# 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/Methyltransf_4.hmm.txt # target sequence database: proteomes/Thermococcus_kodakarensis.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Methyltransf_4 [M=173] Accession: PF02390.16 Description: Putative methyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-06 25.1 0.1 4.4e-06 23.4 0.1 1.8 2 tr|Q5JFS6|Q5JFS6_THEKO Predicted SAM-dependent methyltransfe 3.4e-05 20.5 0.1 0.00032 17.3 0.0 2.1 2 tr|Q5JEW7|Q5JEW7_THEKO tRNA/rRNA cytosine-C5-methylase, NOL1 0.00025 17.6 0.0 0.00066 16.3 0.0 1.7 1 tr|Q5JEM0|Q5JEM0_THEKO Predicted N6-adenine-specific DNA met 0.00053 16.6 0.0 0.00078 16.1 0.0 1.2 1 tr|Q5JEE1|Q5JEE1_THEKO Protein-L-isoaspartate O-methyltransf 0.00072 16.2 0.0 0.0016 15.0 0.0 1.6 2 tr|Q5JGN8|Q5JGN8_THEKO SAM-dependent methyltransferase, UbiE 0.0034 14.0 0.0 0.012 12.2 0.0 1.7 2 tr|Q5JJ79|Q5JJ79_THEKO Predicted SAM-dependent methyltransfe Domain annotation for each sequence (and alignments): >> tr|Q5JFS6|Q5JFS6_THEKO Predicted SAM-dependent methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918 / # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 23.4 0.1 1.1e-08 4.4e-06 5 63 .. 61 118 .. 58 145 .. 0.81 2 ? -0.5 0.0 0.24 92 98 127 .. 140 170 .. 136 182 .. 0.74 Alignments for each domain: == domain 1 score: 23.4 bits; conditional E-value: 1.1e-08 EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCH CS Methyltransf_4 5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkv 63 vl++GcG G ++ ++A kn ++G++ +++v++ + ++ +++ kN + ++g+ l++ tr|Q5JFS6|Q5JFS6_THEKO 61 VLDVGCGTGVLTFKMALKNGVEMVVGVDRKEEVIEFC-NRLGDRVTKNAKFVQGNFLEM 118 79**************************999999766.567778899999999996543 PP == domain 2 score: -0.5 bits; conditional E-value: 0.24 HHHHHHHHHEEEEEEEEE.EESHHHHHHHHH CS Methyltransf_4 98 ellkelarvLkkgGvlel.aTDveeyaeeml 127 +l+ + +vL++gG + + D++++ +++ tr|Q5JFS6|Q5JFS6_THEKO 140 PFLERALEVLEEGGRVIVgDFDINDLRKRIR 170 68999999******87551456666666655 PP >> tr|Q5JEW7|Q5JEW7_THEKO tRNA/rRNA cytosine-C5-methylase, NOL1/NOP2/Sun family, containing RNA-binding PUA domain OS=T # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 17.3 0.0 8.3e-07 0.00032 4 65 .. 201 262 .. 198 269 .. 0.86 2 ? 0.6 0.0 0.11 43 96 128 .. 302 334 .. 300 350 .. 0.81 Alignments for each domain: == domain 1 score: 17.3 bits; conditional E-value: 8.3e-07 EEEEET-TTSHHHHHHHH.HSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHH CS Methyltransf_4 4 vvleiGcGkGeflvalAk.knPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvll 65 +++++ + G+ ++++A+ ++ ++++i++++++++k+ ++ ++l++kN+r+++ da + l+ tr|Q5JEW7|Q5JEW7_THEKO 201 LIIDMAAAPGGKTSHIAQlMQNRGEIIAIDKSRNRLRKMEEELKRLGVKNVRLIHMDA-RKLP 262 6788888889999999984567789********************************9.5555 PP == domain 2 score: 0.6 bits; conditional E-value: 0.11 SHHHHHHHHHHEEEEEEEEEEESHHHHHHHHHH CS Methyltransf_4 96 qpellkelarvLkkgGvlelaTDveeyaeemlk 128 q++++ ++ + L+kgG l+ T y e+ ++ tr|Q5JEW7|Q5JEW7_THEKO 302 QRAFIWAAIKSLRKGGTLVYSTCTISYEENEAN 334 6778888999**********9998888877554 PP >> tr|Q5JEM0|Q5JEM0_THEKO Predicted N6-adenine-specific DNA methylase OS=Thermococcus kodakarensis (strain ATCC BAA-918 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.3 0.0 1.7e-06 0.00066 6 70 .. 222 286 .. 218 331 .. 