# 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/UPF0020.hmm.txt # target sequence database: proteomes/Natronomonas_moolapensis.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: UPF0020 [M=197] Accession: PF01170.17 Description: Putative RNA methylase family UPF0020 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-28 96.4 0.0 1e-27 94.5 0.0 1.8 1 tr|M1XLM2|M1XLM2_NATM8 tRNA (Guanine(6)-N(2))-dimethyltransf 2.2e-22 77.0 0.2 1.5e-21 74.3 0.2 2.0 1 tr|M1XLF5|M1XLF5_NATM8 tRNA (Guanine(10),N(2))-dimethyltrans 5.2e-11 39.9 0.0 5e-10 36.7 0.0 2.0 1 tr|M1XS10|M1XS10_NATM8 Probable rRNA methyltransferase OS=Na 2e-07 28.2 0.0 0.0053 13.8 0.0 2.4 2 tr|M1Y2L8|M1Y2L8_NATM8 Adenine-specific DNA modification met 2.3e-07 28.0 0.0 0.0036 14.3 0.0 2.6 2 tr|M1XNX9|M1XNX9_NATM8 Adenine-specific DNA modification met 2.6e-06 24.6 0.0 7.7e-06 23.1 0.0 1.8 1 tr|M1Y4D2|M1Y4D2_NATM8 Probable S-adenosylmethionine-depende 2.8e-06 24.5 0.0 5.6e-06 23.5 0.0 1.4 1 tr|M1XL08|M1XL08_NATM8 Probable arsenite(III)-methyltransfer 6e-06 23.4 0.0 0.014 12.4 0.0 2.5 2 tr|M1XS34|M1XS34_NATM8 Adenine-specific DNA modification met 7.8e-06 23.0 0.1 1.9e-05 21.7 0.1 1.6 1 tr|M1Y3X8|M1Y3X8_NATM8 tRNA (Guanine(37)-N(1))-methyltransfe 0.00038 17.5 0.0 0.00078 16.5 0.0 1.5 2 tr|M1XK62|M1XK62_NATM8 tRNA (guanine(26)-N(2))-dimethyltrans 0.0017 15.4 0.0 0.75 6.8 0.0 2.2 2 tr|M1XKR6|M1XKR6_NATM8 Modification methylase OS=Natronomona ------ inclusion threshold ------ 0.015 12.3 0.0 0.023 11.7 0.0 1.3 1 tr|M1XZU1|M1XZU1_NATM8 Protein-L-isoaspartate O-methyltransf 0.028 11.4 0.0 0.3 8.1 0.0 2.1 1 tr|M1XRL7|M1XRL7_NATM8 Probable S-adenosylmethionine-depende Domain annotation for each sequence (and alignments): >> tr|M1XLM2|M1XLM2_NATM8 tRNA (Guanine(6)-N(2))-dimethyltransferase OS=Natronomonas moolapensis (strain DSM 18674 / JC # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 94.5 0.0 4.8e-30 1e-27 1 169 [. 161 356 .. 161 362 .. 0.86 Alignments for each domain: == domain 1 score: 94.5 bits; conditional E-value: 4.8e-30 -SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SS....................... CS UPF0020 1 RgyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvle....................... 64 R yR +++ ap + tLA+a++r+agw+p+++l+DPm Gs ti+ Eaal ++ ++p e + tr|M1XLM2|M1XLM2_NATM8 161 RPYRICEHDAPVRGTLAYAMLRIAGWTPTDRLVDPMAGSATIPTEAALAATGAVPRPDLEPSFGalpgydvdrfrrrrdayadppsg 247 78*************************************************999854433333389********************* PP ..........HHHHHHHHHH.HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHH CS UPF0020 65 ..........lkaeaeeear.aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskka 140 + + l + + ++ +r ++ar N e+ag++d ++++ada++ ++ + d +vtn+P+G r+g+ + tr|M1XLM2|M1XLM2_NATM8 248 pgttrggspaDRPSTGGALDaSALDIEAREIRSRWRRCARVNREAAGLEDAFDVVDADARE---ASIDADRVVTNLPFGVRTGT--D 329 ***999887523222222223666699*********************************5...55678************997..6 PP HHHHHHHHHHHHHHH-TT..-EEEEEESS CS UPF0020 141 lekLYseflrelkrvlrgggrlvlltsen 169 l++LY +f ++l+ grlv+lt++ tr|M1XLM2|M1XLM2_NATM8 330 LRELYGAFVDRLEA--GDIGRLVALTTSP 356 99**********98..4447999999875 PP >> tr|M1XLF5|M1XLF5_NATM8 tRNA (Guanine(10),N(2))-dimethyltransferase OS=Natronomonas moolapensis (strain DSM 18674 / J # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 74.3 0.2 7.2e-24 1.5e-21 2 181 .. 149 296 .. 148 313 .. 