# hmmsearch :: search profile(s) against a sequence 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 HMM file: pfam_list/Methyltr_RsmB-F.hmm.txt # target sequence database: proteomes/Ciona_intestinalis.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Methyltr_RsmB-F [M=200] Accession: PF01189.16 Description: 16S rRNA methyltransferase RsmB/F Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-74 249.7 0.2 4.8e-74 248.2 0.0 1.8 2 tr|H2XZT6|H2XZT6_CIOIN Uncharacterized protein OS=Ciona inte 2.9e-39 134.7 0.0 1.4e-38 132.4 0.0 2.1 1 tr|F6XKA2|F6XKA2_CIOIN Uncharacterized protein OS=Ciona inte 2.7e-34 118.4 0.1 4.5e-34 117.7 0.1 1.3 1 tr|H2XZ35|H2XZ35_CIOIN Uncharacterized protein OS=Ciona inte 5.3e-31 107.7 0.1 8.6e-31 107.0 0.1 1.3 1 tr|H2XS72|H2XS72_CIOIN Uncharacterized protein OS=Ciona inte 3e-16 59.6 0.0 4.6e-16 59.0 0.0 1.3 1 tr|F6ZY66|F6ZY66_CIOIN Uncharacterized protein OS=Ciona inte 1.1e-14 54.4 0.0 1.5e-14 54.0 0.0 1.5 1 tr|F7AFH3|F7AFH3_CIOIN Uncharacterized protein OS=Ciona inte 6.2e-05 22.6 0.0 0.00011 21.8 0.0 1.4 1 tr|F6QVW6|F6QVW6_CIOIN Uncharacterized protein OS=Ciona inte ------ inclusion threshold ------ 0.018 14.6 0.0 0.041 13.4 0.0 1.5 1 tr|F6TIA8|F6TIA8_CIOIN Uncharacterized protein OS=Ciona inte 0.025 14.1 0.0 0.041 13.4 0.0 1.3 1 tr|F7A5J2|F7A5J2_CIOIN rRNA 2'-O-methyltransferase fibrillar Domain annotation for each sequence (and alignments): >> tr|H2XZT6|H2XZT6_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.4 0.2 1.5 2.8e+03 97 129 .. 37 71 .. 32 106 .. 0.68 2 ! 248.2 0.0 2.6e-77 4.8e-74 1 200 [] 380 588 .. 380 588 .. 0.94 Alignments for each domain: == domain 1 score: -2.4 bits; conditional E-value: 1.5 T-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHE..E CS Methyltr_RsmB-F 97 rdpdvklrrkekdiaqlaklqkellsaaidll..k 129 ++p+ k++ + k a+ l+k+ll+++++ k tr|H2XZT6|H2XZT6_CIOIN 37 QEPNKKISSRAKVRAKKRDLKKQLLTSLVEAKaeK 71 56666777777777777889999999988765333 PP == domain 2 score: 248.2 bits; conditional E-value: 2.6e-77 HHHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC--EEEEEEEE CS Methyltr_RsmB-F 1 allLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDa 87 +++Lapq++e++lD+caaPGgKTt+ia+lmkn+g ++ +d+nk Rlk+v+ n++r+gv n ++++Dar +++++g+ f r+LlDa tr|H2XZT6|H2XZT6_CIOIN 380 VMALAPQPGERVLDMCAAPGGKTTYIAQLMKNSGFIFVNDINKARLKAVVGNMHRMGVSNSVISNYDARSFPTIMGN--FSRVLLDA 464 589*************************************************************************8..******** PP --CCGGGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHE....EEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESSBSTTS CS Methyltr_RsmB-F 88 PCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidll....kkgGvlvYsTCsvlveEneevieeaLkkredvelvetelsep 170 PCsgtgvi++dp+vk++++++di+++++lqkel+ aaid+ ++gG++vY+TCsv veEneev+++aLkkr +v+lv+t l+ + tr|H2XZT6|H2XZT6_CIOIN 465 PCSGTGVISKDPSVKTSKDDSDITKCSHLQKELILAAIDSCnaqaQNGGYIVYCTCSVMVEENEEVVNYALKKR-NVKLVQTGLEFG 550 ****************************************999999***************************9.9******66544 PP TTSSECEEC........T-EEE-TTTTS.-SEEEEEEE CS Methyltr_RsmB-F 171 kglklgeea........gtlrllPhtenkdgffiaklk 200 ++ ++ + +t+r++Ph++n+dgff+ak+k tr|H2XZT6|H2XZT6_CIOIN 551 VEGFCKYRQyrfhpslkQTRRFYPHSHNMDGFFVAKFK 588 433333333789999999******************96 PP >> tr|F6XKA2|F6XKA2_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=3 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 132.4 0.0 7.8e-42 1.4e-38 2 200 .] 136 392 .. 135 392 .. 0.92 Alignments for each domain: == domain 1 score: 132.4 bits; conditional E-value: 7.8e-42 HHH---TT-EEEECS-TT-HHHHHHHHHTTT.......TSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.... CS Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmkn.......kgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.... 