0.86 Alignments for each domain: == domain 1 score: 16.3 bits; conditional E-value: 1.7e-06 EEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHH.HHHHHCTTSSEEEEES-CCCHHHHCS-T CS Methyltransf_4 6 leiGcGkGeflvalAkknPdknflGiEirvkvvakvl.kkiealelkNlrilrgdalkvllelled 70 ++ cG+G++l++lA + + ++G+E+++k ++ + ++ a l ++ ++gda + l++++e tr|Q5JEM0|Q5JEM0_THEKO 222 IDPFCGSGTILIELALRGYKGRIIGLEKYRKHIRGAEmNALSAGVLDKIEFIQGDA-TKLSQYVES 286 5556*****************************998614555668999********.889999876 PP >> tr|Q5JEE1|Q5JEE1_THEKO Protein-L-isoaspartate O-methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.1 0.0 2e-06 0.00078 4 64 .. 80 139 .. 77 148 .. 0.87 Alignments for each domain: == domain 1 score: 16.1 bits; conditional E-value: 2e-06 EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHH CS Methyltransf_4 4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvl 64 vleiG+G+G+ + + ++++ iE ++v+ + ++ e+ ++kN++++ gd +k + tr|Q5JEE1|Q5JEE1_THEKO 80 NVLEIGTGSGWNAALI-SELVKTDVYTIERIPELVEFARRNLERAGVKNVHVILGDGTKGF 139 589*******876555.567899999******************************97765 PP >> tr|Q5JGN8|Q5JGN8_THEKO SAM-dependent methyltransferase, UbiE/COQ5 family OS=Thermococcus kodakarensis (strain ATCC B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 15.0 0.0 4.2e-06 0.0016 4 80 .. 44 113 .. 41 115 .. 0.82 2 ? -3.6 0.0 2.2 8.3e+02 98 113 .. 126 141 .. 125 143 .. 0.81 Alignments for each domain: == domain 1 score: 15.0 bits; conditional E-value: 4.2e-06 EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEEEEES CS Methyltransf_4 4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgslekifilF 80 vl++ cG G +++lA++ ++lG+++++++++ + +k+ea++l N++ +rg+al+ ++e+ +++ + ++F tr|Q5JGN8|Q5JGN8_THEKO 44 RVLDLACGTGIPTLELAERG--YEVLGLDLHEEMLRVARRKAEARGL-NVKFIRGNALD---ISFEE-EFDAVTMFF 113 589**************986..678*********9999999888776.9********54...45555.677777776 PP == domain 2 score: -3.6 bits; conditional E-value: 2.2 HHHHHHHHHEEEEEEE CS Methyltransf_4 98 ellkelarvLkkgGvl 113 el + + r+L++gGv+ tr|Q5JGN8|Q5JGN8_THEKO 126 ELFNSVRRTLRPGGVF 141 567889999****986 PP >> tr|Q5JJ79|Q5JJ79_THEKO Predicted SAM-dependent methyltransferase, DUF890 family OS=Thermococcus kodakarensis (strain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 12.2 0.0 3.2e-05 0.012 5 71 .. 85 149 .. 82 162 .. 0.85 2 ? -1.1 0.0 0.37 1.4e+02 98 132 .. 188 223 .. 185 230 .. 0.75 Alignments for each domain: == domain 1 score: 12.2 bits; conditional E-value: 3.2e-05 EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TT CS Methyltransf_4 5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledg 71 vleiG+G ++ +A++ ++++ + E+ ++ +++ ++ie+++ N++ ++++ +++ ++++g tr|Q5JJ79|Q5JJ79_THEKO 85 VLEIGTGHTAMMALMAERLFNCDVTATELDEEFFEYAKRNIEKNG-ANVKPIKSNG-GIIRGVVPKG 149 89***********************************99998765.6999999997.7777777765 PP == domain 2 score: -1.1 bits; conditional E-value: 0.37 HHHHHHHHHEEEEEEEEE.EESHHHHHHHHHHHHHC CS Methyltransf_4 98 ellkelarvLkkgGvlel.aTDveeyaeemlkvlee 132 l++e+ + L++gG + l D e++ e ++++ +e tr|Q5JJ79|Q5JJ79_THEKO 188 RLIEEALEYLNPGGKVALfLPDKEPLIEAIAEKGKE 223 678899999999999975157888888887777655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (173 nodes) Target sequences: 2301 (637680 residues searched) Passed MSV filter: 88 (0.0382442); expected 46.0 (0.02) Passed bias filter: 75 (0.0325945); expected 46.0 (0.02) Passed Vit filter: 17 (0.00738809); expected 2.3 (0.001) Passed Fwd filter: 6 (0.00260756); expected 0.0 (1e-05) Initial search space (Z): 2301 [actual number of targets] Domain search space (domZ): 6 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11031.86 // [ok]