Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate PP_1000 PP_1000 ornithine carbamoyltransferase, catabolic
Query= SwissProt::P08308 (336 letters) >FitnessBrowser__Putida:PP_1000 Length = 336 Score = 634 bits (1634), Expect = 0.0 Identities = 309/336 (91%), Positives = 325/336 (96%) Query: 1 MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60 MAFN+HNRNLLSL HH+TRELRYLLDLSRDLKRAKYTGTEQQHLK NIALIFEKTSTRT Sbjct: 1 MAFNIHNRNLLSLEHHTTRELRYLLDLSRDLKRAKYTGTEQQHLKGNNIALIFEKTSTRT 60 Query: 61 RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120 RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK Sbjct: 61 RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120 Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180 FAGVPVFNGLTDEYHPTQM+ADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL Sbjct: 121 FAGVPVFNGLTDEYHPTQMIADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180 Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240 GMDVRIAAPKALWPHD+ V +CK++AEESGA++TLTEDPK AVKGVDFVHTDVWVSMGEP Sbjct: 181 GMDVRIAAPKALWPHDDLVERCKQYAEESGARITLTEDPKAAVKGVDFVHTDVWVSMGEP 240 Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300 +EAWGERIK+L PYQVN E+MK+TGNPR KFMHCLPAFHNSETKVGKQIAEQYP+LANGI Sbjct: 241 IEAWGERIKQLKPYQVNAELMKSTGNPRTKFMHCLPAFHNSETKVGKQIAEQYPDLANGI 300 Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLADI 336 EVT+DVFESP IAFEQAENRMHTIKAILVSTLAD+ Sbjct: 301 EVTDDVFESPACIAFEQAENRMHTIKAILVSTLADL 336 Lambda K H 0.318 0.133 0.387 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 500 Number of extensions: 6 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 336 Length of database: 336 Length adjustment: 28 Effective length of query: 308 Effective length of database: 308 Effective search space: 94864 Effective search space used: 94864 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate PP_1000 PP_1000 (ornithine carbamoyltransferase, catabolic)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00658.hmm # target sequence database: /tmp/gapView.23395.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00658 [M=304] Accession: TIGR00658 Description: orni_carb_tr: ornithine carbamoyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-138 446.2 0.0 3.2e-138 446.0 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_1000 PP_1000 ornithine carbamoyltrans Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_1000 PP_1000 ornithine carbamoyltransferase, catabolic # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 446.0 0.0 3.2e-138 3.2e-138 1 303 [. 8 333 .. 8 334 .. 0.99 Alignments for each domain: == domain 1 score: 446.0 bits; conditional E-value: 3.2e-138 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkee 75 r+llsl +++++el++ll+l+++lk++k++g+e+++lkg+++aliFek+stRtR++fevaay++Ga+v+y+++++ lcl|FitnessBrowser__Putida:PP_1000 8 RNLLSLEHHTTRELRYLLDLSRDLKRAKYTGTEQQHLKGNNIALIFEKTSTRTRCAFEVAAYDQGANVTYIDPNS 82 78************************************************************************* PP TIGR00658 76 lqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklg.klkev 149 +q+g+kes+kDtarvl+r++dai +R++k+e+veelak+a+vPv+ngLtd+ hP+q++aD+lt++e+ + l+++ lcl|FitnessBrowser__Putida:PP_1000 83 SQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAKFAGVPVFNGLTDEYHPTQMIADVLTMREHSDkPLHDI 157 *********************************************************************99**** PP TIGR00658 150 klvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytD 223 +++y+GDa nn++nslll++aklG+dv++a+P++l+p+ ++v+++k+ a+e+g++++ltedpk avk++d+++tD lcl|FitnessBrowser__Putida:PP_1000 158 SYAYLGDArNNMGNSLLLIGAKLGMDVRIAAPKALWPHDDLVERCKQYAEESGARITLTEDPKAAVKGVDFVHTD 232 *************************************************************************** PP TIGR00658 224 vwvsmGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr...................Geevtdevl 277 vwvsmGe e++ er+k+lkpyqvn el++ + +p +kf+hCLPa++ G evtd+v+ lcl|FitnessBrowser__Putida:PP_1000 233 VWVSMGEpIEAWGERIKQLKPYQVNAELMKSTgNPRTKFMHCLPAFHnsetkvgkqiaeqypdlanGIEVTDDVF 307 *******8899*********************9****************************************** PP TIGR00658 278 egeasivfdeaenRlhaqkavlkall 303 e++a i f++aenR+h++ka+l+ +l lcl|FitnessBrowser__Putida:PP_1000 308 ESPACIAFEQAENRMHTIKAILVSTL 333 **********************9887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (336 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.82 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory