgrGttftftl 107 +g +++ ++ ++Gt++ f++ 23726_FusoPortal_Gene_840 532 YGEGLNI-KKLEQGTRINFRI 551 9999999.66679***99976 PP >> SpoVT_C Stage V sporulation protein T C-terminal, transcription factor # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.9 0.1 4.1 6.2e+03 24 38 .. 26 40 .. 4 44 .. 0.59 2 ! 21.7 1.9 9.7e-08 0.00015 7 126 .] 226 348 .. 222 348 .. 0.84 3 ? -0.8 0.1 0.92 1.4e+03 40 63 .. 483 506 .. 475 524 .. 0.75 Alignments for each domain: == domain 1 score: -2.9 bits; conditional E-value: 4.1 SpoVT_C 24 tDrdqiiavagaskk 38 +Dr +ii + a+ k 23726_FusoPortal_Gene_840 26 IDRANIIIKSKAKTK 40 588888888876644 PP == domain 2 score: 21.7 bits; conditional E-value: 9.7e-08 SpoVT_C 7 keyaeslaetlghi.vlitDrdqiiavagaskkellekeiske.leklmeerktvlakkeekkli..veeeeeeysaqviaPIi 86 +e+++ +ae lg + ++itD+ iia + k e+ i+++ k+++ + +l+ ke++++i + + ++++ +i P+ 23726_FusoPortal_Gene_840 226 SEVCKIIAENLGAKaTVITDKKDIIAGFSFDKAEITRTAIKSNnTRKVLKTGEVMLVIKEDDEIIedFLDISPHIKSCIILPLK 309 577888888888652789**********************76649999**9999999988888886656667799********* PP SpoVT_C 87 aeGdviGaVillskeekkklgelekklaetaAsFLgkqme 126 + dv G+ ++ ++ + k++e + l+ +++++ qme 23726_FusoPortal_Gene_840 310 EKNDVNGTLKIFFDTAE-KITEKNRYLMIGLSHLISTQME 348 *********99955544.5899999999999999999998 PP == domain 3 score: -0.8 bits; conditional E-value: 0.92 SpoVT_C 40 llekeiskeleklmeerktvlakk 63 ++ k+i k++e ++e++ ++++ 23726_FusoPortal_Gene_840 483 VIVKKIDKDIEVIIEDDGVGIEQT 506 577999999999999987755554 PP >> GAF_3 GAF domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.8 0.0 4e-06 0.006 6 128 .. 225 348 .. 222 349 .. 0.74 Alignments for each domain: == domain 1 score: 16.8 bits; conditional E-value: 4e-06 GAF_3 6 lekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesldedsalarralssgevvse.psfae..edg....lpdra 82 l++++k +++ lga++ ++ +d++++ + ++d ++ ++++ ++ r +l++gev + ++ +e ed + + 23726_FusoPortal_Gene_840 225 LSEVCKIIAENLGAKATVI----TDKKDIIAGFSFDKAEITRTAIKSNNT--RKVLKTGEVMLViKEDDEiiEDFldisPHIKS 302 5667777788888888777....688889888888655555667775555..99999999855533333334333222234566 PP GAF_3 83 alavPLvagrqviGvlalastkprafdaedlelleslArqiataie 128 +++PL+ ++ v G+l + + +++++++++l+ l+ +i+t++e 23726_FusoPortal_Gene_840 303 CIILPLKEKNDVNGTLKIFFDTAEKITEKNRYLMIGLSHLISTQME 348 7999**************9999999******************998 PP >> HATPase_c_3 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.3 0.0 0.17 2.6e+02 83 111 .. 235 263 .. 208 285 .. 0.75 2 ? 12.4 0.2 6.5e-05 0.099 10 52 .. 463 510 .. 458 547 .. 