# 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/Natronomonas_moolapensis.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-13 48.1 1.7 3.2e-13 47.4 1.7 1.4 1 tr|M1Y3V1|M1Y3V1_NATM8 UPF0434 protein Nmlp_3063 OS=Natronom ------ inclusion threshold ------ 0.5 8.4 7.7 0.69 7.9 1.5 3.2 3 tr|M1XKG4|M1XKG4_NATM8 Transcription initiation factor IIB O Domain annotation for each sequence (and alignments): >> tr|M1Y3V1|M1Y3V1_NATM8 UPF0434 protein Nmlp_3063 OS=Natronomonas moolapensis (strain DSM 18674 / JCM 14361 / 8.8.11) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 47.4 1.7 2.4e-16 3.2e-13 1 68 [] 2 49 .. 2 49 .. 0.96 Alignments for each domain: == domain 1 score: 47.4 bits; conditional E-value: 2.4e-16 BTGGCCC-B-TTTHHC--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTEEEEEETT CS Trm112p 1 kllllniLaCpackgpLdwealvevaalglnelpkekpedyellleldieegeLvCpncgraYpIkdG 68 k++ll+iL+Cp++k +L++e++ e +i+eg LvC++cg +YpI+dG tr|M1Y3V1|M1Y3V1_NATM8 2 KETLLDILCCPLDKAELELEVIREDDD--------------------EILEGRLVCTECGEVYPIEDG 49 689**************99***99997....................9*******************9 PP >> tr|M1XKG4|M1XKG4_NATM8 Transcription initiation factor IIB OS=Natronomonas moolapensis (strain DSM 18674 / JCM 14361 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 7.9 1.5 0.00051 0.69 33 60 .. 18 47 .. 3 50 .. 0.60 2 ? 6.8 1.0 0.0011 1.5 8 62 .. 41 67 .. 41 67 .. 0.91 3 ? -0.2 0.0 0.17 2.3e+02 22 52 .. 293 336 .. 283 337 .] 0.71 Alignments for each domain: == domain 1 score: 7.9 bits; conditional E-value: 0.00051 S-SS----S..CHHTTEECCCCEEEETTTT CS Trm112p 33 lpkekpedy..ellleldieegeLvCpncg 60 ++e e e e ++e eLvCp+cg tr|M1XKG4|M1XKG4_NATM8 18 AAEESNESErtENEREAGEDESELVCPECG 47 333333333443334577899********7 PP == domain 2 score: 6.8 bits; conditional E-value: 0.0011 -B-TTTHHC--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTEE CS Trm112p 8 LaCpackgpLdwealvevaalglnelpkekpedyellleldieegeLvCpncgra 62 L+Cp c g+L + d e+ge vC++cg++ tr|M1XKG4|M1XKG4_NATM8 41 LVCPECGGRL------------------------T----ADSEHGETVCTECGLV 67 89********........................6....89999********985 PP == domain 3 score: -0.2 bits; conditional E-value: 0.17 HHHHHH.TT---S-SS----S............CHHTTEECCCC CS Trm112p 22 lvevaa.lglnelpkekpedy............ellleldieeg 52 v++a l ++++ ++ +++ ++lle++++ g tr|M1XKG4|M1XKG4_NATM8 293 AVYAASlLTNEKVTQNAVSEVadisevtirnryHELLEVEQDAG 336 55666666666666666665568888888888899999998766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (68 nodes) Target sequences: 2723 (809592 residues searched) Passed MSV filter: 104 (0.0381932); expected 54.5 (0.02) Passed bias filter: 91 (0.033419); expected 54.5 (0.02) Passed Vit filter: 14 (0.00514139); expected 2.7 (0.001) Passed Fwd filter: 2 (0.000734484); expected 0.0 (1e-05) Initial search space (Z): 2723 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5505.23 // [ok]