# 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/Trm112p.hmm.txt # target sequence database: proteomes/Thermococcus_kodakarensis.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Trm112p [M=68] Accession: PF03966.15 Description: Trm112p-like protein 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.0048 14.6 0.1 0.011 13.5 0.1 1.6 1 tr|Q5JF81|Q5JF81_THEKO Uncharacterized protein OS=Thermococc ------ inclusion threshold ------ 0.011 13.4 0.0 1.3 6.8 0.0 2.2 2 sp|Q5JIH3|HYPA_THEKO Hydrogenase maturation factor HypA OS 0.013 13.2 0.2 0.052 11.3 0.0 1.8 2 tr|Q5JFV9|Q5JFV9_THEKO Probable lysine biosynthesis protein Domain annotation for each sequence (and alignments): >> tr|Q5JF81|Q5JF81_THEKO Uncharacterized protein OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 13.5 0.1 1.4e-05 0.011 9 64 .. 3 55 .. 1 58 [. 0.90 Alignments for each domain: == domain 1 score: 13.5 bits; conditional E-value: 1.4e-05 B-TTTHHC--HHHHHHHHH.TT---.S-SS----SCHHTTEECCCCEEEETTTTEEEE CS Trm112p 9 aCpackgpLdwealvevaa.lglne.lpkekpedyellleldieegeLvCpncgraYp 64 Cp+c + Ldw+ l++++ +g e + k++ ++ e + ++ Cp+cg ++ tr|Q5JF81|Q5JF81_THEKO 3 RCPLCGKALDWAELINQMLeKGVGEdVFKDRDKFME-----TFNDFVFKCPHCGEEFY 55 7******************99*99999999999997.....78899999999999886 PP >> sp|Q5JIH3|HYPA_THEKO Hydrogenase maturation factor HypA OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 1238 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 6.8 0.0 0.0017 1.3 41 60 .. 51 77 .. 12 84 .. 0.76 2 ? 4.8 0.0 0.0072 5.5 4 14 .. 104 114 .. 102 127 .. 0.83 Alignments for each domain: == domain 1 score: 6.8 bits; conditional E-value: 0.0017 S.......CHHTTEECCCCEEEETTTT CS Trm112p 41 y.......ellleldieegeLvCpncg 60 + +e+++ee ++ C+nc+ sp|Q5JIH3|HYPA_THEKO 51 LfagtiaeGAEIEFVEEEAVFKCRNCN 77 1555555534589*************8 PP == domain 2 score: 4.8 bits; conditional E-value: 0.0072 GCCC-B-TTTH CS Trm112p 4 llniLaCpack 14 ++ +LaCp c sp|Q5JIH3|HYPA_THEKO 104 VHAFLACPKCG 114 5899****886 PP >> tr|Q5JFV9|Q5JFV9_THEKO Probable lysine biosynthesis protein OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 0.1 0.0 0.2 1.6e+02 8 15 .. 2 9 .. 1 13 [. 0.70 2 ? 11.3 0.0 6.8e-05 0.052 3 17 .. 17 31 .. 15 52 .. 0.61 Alignments for each domain: == domain 1 score: 0.1 bits; conditional E-value: 0.2 -B-TTTHH CS Trm112p 8 LaCpackg 15 + Cp+c + tr|Q5JFV9|Q5JFV9_THEKO 2 VECPVCGS 9 67888865 PP == domain 2 score: 11.3 bits; conditional E-value: 6.8e-05 GGCCC-B-TTTHHC- CS Trm112p 3 lllniLaCpackgpL 17 +l+ i+ Cp+c +L tr|Q5JFV9|Q5JFV9_THEKO 17 ELHQIVECPVCGAEL 31 69***********77 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (68 nodes) Target sequences: 2301 (637680 residues searched) Passed MSV filter: 85 (0.0369405); expected 46.0 (0.02) Passed bias filter: 80 (0.0347675); expected 46.0 (0.02) Passed Vit filter: 15 (0.0065189); expected 2.3 (0.001) Passed Fwd filter: 3 (0.00130378); expected 0.0 (1e-05) Initial search space (Z): 2301 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4336.22 // [ok]