# 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/Dictyostelium_discoideum.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-10 40.6 0.0 3.3e-10 39.9 0.0 1.4 1 sp|Q54N57|TR112_DICDI Multifunctional methyltransferase sub ------ inclusion threshold ------ 5.8 7.1 7.2 15 5.8 0.1 3.3 3 tr|Q54EY5|Q54EY5_DICDI LIM domain protein OS=Dictyostelium d Domain annotation for each sequence (and alignments): >> sp|Q54N57|TR112_DICDI Multifunctional methyltransferase subunit TRM112-like protein OS=Dictyostelium discoideum OX=4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 39.9 0.0 5.2e-14 3.3e-10 2 68 .] 3 111 .. 2 111 .. 0.86 Alignments for each domain: == domain 1 score: 39.9 bits; conditional E-value: 5.2e-14 TGGCCC-B-TTTHH......C-..........................-HHHHHHHHH.TT---.S-SS----S.........CHHTT CS Trm112p 2 llllniLaCpackg......pL..........................dwealvevaa.lglne.lpkekpedy.........ellle 46 l++n++aC k+ pL dw + e + ++++ l +k + +ll + sp|Q54N57|TR112_DICDI 3 ILTHNMMACT-KKQcmgkgfPLkvesteqivleqefnyeftkniypklDWLGIAEISIkFNIPIqLDTTKHSLEdeeflktlhNLLCN 89 58********.999999***998888888888888888888888888888888888887777776666666666999******9**** PP EECCCCEEEETTTTEEEEEETT CS Trm112p 47 ldieegeLvCpncgraYpIkdG 68 l++++g+L+Cpnc+r+YpI++G sp|Q54N57|TR112_DICDI 90 LKVITGSLTCPNCQRVYPIDKG 111 *******************998 PP >> tr|Q54EY5|Q54EY5_DICDI LIM domain protein OS=Dictyostelium discoideum OX=44689 GN=limD PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 5.8 0.1 0.0024 15 41 60 .. 496 524 .. 448 525 .. 0.73 2 ? -0.1 0.3 0.16 1e+03 51 64 .. 600 613 .. 578 616 .. 0.71 3 ? 3.1 0.3 0.016 1e+02 41 64 .. 644 680 .. 626 680 .. 0.70 Alignments for each domain: == domain 1 score: 5.8 bits; conditional E-value: 0.0024 S............CHHTTEECCCCEEEETTTT CS Trm112p 41 y............ellleldieegeLvCpncg 60 +ld e+geLvC +cg tr|Q54EY5|Q54EY5_DICDI 496 ShqnssnslnkspR---KLDGENGELVCARCG 524 04566666664441...59999*********8 PP == domain 2 score: -0.1 bits; conditional E-value: 0.16 CCEEEETTTTEEEE CS Trm112p 51 egeLvCpncgraYp 64 ++ +vC+nc+ +p tr|Q54EY5|Q54EY5_DICDI 600 SECFVCSNCHSSFP 613 56689999999998 PP == domain 3 score: 3.1 bits; conditional E-value: 0.016 S.............CHHTTEECCCCEEEETTTTEEEE CS Trm112p 41 y.............ellleldieegeLvCpncgraYp 64 +l +++ +vC+ c+ ++p tr|Q54EY5|Q54EY5_DICDI 644 ChqeidsksdgvikVLGSKYHNNGKCFVCRGCQTVFP 680 34555555556676444579999999**********9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (68 nodes) Target sequences: 12739 (6856946 residues searched) Passed MSV filter: 385 (0.0302222); expected 254.8 (0.02) Passed bias filter: 249 (0.0195463); expected 254.8 (0.02) Passed Vit filter: 16 (0.00125599); expected 12.7 (0.001) Passed Fwd filter: 2 (0.000156998); expected 0.1 (1e-05) Initial search space (Z): 12739 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.09u 0.00s 00:00:00.09 Elapsed: 00:00:00.05 # Mc/sec: 9325.45 // [ok]