Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate GFF2391 PGA1_c24220 ornithine carbamoyltransferase ArgF
Query= BRENDA::Q98BB6 (303 letters) >FitnessBrowser__Phaeo:GFF2391 Length = 308 Score = 343 bits (879), Expect = 4e-99 Identities = 174/308 (56%), Positives = 221/308 (71%), Gaps = 7/308 (2%) Query: 3 VRHFTDLSTVSEGDLRFMLDDA-VVRKARL----KAGERTRPLEGKVLAMIFDKPSTRTR 57 + HF D+ DLR ++D A ++ARL A + PL+ +++A+IF+KPSTRTR Sbjct: 1 MNHFLDIHKTDATDLRAIIDQASATKQARLGRPKAAPDDELPLKDRMVALIFEKPSTRTR 60 Query: 58 VSFDVGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTEN 117 VSFDVG+RQ+GG+T++L+G +MQLG ETIADTA+VLSRYVD IMIRT L E+ E Sbjct: 61 VSFDVGVRQMGGQTMVLSGNDMQLGHGETIADTARVLSRYVDMIMIRTFDETVLTEMAEY 120 Query: 118 ATVPVINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFN 177 A+VPVINGLTD THPCQ+MAD++T+EEHRGP+ GK + W GDGNNV S L A+A+F F+ Sbjct: 121 ASVPVINGLTDRTHPCQIMADVLTYEEHRGPIKGKKVVWCGDGNNVCASFLHAAAQFGFD 180 Query: 178 LNVAVPEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSM--GQEHRARG 235 L P +P + I ++ G ++ R +AV+ AD VV D WVSM Q + R Sbjct: 181 LTFTGPAQLDPEPEFIGLARNAGSQVIIERDAAKAVEGADLVVADTWVSMHDSQSSKERR 240 Query: 236 HNVFSPYQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKA 295 HN+ YQVN LMAHAKPDALFMHCLPAHR EEVT V+DGP SV+FDEAENRLHAQKA Sbjct: 241 HNMLRGYQVNDALMAHAKPDALFMHCLPAHREEEVTSAVMDGPQSVIFDEAENRLHAQKA 300 Query: 296 VLAWCLGA 303 ++ +CLGA Sbjct: 301 IMRYCLGA 308 Lambda K H 0.320 0.133 0.400 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: 333 Number of extensions: 7 Number of successful extensions: 3 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: 303 Length of database: 308 Length adjustment: 27 Effective length of query: 276 Effective length of database: 281 Effective search space: 77556 Effective search space used: 77556 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate GFF2391 PGA1_c24220 (ornithine carbamoyltransferase ArgF)
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.3491.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-116 372.5 0.0 8.8e-116 372.3 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF2391 PGA1_c24220 ornithine carbamoylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF2391 PGA1_c24220 ornithine carbamoyltransferase ArgF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 372.3 0.0 8.8e-116 8.8e-116 2 303 .. 3 306 .. 2 307 .. 0.96 Alignments for each domain: == domain 1 score: 372.3 bits; conditional E-value: 8.8e-116 TIGR00658 2 hllslldlseeelkellelakklkkekkkgke.....ekklkgktlaliFekrstRtRvsfevaayelGaqvlyln 72 h+l++++ + +l+ ++++a+ k+++ + e lk + +aliFek+stRtRvsf+v++ ++G+q+++l+ lcl|FitnessBrowser__Phaeo:GFF2391 3 HFLDIHKTDATDLRAIIDQASATKQARLGRPKaapddELPLKDRMVALIFEKPSTRTRVSFDVGVRQMGGQTMVLS 78 9***********************9876543345555899************************************ PP TIGR00658 73 keelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklke 148 +++qlg++e+i+Dtarvlsryvd+i++R+++++ ++e+a+yasvPvingLtd +hPcqi+aD+lt +e+ g +k+ lcl|FitnessBrowser__Phaeo:GFF2391 79 GNDMQLGHGETIADTARVLSRYVDMIMIRTFDETVLTEMAEYASVPVINGLTDRTHPCQIMADVLTYEEHRGPIKG 154 **************************************************************************** PP TIGR00658 149 vklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDv 224 k+v+ GD+nnv+ s+l aaa++G+d++ ++P +l+pe+e + a ++ g+++ + +d +kav++ad+++ D+ lcl|FitnessBrowser__Phaeo:GFF2391 155 KKVVWCGDGNNVCASFLHAAAQFGFDLTFTGPAQLDPEPEFIGLA----RNAGSQVIIERDAAKAVEGADLVVADT 226 ******************************************988....569************************ PP TIGR00658 225 wvsmGe.eekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavl 299 wvsm + +++ke r ++l++yqvn+ l+++akp++ f+hCLPa+r eevt v++g++s++fdeaenRlhaqka++ lcl|FitnessBrowser__Phaeo:GFF2391 227 WVSMHDsQSSKERRHNMLRGYQVNDALMAHAKPDALFMHCLPAHREEEVTSAVMDGPQSVIFDEAENRLHAQKAIM 302 *****95667777889************************************************************ PP TIGR00658 300 kall 303 ++l lcl|FitnessBrowser__Phaeo:GFF2391 303 RYCL 306 9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (308 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: 7.76 // [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