# 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/GCD14.hmm.txt # target sequence database: proteomes/Petromyzon_marinus.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: GCD14 [M=247] Accession: PF08704.9 Description: tRNA methyltransferase complex GCD14 subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-96 319.8 0.0 1.3e-95 319.4 0.0 1.2 1 tr|S4RY21|S4RY21_PETMA tRNA (adenine(58)-N(1))-methyltransfe 3.5e-07 29.8 0.0 4.6e-07 29.4 0.0 1.2 1 tr|S4R827|S4R827_PETMA Protein-L-isoaspartate (D-aspartate) 4.6e-05 22.8 0.0 9.5e-05 21.8 0.0 1.5 2 tr|S4RW29|S4RW29_PETMA Protein-L-isoaspartate O-methyltransf 0.0001 21.6 0.1 0.00021 20.6 0.1 1.4 1 tr|S4RTL8|S4RTL8_PETMA Fibrillarin OS=Petromyzon marinus OX= 0.002 17.4 0.0 0.018 14.4 0.0 2.1 2 tr|S4RHT4|S4RHT4_PETMA tRNA (guanine(26)-N(2))-dimethyltrans ------ inclusion threshold ------ 0.022 14.0 0.1 0.03 13.6 0.1 1.2 1 tr|S4RCL0|S4RCL0_PETMA Uncharacterized protein OS=Petromyzon Domain annotation for each sequence (and alignments): >> tr|S4RY21|S4RY21_PETMA tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A OS=Petromyzon marinus OX= # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 319.4 0.0 5.7e-99 1.3e-95 1 246 [. 65 305 .. 65 306 .. 0.92 Alignments for each domain: == domain 1 score: 319.4 bits; conditional E-value: 5.7e-99 GCD14 1 gfvyvlaptPeLWtlaLphrtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefre 87 g++y l+ptPeLWt +Lphrtqily++Di++++ +L+l+pGsvv+esGtGsgslsha++rt+aP Ghl+t+efheqra +a eef++ tr|S4RY21|S4RY21_PETMA 65 GWAYALHPTPELWTRSLPHRTQILYSTDIAMVTLMLDLRPGSVVCESGTGSGSLSHALLRTIAPSGHLHTVEFHEQRAASAAEEFER 151 8************************************************************************************** PP GCD14 88 helsqlvtvthrDvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteietlevll 174 h++ l tv+ rDvc++Gf +v g++DavfLD+P+Pw+a+pha +a+k++ggrlCsfsPCieqvqrtc+aL+ lgf+e +t+evll tr|S4RY21|S4RY21_PETMA 152 HGVGRLATVRCRDVCRDGF--GVAGVADAVFLDIPSPWDAVPHARDAMKTSGGRLCSFSPCIEQVQRTCQALAGLGFVEPSTVEVLL 236 *******************..9***************************************************************** PP GCD14 175 rtyevrkskleeidlaekrleenerkriekakrrkaskdakvedkssksstevllkPvselkghtgyLtfat 246 r +vr+++l++ dl++ + + + + +a v+ ++ + + P +e+ ghtgyLtfat tr|S4RY21|S4RY21_PETMA 237 RPLDVRTVSLPVPDLGQGGVRASGDG--GRPRPPHAVPAGVVDSSRGV-YSFKAGCPPREMPGHTGYLTFAT 305 ***************99988877544..23333445555666666666.555566788*************8 PP >> tr|S4R827|S4R827_PETMA Protein-L-isoaspartate (D-aspartate) O-methyltransferase OS=Petromyzon marinus OX=7757 PE=4 S # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 29.4 0.0 2e-10 4.6e-07 35 106 .. 75 146 .. 57 187 .. 0.77 Alignments for each domain: == domain 1 score: 29.4 bits; conditional E-value: 2e-10 GCD14 35 kLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGf 106 + +l +G+ v++ G Gsg l+ iar v+ G++f +++ ++ +++a+++ +++++s l ++ v +G tr|S4R827|S4R827_PETMA 75 QDHLFEGASVLDVGSGSGYLTACIARMVGSSGKVFGIDHIQELVDEAIKNVNKDDMSLLSSGQVTLVVGDGR 146 456789*************************************************95544444444444443 PP >> tr|S4RW29|S4RW29_PETMA Protein-L-isoaspartate O-methyltransferase OS=Petromyzon marinus OX=7757 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 21.8 0.0 4.2e-08 9.5e-05 35 87 .. 96 148 .. 86 169 .. 0.89 2 ? -2.9 0.0 1.4 3.2e+03 45 68 .. 179 202 .. 170 203 .. 