# 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/Ciona_savignyi.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-15 56.3 0.0 2.7e-15 56.1 0.0 1.1 1 tr|H2YV57|H2YV57_CIOSA Uncharacterized protein OS=Ciona savi ------ inclusion threshold ------ 3.5 7.7 7.3 5.3 7.1 6.4 1.7 2 tr|H2ZCX8|H2ZCX8_CIOSA Uncharacterized protein OS=Ciona savi 5.5 7.0 13.0 0.089 12.8 3.7 2.8 3 tr|H2ZD14|H2ZD14_CIOSA Uncharacterized protein OS=Ciona savi Domain annotation for each sequence (and alignments): >> tr|H2YV57|H2YV57_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 56.1 0.0 7.1e-19 2.7e-15 2 68 .] 11 120 .. 10 120 .. 0.98 Alignments for each domain: == domain 1 score: 56.1 bits; conditional E-value: 7.1e-19 TGGCCC-B-TTTHH.....C-..........................-HHHHHHHHH.TT---.S-SS----S...........CHH CS Trm112p 2 llllniLaCpackg.....pL..........................dwealvevaa.lglne.lpkekpedy...........ell 44 l ++n+L+++ +kg pL +w+al ++++ +g ++ lp e p+dy ++l tr|H2YV57|H2YV57_CIOSA 11 LITHNMLTSH-VKGvkngyPLlitakdvkeqevdfnpdfvskmitriEWPALTKAMEmVGKTDlLPTEVPKDYetdndflkkahHAL 96 689*******.**************************************************************************** PP TTEECCCCEEEETTTTEEEEEETT CS Trm112p 45 leldieegeLvCpncgraYpIkdG 68 +e++i++g L Cp++gr +pI +G tr|H2YV57|H2YV57_CIOSA 97 MEIEIISGCLSCPETGREFPITNG 120 **********************99 PP >> tr|H2ZCX8|H2ZCX8_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 7.1 6.4 0.0014 5.3 6 60 .. 8 53 .. 4 55 .. 0.73 2 ? -3.8 0.0 3 1.2e+04 30 54 .. 81 101 .. 75 104 .. 0.58 Alignments for each domain: == domain 1 score: 7.1 bits; conditional E-value: 0.0014 CC-B-TTTHHC--HHHHHHHHHTT---.S-SS----S..CHHTTEECCC.CEEEETTTT CS Trm112p 6 niLaCpackgpLdwealvevaalglne.lpkekpedy..ellleldiee.geLvCpncg 60 ++L C++c +pL ++n+ lp + +l+l++ +++ eL Cp+c+ tr|H2ZCX8|H2ZCX8_CIOSA 8 DLLECSVCLKPL----------DEQNKvLPCQH---TfcKLCLQTIVKShKELRCPECR 53 79**********..........34444344333...25578998877766********8 PP == domain 2 score: -3.8 bits; conditional E-value: 3 ---.S-SS----SCHHTTEECCCCEE CS Trm112p 30 lne.lpkekpedyellleldieegeL 54 +n+ + ekp+++ + +eg L tr|H2ZCX8|H2ZCX8_CIOSA 81 NNKpQATEKPDFR-----RHSVEGIL 101 4444556677766.....35666655 PP >> tr|H2ZD14|H2ZD14_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 3.5 0.5 0.018 71 46 60 .. 121 135 .. 59 137 .. 0.73 2 ? 12.8 3.7 2.3e-05 0.089 3 61 .. 124 192 .. 122 193 .. 0.83 3 ? -2.3 0.1 1.2 4.6e+03 8 16 .. 203 211 .. 201 220 .. 0.75 Alignments for each domain: == domain 1 score: 3.5 bits; conditional E-value: 0.018 TEECCCCEEEETTTT CS Trm112p 46 eldieegeLvCpncg 60 e+d++ +++vCp c+ tr|H2ZD14|H2ZD14_CIOSA 121 EYDDTVNVFVCPVCK 135 466666666666665 PP == domain 2 score: 12.8 bits; conditional E-value: 2.3e-05 GGCCC-B-TTTHH..C--HHHHHHHHH.TT---.S-SS----S......CHHTTEECCCCEEEETTTTE CS Trm112p 3 lllniLaCpackg..pLdwealvevaa.lglne.lpkekpedy......ellleldieegeLvCpncgr 61 ++ n+ +Cp+ck L +a+ e + l ++e l+ + + d +ll +l++++ ++ Cp c++ tr|H2ZD14|H2ZD14_CIOSA 124 DTVNVFVCPVCKVenCLTCKAIHEGVScLVYQEkLQNTATNDKsskqtkNLLQRLVKTKDAMHCPQCNI 192 688999999999998777788888888888888787777777788888999999*************97 PP == domain 3 score: -2.3 bits; conditional E-value: 1.2 -B-TTTHHC CS Trm112p 8 LaCpackgp 16 + C++ck++ tr|H2ZD14|H2ZD14_CIOSA 203 VRCSMCKTE 211 579999975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (68 nodes) Target sequences: 11592 (4231397 residues searched) Passed MSV filter: 409 (0.035283); expected 231.8 (0.02) Passed bias filter: 304 (0.026225); expected 231.8 (0.02) Passed Vit filter: 28 (0.00241546); expected 11.6 (0.001) Passed Fwd filter: 4 (0.000345066); expected 0.1 (1e-05) Initial search space (Z): 11592 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.02 # Mc/sec: 14386.75 // [ok]