Align Ornithine carbamoyltransferase, anabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate GFF771 HP15_750 ornithine carbamoyltransferase
Query= SwissProt::P11724 (305 letters) >FitnessBrowser__Marino:GFF771 Length = 304 Score = 389 bits (999), Expect = e-113 Identities = 193/299 (64%), Positives = 229/299 (76%) Query: 1 MSVRHFLSFMDYSPEELIGLIRRGSELKDLRNRGVLYEPLKSRVLGMVFEKASTRTRLSF 60 M+ RHFL+ D + EL L+ + L++ +G + + LK+RVL M+FEK+STRTR+SF Sbjct: 1 MAARHFLTLNDMTTNELESLVDHATALRNEWRQGKVRDSLKNRVLAMIFEKSSTRTRVSF 60 Query: 61 EAGMIQLGGQAIFLSPRDTQLGRGEPIGDSARVMSRMLDGVMIRTFAHATLTEFAAHSKV 120 EAGM QLGG A+FLSPRDTQLGRGEPI DSA V+S M+D VMIRTFAH T+ FAA S+V Sbjct: 61 EAGMTQLGGSAMFLSPRDTQLGRGEPIEDSAIVISSMVDAVMIRTFAHETVERFAAASRV 120 Query: 121 PVINGLSDDLHPCQLLADMQTFHEHRGSIQGKTVAWIGDGNNMCNSYIEAALKFDFQLRV 180 PVIN L+DD HPCQLLADMQTF EHRGSI+G TVAWIGDGNNMC+SYI AA +FDF L + Sbjct: 121 PVINALTDDFHPCQLLADMQTFREHRGSIRGATVAWIGDGNNMCHSYINAAAQFDFNLNI 180 Query: 181 ACPEGYEPKAEFVALAGDRLRVVRDPREAVAGAHLVSTDVWASMGQEDEAAARIALFRPY 240 ACPEGYEP + DR++V R+P EA A L+ TDVWASMGQEDE AR F Y Sbjct: 181 ACPEGYEPAESMLKGHEDRVKVFREPAEAARNAQLLVTDVWASMGQEDEQKARERAFSGY 240 Query: 241 QVNAALLDGAADDVLFMHCLPAHRGEEISEELLDDPRSVAWDQAENRLHAQKALLELLI 299 Q+N LL A DVLFMHCLPAHRGEEIS ++++ P SV W++AENRLHAQKALLE LI Sbjct: 241 QINPGLLSVADKDVLFMHCLPAHRGEEISADMMEHPASVVWNEAENRLHAQKALLEFLI 299 Lambda K H 0.322 0.136 0.404 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: 306 Number of extensions: 7 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: 305 Length of database: 304 Length adjustment: 27 Effective length of query: 278 Effective length of database: 277 Effective search space: 77006 Effective search space used: 77006 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate GFF771 HP15_750 (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.aa/TIGR00658.hmm # target sequence database: /tmp/gapView.20223.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-119 382.8 0.0 6.5e-119 382.6 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF771 HP15_750 ornithine carbamoyltran Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF771 HP15_750 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 382.6 0.0 6.5e-119 6.5e-119 1 303 [. 4 299 .. 4 300 .. 0.98 Alignments for each domain: == domain 1 score: 382.6 bits; conditional E-value: 6.5e-119 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeel 76 rh+l+l d++++el++l++ a+ l++e ++gk ++ lk++ la+iFek+stRtRvsfe+++++lG+ +++l++ ++ lcl|FitnessBrowser__Marino:GFF771 4 RHFLTLNDMTTNELESLVDHATALRNEWRQGKVRDSLKNRVLAMIFEKSSTRTRVSFEAGMTQLGGSAMFLSPRDT 79 8*************************************************************************** PP TIGR00658 77 qlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevklv 152 qlgr+e+i+D a v+s++vda+++R+++he+ve +a + vPvin+Ltd +hPcq+laD++t +e+ g++ + +++ lcl|FitnessBrowser__Marino:GFF771 80 QLGRGEPIEDSAIVISSMVDAVMIRTFAHETVERFAAASRVPVINALTDDFHPCQLLADMQTFREHRGSIRGATVA 155 **************************************************************************** PP TIGR00658 153 yvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsm 228 ++GD+nn+++s + aaa++ +++++a+Peg+ep ++++k + ++++ ++p++a+++a++++tDvw+sm lcl|FitnessBrowser__Marino:GFF771 156 WIGDGNNMCHSYINAAAQFDFNLNIACPEGYEPAESMLKGH-------EDRVKVFREPAEAARNAQLLVTDVWASM 224 *********************************88777655.......569************************* PP TIGR00658 229 GeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303 G+e+++++r +++ +yq+n ll++a+++v f+hCLPa+rGee++ +++e +as+v++eaenRlhaqka+l++l+ lcl|FitnessBrowser__Marino:GFF771 225 GQEDEQKARERAFSGYQINPGLLSVADKDVLFMHCLPAHRGEEISADMMEHPASVVWNEAENRLHAQKALLEFLI 299 ***********************************************************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (304 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: 00:00:00.00 # Mc/sec: 9.32 // [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