0.84 Alignments for each domain: == domain 1 score: 21.8 bits; conditional E-value: 4.2e-08 GCD14 35 kLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefre 87 + +l++G+ +++ G Gsg l+ +ar ++P+G++ +++ ++ +++a+ + ++ tr|S4RW29|S4RW29_PETMA 96 QDRLQEGASALDVGSGSGYLTACLARMIGPRGKVIGVDHIQELVSEAKVNVQR 148 55899************************************999999887766 PP == domain 2 score: -2.9 bits; conditional E-value: 1.4 GCD14 45 vesGtGsgslshaiartvaPtGhl 68 + G+ ++ + ha++ ++P G+l tr|S4RW29|S4RW29_PETMA 179 IHVGAAAAIVPHALLDQLKPGGRL 202 667888899999999999999997 PP >> tr|S4RTL8|S4RTL8_PETMA Fibrillarin OS=Petromyzon marinus OX=7757 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 20.6 0.1 9.5e-08 0.00021 35 150 .. 164 277 .. 156 293 .. 0.69 Alignments for each domain: == domain 1 score: 20.6 bits; conditional E-value: 9.5e-08 GCD14 35 kLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareef..rehelsqlvtvthrDvckeGfdeevsgkvDavfL 119 ++++kpG +v+ G+ sg+ + ++ v+P G ++++ef ++ + + + +++++ + +++ + + g vD vf tr|S4RTL8|S4RTL8_PETMA 164 QIHIKPGVKVLYLGAASGTTVSHVSDIVGPEGLVYAVEFSHR-SGRDLMNVakKRTNIIPIYKLECSPI-------SLAGMVDVVFA 242 789************************************653.33334343003444444444444444.......456669***** PP GCD14 120 DlPaPwea...iphaakalkkeggrlCsf.sPCie 150 D+ +P++ +a + lk+ g + s + Ci+ tr|S4RTL8|S4RTL8_PETMA 243 DVAQPDQTrivAINAHNFLKNGGHFVISIkANCID 277 *****986321234556665555555554245665 PP >> tr|S4RHT4|S4RHT4_PETMA tRNA (guanine(26)-N(2))-dimethyltransferase OS=Petromyzon marinus OX=7757 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 14.4 0.0 7.8e-06 0.018 37 144 .. 138 246 .. 133 251 .. 0.93 2 ? 0.3 0.0 0.16 3.5e+02 44 80 .. 261 297 .. 249 313 .. 0.89 Alignments for each domain: == domain 1 score: 14.4 bits; conditional E-value: 7.8e-06 GCD14 37 elkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGf.deevsgkvDavfLD.l 121 + ++G +v+e+ + sg s +a+ + + t +f ++ + ++ + +++++lvt + D+ + +++ +++ D v LD tr|S4RHT4|S4RHT4_PETMA 138 KCEEGVKVLEALAASGLRSIRFAKEIPGIKSIITNDFSKNAVAAINKNIEMNQVQHLVTASYSDASMLMYkSKNHKESFDVVDLDpY 224 5678******************************************************************77888999*******56 PP GCD14 122 PaPweaiphaakalkkeggrlCs 144 +P + ++ a++ + +egg lC tr|S4RHT4|S4RHT4_PETMA 225 GSPVQFLDAAVQSV-NEGGLLCV 246 79************.99****96 PP == domain 2 score: 0.3 bits; conditional E-value: 0.16 GCD14 44 vvesGtGsgslshaiartvaPtGhlftfefheqraek 80 + s Gs sl ++ +a + l+ ++ h +r+++ tr|S4RHT4|S4RHT4_PETMA 261 TCYSKYGSMSLKAKFCHEMALRIILHCLDLHSNRYHR 297 567888****************************975 PP >> tr|S4RCL0|S4RCL0_PETMA Uncharacterized protein OS=Petromyzon marinus OX=7757 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.6 0.1 1.3e-05 0.03 10 140 .. 34 175 .. 27 181 .. 0.75 Alignments for each domain: == domain 1 score: 13.6 bits; conditional E-value: 1.3e-05 GCD14 10 PeLW..tlaLphrtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehel.... 90 P L+ tl ++ + i y + i +i+ + +k G v G s+ + + tv Gh+ + + e+ + a+ + + + tr|S4RCL0|S4RCL0_PETMA 34 PSLYefTLFMSRTATIAYPKKIGVIMRTKIVKVGDPVQCGGVASARFGIVASATVWEPGHVVSCDVREDHLHVAQRNVASWRSaweq 120 55651155556666899************************************************9988888777665433322223 PP GCD14 91 .......sqlvtvthrDvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkegg 140 ++ + Dv ++ ++ + + Dav LD+ + a+ + alk gg tr|S4RCL0|S4RCL0_PETMA 121 argvdswPRNISFLKADVLRDTHLTH-QYTYDAVVLDMLNVHLAVSCVLPALK-PGG 175 33333333478888899998887333.3589*******999999999988884.444 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (247 nodes) Target sequences: 13539 (5048892 residues searched) Passed MSV filter: 503 (0.0371519); expected 270.8 (0.02) Passed bias filter: 377 (0.0278455); expected 270.8 (0.02) Passed Vit filter: 30 (0.00221582); expected 13.5 (0.001) Passed Fwd filter: 7 (0.000517025); expected 0.1 (1e-05) Initial search space (Z): 13539 [actual number of targets] Domain search space (domZ): 6 [number of targets reported over threshold] # CPU time: 0.15u 0.01s 00:00:00.16 Elapsed: 00:00:00.04 # Mc/sec: 31176.91 // [ok]