0.80 Alignments for each domain: == domain 1 score: 74.3 bits; conditional E-value: 7.2e-24 SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHH CS UPF0020 2 gyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrv 88 +++f++p+++ + A+al ++ag+ pg ++lDPmCG+G+il+Ea+l ga+++ g+D ++++ tr|M1XLF5|M1XLF5_NATM8 149 TKKPFFQPGSMAPMDARALANIAGAAPGARILDPMCGTGGILVEAGLAGASVV--------------------------GVDAQAKM 209 5789*************************************************..........................******** PP HHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------H.HHHHHHHHHHHHHHHHH-TT..-EEEEEESSHHHHH CS UPF0020 89 vqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgsk.kalekLYseflrelkrvlrgggrlvlltsenkalek 174 v+g+++N+ ++ ++++ da+ L+l++++vd v + PYG+ + + ++l +L +l+el rv + +++ +++ + tr|M1XLF5|M1XLF5_NATM8 210 VRGTERNLAAYLGEGSVL--RGDATRLPLADDSVDGAVLDAPYGRQSKVAgGSLSALVGGTLSELRRVAPR-----AVLVGDRVWSD 289 ********9998888775..567999999999************987654145577777777777775444.....55556666667 PP CC---ES CS UPF0020 175 aleeral 181 a+e + + tr|M1XLF5|M1XLF5_NATM8 290 AAEAAGW 296 6666644 PP >> tr|M1XS10|M1XS10_NATM8 Probable rRNA methyltransferase OS=Natronomonas moolapensis (strain DSM 18674 / JCM 14361 / 8 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 36.7 0.0 2.4e-12 5e-10 14 146 .. 37 147 .. 30 170 .. 0.89 Alignments for each domain: == domain 1 score: 36.7 bits; conditional E-value: 2.4e-12 HHHHHHHHHHTT--...TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHH CS UPF0020 14 etLAaalvrlagwk...pgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNae 97 + LAa +v +a+++ +g++ lD CG+G +++ aal g + + +g+D+d++ + +areN + tr|M1XS10|M1XS10_NATM8 37 PDLAAHIVHVADLNgdvEGRTVLDLGCGTGMLALGAALRGPELV-------------------------VGVDIDPAPLSTARENER 98 679999999988863336799*********************99.........................8***************** PP HTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHHHHH CS UPF0020 98 kagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYs 146 + g ++++ d+++L+l g +++ npP+G g+++a +++ + tr|M1XS10|M1XS10_NATM8 99 RVGAMTDVSWVRGDVTDLPLVPGGDATVLMNPPFGAQSGNEGADRAFLE 147 *******************77776779************9999877655 PP >> tr|M1Y2L8|M1Y2L8_NATM8 Adenine-specific DNA modification methylase OS=Natronomonas moolapensis (strain DSM 18674 / J # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.8 0.0 0.00011 0.022 29 58 .. 125 154 .. 122 204 .. 0.77 2 ! 13.8 0.0 2.5e-05 0.0053 102 133 .. 520 550 .. 510 557 .. 0.86 Alignments for each domain: == domain 1 score: 11.8 bits; conditional E-value: 0.00011 TS-EEETT-TTSHHHHHHHHHHTT--TTTT CS UPF0020 29 gepllDPmCGsGtilIEaallganiapgll 58 ++++lDP+ G+Gt l+Ea g + + l tr|M1Y2L8|M1Y2L8_NATM8 125 DKKILDPFMGGGTSLVEASRFGVESVGVDL 154 789***************999888775444 PP == domain 2 score: 13.8 bits; conditional E-value: 2.5e-05 GGGEEEEE--GGG--STTS---EEEE------ CS UPF0020 102 gdliefsqadaakLrlkegevdvivtnpPYGe 133 g+ ++ q d++ L +e+e+dv++t+pPY tr|M1Y2L8|M1Y2L8_NATM8 520 GQNSDVFQGDMRRLD-AEEEYDVVITDPPYYH 550 566677899******.888***********65 PP >> tr|M1XNX9|M1XNX9_NATM8 Adenine-specific DNA modification methylase OS=Natronomonas moolapensis (strain DSM 18674 / J # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 10.8 0.0 0.0002 0.042 28 64 .. 124 160 .. 118 205 .. 0.75 2 ! 14.3 0.0 1.7e-05 0.0036 93 134 .. 504 544 .. 497 555 .. 