Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate AO356_05275 AO356_05275 ornithine carbamoyltransferase
Query= SwissProt::P08308 (336 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05275 Length = 336 Score = 595 bits (1534), Expect = e-175 Identities = 288/336 (85%), Positives = 313/336 (93%) Query: 1 MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60 MAFNM NR+LLSLMHH+ REL YLLDLSRDLKRAKYTGTEQ HLK KNIALIFEKTSTRT Sbjct: 1 MAFNMRNRSLLSLMHHTNRELHYLLDLSRDLKRAKYTGTEQPHLKGKNIALIFEKTSTRT 60 Query: 61 RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120 RCAFEVAA+DQGA+VTYIDP SSQIGHKESMKDTARVLGRM+DAIEYRGF+QEIVEELAK Sbjct: 61 RCAFEVAAHDQGAHVTYIDPVSSQIGHKESMKDTARVLGRMFDAIEYRGFEQEIVEELAK 120 Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180 FAGVPVFNGLT E+HPTQM+AD LTMREHSDKPLHDISYAYLGDAR NMGNSLL+IGAKL Sbjct: 121 FAGVPVFNGLTAEFHPTQMIADTLTMREHSDKPLHDISYAYLGDARYNMGNSLLMIGAKL 180 Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240 GMDVRI APKALWPH +F+ QC+ FA ESG ++T+TEDPK AVKGVDF+HTD+WVSMGEP Sbjct: 181 GMDVRIGAPKALWPHQDFIDQCQAFAAESGGRITITEDPKAAVKGVDFIHTDIWVSMGEP 240 Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300 VEAW ERI++LLPYQVN ++MKA+GNPR KFMHCLPAFHNSETKVGK IA +YPNLANG+ Sbjct: 241 VEAWDERIEQLLPYQVNAQMMKASGNPRVKFMHCLPAFHNSETKVGKDIAARYPNLANGV 300 Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLADI 336 EVTE+VFESP NIAFEQAENRMHTIKAILVS LADI Sbjct: 301 EVTEEVFESPANIAFEQAENRMHTIKAILVSALADI 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: 484 Number of extensions: 8 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 AO356_05275 AO356_05275 (ornithine carbamoyltransferase)
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.carbon/TIGR00658.hmm # target sequence database: /tmp/gapView.4252.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-132 426.0 0.0 4.5e-132 425.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05275 AO356_05275 ornithine carbamoylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05275 AO356_05275 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 425.8 0.0 4.5e-132 4.5e-132 1 303 [. 8 333 .. 8 334 .. 0.99 Alignments for each domain: == domain 1 score: 425.8 bits; conditional E-value: 4.5e-132 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaaye 63 r+llsl++++++el++ll+l+++lk++k++g+e+ +lkgk++aliFek+stRtR++fevaa + lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05275 8 RSLLSLMHHTNRELHYLLDLSRDLKRAKYTGTEQPHLKGKNIALIFEKTSTRTRCAFEVAAHD 70 78************************************************************* PP TIGR00658 64 lGaqvlylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdl 126 +Ga+v+y+++ ++q+g+kes+kDtarvl+r++dai +R++++e+veelak+a+vPv+ngLt + lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05275 71 QGAHVTYIDPVSSQIGHKESMKDTARVLGRMFDAIEYRGFEQEIVEELAKFAGVPVFNGLTAE 133 *************************************************************** PP TIGR00658 127 ehPcqilaDlltikeklg.klkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepea 187 +hP+q++aD lt++e+ + l++++++y+GDa n++nsll+++aklG+dv++ +P++l+p++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05275 134 FHPTQMIADTLTMREHSDkPLHDISYAYLGDArYNMGNSLLMIGAKLGMDVRIGAPKALWPHQ 196 ******************99************99***************************** PP TIGR00658 188 eivkkakkiakenggkleltedpkkavkdadviytDvwvsmGe.eekkeerlkllkpyqvnee 249 + +++++++a+e+gg++++tedpk avk++d+i+tD+wvsmGe e+++er+++l pyqvn + lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05275 197 DFIDQCQAFAAESGGRITITEDPKAAVKGVDFIHTDIWVSMGEpVEAWDERIEQLLPYQVNAQ 259 *******************************************9999**************** PP TIGR00658 250 llela.kpevkflhCLPavr...................GeevtdevlegeasivfdeaenRl 292 +++ + +p vkf+hCLPa++ G evt+ev+e++a+i f++aenR+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05275 260 MMKASgNPRVKFMHCLPAFHnsetkvgkdiaarypnlanGVEVTEEVFESPANIAFEQAENRM 322 ****99********************************************************* PP TIGR00658 293 haqkavlkall 303 h++ka+l+ l lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05275 323 HTIKAILVSAL 333 ******99766 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.01 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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