Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate AZOBR_RS13250 AZOBR_RS13250 ornithine carbamoyltransferase
Query= SwissProt::P08308 (336 letters) >FitnessBrowser__azobra:AZOBR_RS13250 Length = 334 Score = 490 bits (1262), Expect = e-143 Identities = 235/335 (70%), Positives = 283/335 (84%), Gaps = 1/335 (0%) Query: 1 MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60 M+FN+ NR+LL++ ++ RE RY+LDL+RDLKRAKY TEQQHL+ K I LIFEKTSTRT Sbjct: 1 MSFNLRNRSLLTVQDYTPREFRYVLDLARDLKRAKYARTEQQHLRGKEICLIFEKTSTRT 60 Query: 61 RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120 RCAFEVA +DQGANVTY+DP SQIGHKES KDTARVLGRMYDAIEYRG Q VE+LAK Sbjct: 61 RCAFEVACHDQGANVTYLDPAGSQIGHKESFKDTARVLGRMYDAIEYRGAAQGGVEQLAK 120 Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180 +AGVPV+NGLTDEYHPTQMLADV+TMREHSDKP+ DI+YAY+GD R+NMG+SL+++G + Sbjct: 121 YAGVPVYNGLTDEYHPTQMLADVMTMREHSDKPITDITYAYVGDTRSNMGHSLMIVGCLM 180 Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240 GMDVRI P++LWP +E+ A +K A SGA+LT+T++ EAV GVDF+HTDVWVSMGEP Sbjct: 181 GMDVRICGPQSLWPSEEYTAIARKLAAASGARLTITDNTAEAVAGVDFIHTDVWVSMGEP 240 Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300 + W ERI L PYQVN E+M A+GNP+ KFMHCLPAFH+SET +G+QIAE Y + NG+ Sbjct: 241 KDVWRERIALLKPYQVNPELMAASGNPQVKFMHCLPAFHDSETTLGRQIAEDY-GMPNGL 299 Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLAD 335 EVT +VFES NIAFEQAENRMHTIKA+LV+TL + Sbjct: 300 EVTNEVFESEANIAFEQAENRMHTIKALLVATLGE 334 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: 410 Number of extensions: 5 Number of successful extensions: 2 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: 334 Length adjustment: 28 Effective length of query: 308 Effective length of database: 306 Effective search space: 94248 Effective search space used: 94248 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 AZOBR_RS13250 AZOBR_RS13250 (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.20024.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-129 418.0 0.0 1.2e-129 417.8 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS13250 AZOBR_RS13250 ornithine carbamoy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS13250 AZOBR_RS13250 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 417.8 0.0 1.2e-129 1.2e-129 1 303 [. 8 332 .. 8 333 .. 0.99 Alignments for each domain: == domain 1 score: 417.8 bits; conditional E-value: 1.2e-129 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 r+ll+++d++++e++++l+la++lk++k++ +e+++l+gk++ liFek+stRtR++feva ++Ga+v+ lcl|FitnessBrowser__azobra:AZOBR_RS13250 8 RSLLTVQDYTPREFRYVLDLARDLKRAKYARTEQQHLRGKEICLIFEKTSTRTRCAFEVACHDQGANVT 76 789****************************************************************** PP TIGR00658 70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138 yl++ +q+g+kes+kDtarvl+r++dai +R+ ++ ve+lakya+vPv+ngLtd+ hP+q+laD++t lcl|FitnessBrowser__azobra:AZOBR_RS13250 77 YLDPAGSQIGHKESFKDTARVLGRMYDAIEYRGAAQGGVEQLAKYAGVPVYNGLTDEYHPTQMLADVMT 145 ********************************************************************* PP TIGR00658 139 ikeklg.klkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkle 205 ++e+ + + +++++yvGD+ n+++sl++ + ++G+dv++++P+ l+p++e++ a+k+a+++g++l+ lcl|FitnessBrowser__azobra:AZOBR_RS13250 146 MREHSDkPITDITYAYVGDTrSNMGHSLMIVGCLMGMDVRICGPQSLWPSEEYTAIARKLAAASGARLT 214 ******99************9************************************************ PP TIGR00658 206 ltedpkkavkdadviytDvwvsmGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr.... 268 +t+++++av+++d+i+tDvwvsmGe ++ + er++llkpyqvn el++ + +p+vkf+hCLPa++ lcl|FitnessBrowser__azobra:AZOBR_RS13250 215 ITDNTAEAVAGVDFIHTDVWVSMGEpKDVWRERIALLKPYQVNPELMAASgNPQVKFMHCLPAFHdset 283 *************************9999********************99****************** PP TIGR00658 269 ..............GeevtdevlegeasivfdeaenRlhaqkavlkall 303 G evt+ev+e+ea+i f++aenR+h++ka+l+a+l lcl|FitnessBrowser__azobra:AZOBR_RS13250 284 tlgrqiaedygmpnGLEVTNEVFESEANIAFEQAENRMHTIKALLVATL 332 *********************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (334 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: 6.56 // [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