77 llL+ + + ++lD+caaPG+KT+ i el++ +g vA+d++++R +++ + rL +t +++ Da++++++ + tr|F6XKA2|F6XKA2_CIOIN 136 LLLDVHSHHKVLDMCAAPGSKTAQIVELLHRdennsipEGICVANDKDNKRCYMLVHQIGRLHSPSTLIVNHDASNFPEIFIKnddg 222 57999***********************76412222225678*************************************99888999 PP ....--EEEEEEEE--CCGGGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-.TT CS Methyltr_RsmB-F 78 ....elfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkr.ed 159 +DriL D+PCsg g++r++ dv ++ ++++ ++l++ q ++l ++ll +gG lvYsTCs+++ E+e+v+++a+++ tr|F6XKA2|F6XKA2_CIOIN 223 kdilLRYDRILCDVPCSGDGTMRKNTDVWVKWNQANAIYLHRTQYRILLRGLELLASGGQLVYSTCSLNPIEDEAVVAAAIHHCgGA 309 999889**********************9999999********************************************99986258 PP EEEESSBSTTSTTSSECEEC...........................................T-EEE-TTTTS.-SEEEEEEE CS Methyltr_RsmB-F 160 velvetelsepkglklgeea...........................................gtlrllPhtenkdgffiaklk 200 velv+++l + + + g+ + +rllPh++++ gff+a l+ tr|F6XKA2|F6XKA2_CIOIN 310 VELVSVSLPG-LKWSPGVSSwrvmdsdmnwydthdqvpekkknisysmfppggqdvmeamhleRCMRLLPHQQDTGGFFVAVLR 392 99***98887.777788888999**************************************99999***************885 PP >> tr|H2XZ35|H2XZ35_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 117.7 0.1 2.5e-37 4.5e-34 2 199 .. 207 410 .. 206 411 .. 0.82 Alignments for each domain: == domain 1 score: 117.7 bits; conditional E-value: 2.5e-37 HHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.--EEEEEEEE CS Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.elfDriLlDa 87 +L+p ++ +++D+caaPG KT+h++++m+n+g+++A+d+++eR++ +++ lk+ +v+n v++ D + + + ++++ iL+D tr|H2XZ35|H2XZ35_CIOIN 207 FVLNPSPNSHVIDACAAPGNKTSHLSAIMNNTGKLFAIDRSSERIEVMKKQLKKASVKNCEVINSDFLILKPTDEKfKQVEYILVDP 293 69****************************************************************97775555555789******* PP --CCGGGTTT-TTH...HHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESS..BSTT CS Methyltr_RsmB-F 88 PCsgtgvirrdpdv...klrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelvet..else 169 C+g g+i+r+ + k ++ k + +l+k q ++l+ a+ + +vYsTCs++ eEne ++ a +++ + l+++ ++++ tr|H2XZ35|H2XZ35_CIOIN 294 SCTGSGIISRQLEHteeKDSKCSKRLESLSKFQLKVLNHALSFP-NVKRVVYSTCSIHEEENELIVKLAVEQNSNFDLKKVlpKWHN 379 **********7665111556666777778888888888776543.33469*************************999987334444 PP STTS.SECEECT-EEE-TTTTS.-SEEEEEE CS Methyltr_RsmB-F 170 pkgl.klgeeagtlrllPhtenkdgffiakl 199 + + + ++ +r P+ + ++gff+a + tr|H2XZ35|H2XZ35_CIOIN 380 RGLIsDSFNAEKCVRCDPNVDFTNGFFVALF 410 33220222333699**************987 PP >> tr|H2XS72|H2XS72_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 107.0 0.1 4.6e-34 8.6e-31 2 171 .. 155 335 .. 154 373 .. 0.86 Alignments for each domain: == domain 1 score: 107.0 bits; conditional E-value: 4.6e-34 HHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHH.....HTT--.SEEEEES-CCCCHHHHCC--EEE CS Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlk.....rLgvt.ntivleaDarkidkvlggelfDr 82 l L+pq+++ ilD+c+aPGgK +++ + ++g++vA+d+n++R+ rv++ k +++v+ +++++ Da++ ++ ++ +D+ tr|H2XS72|H2XS72_CIOIN 155 LSLDPQPGDSILDMCSAPGGKLNVMMQAIGDSGRIVANDINTKRVTRVKNVYKeyipkQFSVEkFVKIVKFDATQWTEIETE-AYDK 240 679******************************************9999876511111566664589*********888885.9999 PP E.EEEE--C....CGGGTTT-TT.HHHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEE CS Methyltr_RsmB-F 83 i.LlDaPCs....gtgvirrdpd.vklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelv 163 + L+D+PC+ ++ v +r+ d + + ++++ aql +lq +ll+ ai +++G++vYsTC+ + ne v+++a ++ d +++ tr|H2XS72|H2XS72_CIOIN 241 VvLVDVPCTndrhSLYVSDRETDnIFSTLRKRERAQLPHLQCQLLKNAILACRPNGTIVYSTCTASPLQNEFVVQYAVQELMDQHSI 327 5489****93333467888887636566677889***********************************************999999 PP SSBSTTST CS Methyltr_RsmB-F 164 etelsepk 171 + e+++++ tr|H2XS72|H2XS72_CIOIN 328 SCEVQNTR 335 99888754 PP >> tr|F6ZY66|F6ZY66_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=3 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 59.0 0.0 2.5e-19 4.6e-16 3 56 .. 187 240 .] 