0.86 Alignments for each domain: == domain 1 score: 10.8 bits; conditional E-value: 0.0002 TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SS CS UPF0020 28 pgepllDPmCGsGtilIEaallganiapgllrefvle 64 +g+++lDP+ G+Gt IE ga+++ l + + + tr|M1XNX9|M1XNX9_NATM8 124 DGKKILDPFMGGGTSVIESSRFGAEVVGYDLNPVAWF 160 6899***************999999985555444444 PP == domain 2 score: 14.3 bits; conditional E-value: 1.7e-05 HHHHHHTT-GGGEEEEE--GGG--STTS---EEEE------- CS UPF0020 93 reNaekagvgdliefsqadaakLrlkegevdvivtnpPYGer 134 ++N + vg+ ++ q d ++L e+e+d+++t+pPY + tr|M1XNX9|M1XNX9_NATM8 504 KSNSFNQPVGENTTVFQGDSKDLD-YENEFDAVITDPPYYDN 544 5677788899999999********.888***********765 PP >> tr|M1Y4D2|M1Y4D2_NATM8 Probable S-adenosylmethionine-dependent methyltransferase OS=Natronomonas moolapensis (strain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 23.1 0.0 3.7e-08 7.7e-06 76 126 .. 66 116 .. 34 118 .. 0.91 Alignments for each domain: == domain 1 score: 23.1 bits; conditional E-value: 3.7e-08 H--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEE CS UPF0020 76 elklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdviv 126 + ++g+D+ +++++++r++a++agv+++ +f q da L+ +++ +d+++ tr|M1Y4D2|M1Y4D2_NATM8 66 GADIVGMDISEAMLEQGRRKARSAGVDESLSFIQGDAGRLPFPDDHFDAVL 116 4669*************************************9999999986 PP >> tr|M1XL08|M1XL08_NATM8 Probable arsenite(III)-methyltransferase OS=Natronomonas moolapensis (strain DSM 18674 / JCM # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 23.5 0.0 2.7e-08 5.6e-06 75 128 .. 119 171 .. 105 172 .. 0.88 Alignments for each domain: == domain 1 score: 23.5 bits; conditional E-value: 2.7e-08 HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE- CS UPF0020 75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtn 128 ++ +++g+D+ ++++++ar Na++ g + +ef+ ++ +L+ +++++dvi++n tr|M1XL08|M1XL08_NATM8 119 ETGRVIGVDMTPEMIKKARANASQNGAE-NVEFRLGEIEHLPVSDDSIDVIISN 171 45569*******************9975.69***********9999*******9 PP >> tr|M1XS34|M1XS34_NATM8 Adenine-specific DNA modification methylase OS=Natronomonas moolapensis (strain DSM 18674 / J # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 12.4 0.0 6.7e-05 0.014 29 65 .. 125 176 .. 120 206 .. 0.67 2 ! 8.3 0.0 0.0012 0.26 110 135 .. 523 547 .. 513 569 .. 0.84 Alignments for each domain: == domain 1 score: 12.4 bits; conditional E-value: 6.7e-05 TS-EEETT-TTSHHHHHHHHHHTT--TTTT----SS...............H CS UPF0020 29 gepllDPmCGsGtilIEaallganiapgllrefvle...............l 65 +++ lDP+ G+Gt l+Ea ga+++ l + + + l tr|M1XS34|M1XS34_NATM8 125 DKKVLDPFMGGGTSLVEASRFGAEVVGNDLNPVAWFvtkkeleagvtdveeL 176 7889********************9976666665555444444444444440 PP == domain 2 score: 8.3 bits; conditional E-value: 0.0012 --GGG--STTS---EEEE-------- CS UPF0020 110 adaakLrlkegevdvivtnpPYGerl 135 da+ + ke+e+dv++++pPY + + tr|M1XS34|M1XS34_NATM8 523 GDARTID-KEDEFDVVLSDPPYYDNI 547 6899999.999***********7665 PP >> tr|M1Y3X8|M1Y3X8_NATM8 tRNA (Guanine(37)-N(1))-methyltransferase OS=Natronomonas moolapensis (strain DSM 18674 / JCM # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 21.7 0.1 9.3e-08 1.9e-05 74 131 .. 197 254 .. 161 257 .. 0.84 Alignments for each domain: == domain 1 score: 21.7 bits; conditional E-value: 9.3e-08 HHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE---- CS UPF0020 74 raelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPY 131 ++ ++ +g+Dl++++v+ r+Nae+ gv+d++ + +ad+++++ ++ d iv n+P tr|M1Y3X8|M1Y3X8_NATM8 197 KRGAECVGVDLNEAAVEYLRRNAERNGVSDRVIAINADVRDVTGYDDWADRIVMNLPH 254 4455678************************************77779*********6 PP >> tr|M1XK62|M1XK62_NATM8 tRNA (guanine(26)-N(2))-dimethyltransferase OS=Natronomonas moolapensis (strain DSM 18674 / J # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.5 0.0 3.7e-06 0.00078 71 116 .. 