0.83 Alignments for each domain: == domain 1 score: 1.3 bits; conditional E-value: 0.17 HATPase_c_3 83 slgkkltvitkkegesstltldvdkidke 111 lg+k+tvit k++ +++d i + 23726_FusoPortal_Gene_840 235 NLGAKATVITDKKDIIAGFSFDKAEITRT 263 6899*******999999666555555432 PP == domain 2 score: 12.4 bits; conditional E-value: 6.5e-05 HATPase_c_3 10 lvdNsldAdaen......vkievnknrgktgeivieDdGkGmseeelkn 52 lv+Ns+ + vk+ v+k + k+ e+ ieDdG G+++ ++n 23726_FusoPortal_Gene_840 463 LVENSIKHGILKkrengcVKVIVKKID-KDIEVIIEDDGVGIEQTVIDN 510 788888866666677899*******97.79************9987776 PP >> GAF GAF domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 12.4 0.0 0.00011 0.17 6 108 .. 225 321 .. 222 346 .. 0.69 Alignments for each domain: == domain 1 score: 12.4 bits; conditional E-value: 0.00011 HHHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECH........EEEETTSHHHHHHHHHSSSEEESTGGTSTT....HHTTH CS GAF 6 ldtvveelrellgadrvalylpdydGlhydipqasrw........lfmkngrgicgqvlatgqplvipdstpdpr....faqyn 77 l +v++ ++e lga ++ d + i ++ ++ +n++ +vl+tg+++++ +d+ f++ 23726_FusoPortal_Gene_840 225 LSEVCKIIAENLGAKATVIT--DKKD----IIAGFSFdkaeitrtAIKSNNTR---KVLKTGEVMLVIK--EDDEiiedFLD-- 295 67899999999999888883..3444....66666664433322133333444...9***********4..34442222444.. PP HHHHHHHTTCSEEEEEEEEETTEEEEEEEEE CS GAF 78 rrdllenmgirsslvvPlvndgelwGllvlh 108 ++i+s++ +Pl+ ++++ G+l + 23726_FusoPortal_Gene_840 296 -----ISPHIKSCIILPLKEKNDVNGTLKIF 321 .....679*******************9875 PP >> RD3 RD3 protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.8 0.0 0.0002 0.3 49 121 .. 330 406 .. 322 415 .. 0.83 Alignments for each domain: == domain 1 score: 10.8 bits; conditional E-value: 0.0002 RD3 49 erkaetgvDYswlastp....rkrkqisaserleLEelCakikPsecgkvisrfrevlaenevevkeivelfksvlk 121 e+ + ++ s+l+st+ + ++ is + eL l ++i+P +v+ + +++++n+++++e+ ++ l+ 23726_FusoPortal_Gene_840 330 EKNRYLMIGLSHLISTQmeisKVENLISLLKYSELKALQSQINPHFLFNVLNTMTSLIRTNPEKAREVTIDLSNYLR 406 45555568899999998888888999*****************************************9876666665 PP >> MreD rod shape-determining protein MreD # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.8 7.0 0.00012 0.18 48 158 .. 83 195 .. 74 197 .. 0.75 2 ? -2.8 0.0 3.5 5.3e+03 31 45 .. 370 384 .. 349 389 .. 0.76 Alignments for each domain: == domain 1 score: 11.8 bits; conditional E-value: 0.00012 MreD 48 lpervgiitafvlGllyDvl.ygsllGvyalvlslil.ylvaklqkvlrlnrrflpavlqvlllellvlvialliglaeldlig 129 + +v+iit++v+G+ ++ +g + + ++i+ +l a +++ + + r++ ++ ++ +e l++++ l++ + 23726_FusoPortal_Gene_840 83 GGPYVSIITGLVAGIHRAFVnLGRETAIPCAISTIIGgFLTAYVHRFIKNKDRIFFGFFLACTIENLSMGLILILLKDKILAQN 166 567889999999999866541666667766666666526666677666665599999999999999999998888877774556 PP MreD 130 fvvyrllPtlllnfllailLvppvfkLlr 158 v++ ++P +l+n + a +L+++v+ ++ 23726_FusoPortal_Gene_840 167 IVTSFYIPMVLMNSIGASVLILIVEDIIQ 195 6667778****************998776 PP == domain 2 score: -2.8 bits; conditional E-value: 3.5 MreD 31 vlrPhflllvllywv 45 ++Phfl+ vl ++ 23726_FusoPortal_Gene_840 370 QINPHFLFNVLNTMT 384 578999998876554 PP >> ECF_trnsprt ECF transporter, substrate-specific component # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.9 18.1 0.00011 0.17 11 168 .. 