185 240 .] 0.96 Alignments for each domain: == domain 1 score: 59.0 bits; conditional E-value: 2.5e-19 HH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHT CS Methyltr_RsmB-F 3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrL 56 +L+pqe++ +lD+caaPGgKT+hi l++ +g++vAvd+++++++++++n +L tr|F6ZY66|F6ZY66_CIOIN 187 VLNPQEGDIVLDMCAAPGGKTSHIVSLLRGRGRLVAVDRSSSKVEKIKQNAAKL 240 8*************************************************9876 PP >> tr|F7AFH3|F7AFH3_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=3 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 54.0 0.0 8.1e-18 1.5e-14 108 185 .. 2 75 .. 1 136 [. 0.87 Alignments for each domain: == domain 1 score: 54.0 bits; conditional E-value: 8.1e-18 CHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESSBSTTSTTSSECEECT-EEE- CS Methyltr_RsmB-F 108 kdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelvetelsepkglklgeeagtlrll 185 k+i+++ lq++l+++a+ llk+gG+lvYsTC+ +v+Ene +e aL k++ +l++ p++ +g+++ +l tr|F7AFH3|F7AFH3_CIOIN 2 KNIKSYPALQRQLFNTAVRLLKPGGTLVYSTCTTTVDENEGLVEWALDKHPCLKLSQH---TPHIGGTGRQE-VTNLS 75 68999************************************************99987...34455555555.44444 PP >> tr|F6QVW6|F6QVW6_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=3 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 21.8 0.0 6.1e-08 0.00011 4 92 .. 13 104 .. 10 118 .. 0.86 Alignments for each domain: == domain 1 score: 21.8 bits; conditional E-value: 6.1e-08 H---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.....--EEEEEE CS Methyltr_RsmB-F 4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.....elfDriLl 85 L+ + ++ i+D+ + Gg T +i+e ++ +v+A+d++++ + ++ k++ + +i l + ++ dk l++ + + +Ll tr|F6QVW6|F6QVW6_CIOIN 13 LNIKRGDVIIDMTFGAGGHTKFIMEN-YKHCKVIALDRDEKAFEIAQDLSKKFKGR-IIPLLGKFSELDKLLSEngiveNSLNAALL 97 89999********************8.6678899****998777666666666666.888999999999999998898899****** PP EE--CCG CS Methyltr_RsmB-F 86 DaPCsgt 92 Da Cs++ tr|F6QVW6|F6QVW6_CIOIN 98 DAGCSSM 104 *****86 PP >> tr|F6TIA8|F6TIA8_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.4 0.0 2.2e-05 0.041 7 73 .. 330 395 .. 325 413 .. 0.88 Alignments for each domain: == domain 1 score: 13.4 bits; conditional E-value: 2.2e-05 -TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHH CS Methyltr_RsmB-F 7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidk 73 +e++ ++D c++ G +a+l + +++ v++++e l+r ++ ++ L+++n+++ + + ++ k tr|F6TIA8|F6TIA8_CIOIN 330 EEGDVLVDFCSGGGHVGIVLAHL-LPLCKIILVENKEESLERAMQRIQELNLKNIMIYQCNLDQFMK 395 688999****9988888888888.67889999**************************999988855 PP >> tr|F7A5J2|F7A5J2_CIOIN rRNA 2'-O-methyltransferase fibrillarin isoform X1 OS=Ciona intestinalis OX=7719 GN=LOC100186 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.4 0.0 2.2e-05 0.041 6 87 .. 144 224 .. 140 235 .. 0.78 Alignments for each domain: == domain 1 score: 13.4 bits; conditional E-value: 2.2e-05 --TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.--EEEEEEEE CS Methyltr_RsmB-F 6 pqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.elfDriLlDa 87 +++ ++l l aa G +h+++++ ++g v+Av+ +++ + +++ k+ tn+i + Dar+++k+ ++D i D+ tr|F7A5J2|F7A5J2_CIOIN 144 IKPGSKVLYLGAASGTTVSHVSDIVGPEGLVYAVEFSHRSGRDLINVAKK--RTNIIPIIEDARHPHKYRMLvGMVDTIFADV 224 567788999**************************987665555544433..3456777889999988754335788887775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (200 nodes) Target sequences: 16678 (5370518 residues searched) Passed MSV filter: 580 (0.0347764); expected 333.6 (0.02) Passed bias filter: 400 (0.0239837); expected 333.6 (0.02) Passed Vit filter: 39 (0.00233841); expected 16.7 (0.001) Passed Fwd filter: 9 (0.000539633); expected 0.2 (1e-05) Initial search space (Z): 16678 [actual number of targets] Domain search space (domZ): 9 [number of targets reported over threshold] # CPU time: 0.11u 0.00s 00:00:00.11 Elapsed: 00:00:00.04 # Mc/sec: 26852.59 // [ok]