67 112 .. 35 128 .. 0.82 2 ? -3.9 0.0 6.7 1.4e+03 79 115 .. 325 361 .. 313 363 .. 0.70 Alignments for each domain: == domain 1 score: 16.5 bits; conditional E-value: 3.7e-06 HHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG-- CS UPF0020 71 eearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLr 116 ++a+a + g D+d+++v+ ar+N+e+ g++++i+ ++ +a + + tr|M1XK62|M1XK62_NATM8 67 RAAEAGYAATGCDIDEAAVDLARSNLERNGLSGTIHHRNVNAHMHE 112 4556777899*****************************9988433 PP == domain 2 score: -3.9 bits; conditional E-value: 6.7 EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG- CS UPF0020 79 lygsDldrrvvqgareNaekagvgdliefsqadaakL 115 + ++D +++ a a+++ g++ +a +a++ tr|M1XK62|M1XK62_NATM8 325 NTAMDEFLGALREAGHEASRTHYGGTTFKTDAGVAEI 361 5677777777888888888888777776666666655 PP >> tr|M1XKR6|M1XKR6_NATM8 Modification methylase OS=Natronomonas moolapensis (strain DSM 18674 / JCM 14361 / 8.8.11) OX # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 6.8 0.0 0.0036 0.75 107 177 .. 7 74 .. 1 80 [. 0.72 2 ! 6.6 0.0 0.0041 0.87 29 58 .. 231 260 .. 222 312 .. 0.76 Alignments for each domain: == domain 1 score: 6.8 bits; conditional E-value: 0.0036 EEE--GGG--.STTS---EEEE----------HHHHHHHHHHHHHHHHHH-TT..-EEEEEESSHHHHHCC- CS UPF0020 107 fsqadaakLr.lkegevdvivtnpPYGerlgskkalekLYseflrelkrvlrgggrlvlltsenkalekale 177 +++ d ++L ++++v+++vt pPY ++ ++L+se+ e+ l+ g +++ + +++lek+ + tr|M1XKR6|M1XKR6_NATM8 7 IVTGDSRSLSkTDDDSVELVVTSPPYPM----IEMWDELFSELNPEITASLEAGEGHAAASQMHEELEKVWK 74 567788999966677***********64....4566667777777776666666667777777777777655 PP == domain 2 score: 6.6 bits; conditional E-value: 0.0041 TS-EEETT-TTSHHHHHHHHHHTT--TTTT CS UPF0020 29 gepllDPmCGsGtilIEaallganiapgll 58 g++ lDP+ G+Gt a + g+n + l tr|M1XKR6|M1XKR6_NATM8 231 GDTVLDPFWGTGTTSFAAMVAGRNSVGYEL 260 7999*********99988888888874444 PP >> tr|M1XZU1|M1XZU1_NATM8 Protein-L-isoaspartate O-methyltransferase OS=Natronomonas moolapensis (strain DSM 18674 / JC # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.7 0.0 0.00011 0.023 71 105 .. 95 129 .. 64 152 .. 0.78 Alignments for each domain: == domain 1 score: 11.7 bits; conditional E-value: 0.00011 HHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGE CS UPF0020 71 eearaelklygsDldrrvvqgareNaekagvgdli 105 +e +e+++ g+D+ rr+v ar+N+++ag ++ tr|M1XZU1|M1XZU1_NATM8 95 AELTDEASVHGIDIARRLVYDARSNLSAAGYSGVL 129 44458899**********************98754 PP >> tr|M1XRL7|M1XRL7_NATM8 Probable S-adenosylmethionine-dependent methyltransferase PrmC OS=Natronomonas moolapensis (s # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 8.1 0.0 0.0014 0.3 105 132 .. 75 101 .. 45 172 .. 0.64 Alignments for each domain: == domain 1 score: 8.1 bits; conditional E-value: 0.0014 EEEEE--GGG--STTS---EEEE----- CS UPF0020 105 iefsqadaakLrlkegevdvivtnpPYG 132 ie++ d ++ +++d++v npPY tr|M1XRL7|M1XRL7_NATM8 75 IEAVRSDLTHAF-LADSFDAVVFNPPYL 101 333444444333.4569**********7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (197 nodes) Target sequences: 2723 (809592 residues searched) Passed MSV filter: 103 (0.0378259); expected 54.5 (0.02) Passed bias filter: 95 (0.034888); expected 54.5 (0.02) Passed Vit filter: 24 (0.00881381); expected 2.7 (0.001) Passed Fwd filter: 13 (0.00477415); expected 0.0 (1e-05) Initial search space (Z): 2723 [actual number of targets] Domain search space (domZ): 13 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 7974.48 // [ok]