45 190 .. 41 194 .. 0.72 Alignments for each domain: == domain 1 score: 11.9 bits; conditional E-value: 0.00011 HHHHHHHH...H.HEEE.STS...EEESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHHHHHHHHHHCHHHHH CS ECF_trnsprt 11 Aisivlsl...l.gyiplpni...kitiihipvllggllfGpikGailgiitsvlkailtggtgalssfvpiaflsriliglia 87 A+s+ +sl +yi l + + + + v+ gg+l Gp + +i g++ + +a+++ g+ + ++s i+ g+++ 23726_FusoPortal_Gene_840 45 ALSFFFSLlsiSgTYIGLN-FngaILNTRNVGVIAGGILGGPYVSIITGLVAGIHRAFVNLGRETA----IPCAISTIIGGFLT 123 4455555444433666665.3232577788999999***********************9888655....8899********** PP HHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHHHHHCCCHHHHS.............--HHHHHHHHHCCTTCCHHHHHHHH CS ECF_trnsprt 88 gllykkgkkknlkeivvsfilagvlgtivatllvlliilplylklktakaiaiagkallaailgpiivkglieaiiaaiiv 168 +++ +++k+k + ++++ +l + + l+ +++il+l k+ +i+ ++ ++ + +p ++ + i a + ++iv 23726_FusoPortal_Gene_840 124 AYVHRFIKNKDR------IFFGFFLACTIENLS-MGLILILL-KD------KILAQNIVTSFYIPMVLMNSIGASVLILIV 190 **********98......444444445555554.55555555.23......345567888888888888888888888887 PP >> ThiW Thiamine-precursor transporter protein (ThiW) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.2 0.1 0.61 9.3e+02 111 143 .. 28 64 .. 6 71 .. 0.62 2 ? 10.6 11.7 0.00029 0.44 19 143 .. 59 190 .. 42 197 .. 0.68 Alignments for each domain: == domain 1 score: -0.2 bits; conditional E-value: 0.61 ThiW 111 vaklllgkeaal....lvlvisFilstliGsviallv 143 a+++++++a++ ++l F l +++G+ i+l + 23726_FusoPortal_Gene_840 28 RANIIIKSKAKTkkdiVALSFFFSLLSISGTYIGLNF 64 4566666555555532444555555688999999865 PP == domain 2 score: 10.6 bits; conditional E-value: 0.00029 ThiW 19 sipvgvakvaPvqhvvNvvaavll.GPwyalavalvisliRnllgtgtllalpGs...iiGallagllyrltrkl.......ll 91 +i + +++++ v v+a+ +l GP+ ++++ lv ++ R ++ +g a+p + iiG +l+++++r+ ++ +l 23726_FusoPortal_Gene_840 59 YIGLNFNGAILNTRNVGVIAGGILgGPYVSIITGLVAGIHRAFVNLGRETAIPCAistIIGGFLTAYVHRFIKNKdriffgfFL 142 46667778888888899999866637***************************8633369************998333333344 PP ThiW 92 aalgEvlGtgiiGallaypvaklllgkeaallvlvisFilstliGsviallv 143 a++ E l g+i +++ +l ++ ++ ++++ ++ ++ sv+ l+v 23726_FusoPortal_Gene_840 143 ACTIENLSMGLI----LILLKDKILAQNIVTSFYIPMVLMNSIGASVLILIV 190 444454444444....334445555666666777777777776666665555 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (559 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 776 (0.0464337); expected 334.2 (0.02) Passed bias filter: 351 (0.0210029); expected 334.2 (0.02) Passed Vit filter: 38 (0.00227382); expected 16.7 (0.001) Passed Fwd filter: 11 (0.00065821); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 11 [number of targets reported over threshold] # CPU time: 0.30u 0.23s 00:00:00.53 Elapsed: 00:00:00.31 # Mc/sec: 5242.04 // [ok]