Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_012706739.1 NGR_RS12140 ornithine carbamoyltransferase
Query= BRENDA::Q98BB6 (303 letters) >NCBI__GCF_000018545.1:WP_012706739.1 Length = 305 Score = 472 bits (1214), Expect = e-138 Identities = 228/302 (75%), Positives = 257/302 (85%) Query: 2 SVRHFTDLSTVSEGDLRFMLDDAVVRKARLKAGERTRPLEGKVLAMIFDKPSTRTRVSFD 61 + RHF DLS ++ DLR ++DDA VRK KAG +PL GK+LAMIF+KPSTRTRVSFD Sbjct: 3 ATRHFLDLSAMTGADLRTIIDDARVRKTATKAGTAEKPLAGKMLAMIFEKPSTRTRVSFD 62 Query: 62 VGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENATVP 121 VGMRQLGGET+ L+GTEMQLGR+ETI DTAKVLSRYVDAIMIRTT H RLLEL E+ATVP Sbjct: 63 VGMRQLGGETLFLSGTEMQLGRAETIGDTAKVLSRYVDAIMIRTTDHRRLLELAEHATVP 122 Query: 122 VINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNLNVA 181 VINGLTDDTHPCQ+MADIMTFEEHRGPV GKTIAWTGDGNNVLHSL+E SARF + +N+A Sbjct: 123 VINGLTDDTHPCQIMADIMTFEEHRGPVQGKTIAWTGDGNNVLHSLIEGSARFGYRMNMA 182 Query: 182 VPEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRARGHNVFSP 241 VP GSEP K ++W++ +GG++ E+AV A CVVTD WVSM QEHRARGHNVF P Sbjct: 183 VPLGSEPQDKFLNWARNNGGEILLCHEAEQAVAGAHCVVTDTWVSMNQEHRARGHNVFQP 242 Query: 242 YQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAVLAWCL 301 YQVNA LM HA P+A+FMHCLPAHRGEEVTDEVIDGP SVVFD AENRLHAQK++LAWCL Sbjct: 243 YQVNAALMKHAVPEAVFMHCLPAHRGEEVTDEVIDGPQSVVFDAAENRLHAQKSILAWCL 302 Query: 302 GA 303 GA Sbjct: 303 GA 304 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: 411 Number of extensions: 16 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: 303 Length of database: 305 Length adjustment: 27 Effective length of query: 276 Effective length of database: 278 Effective search space: 76728 Effective search space used: 76728 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 WP_012706739.1 NGR_RS12140 (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.2493593.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-119 383.3 0.0 4.5e-119 383.1 0.0 1.0 1 NCBI__GCF_000018545.1:WP_012706739.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000018545.1:WP_012706739.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 383.1 0.0 4.5e-119 4.5e-119 1 303 [. 5 302 .. 5 303 .. 0.98 Alignments for each domain: == domain 1 score: 383.1 bits; conditional E-value: 4.5e-119 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnk 73 rh+l+l ++ ++l+++++ a+ k+++k+g+ ek l gk la+iFek+stRtRvsf+v++ +lG+++l+l+ NCBI__GCF_000018545.1:WP_012706739.1 5 RHFLDLSAMTGADLRTIIDDARVRKTATKAGTAEKPLAGKMLAMIFEKPSTRTRVSFDVGMRQLGGETLFLSG 77 8************************************************************************ PP TIGR00658 74 eelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgkl 146 e+qlgr e+i Dta+vlsryvdai++R+++h+ + ela++a+vPvingLtd +hPcqi+aD++t +e+ g + NCBI__GCF_000018545.1:WP_012706739.1 78 TEMQLGRAETIGDTAKVLSRYVDAIMIRTTDHRRLLELAEHATVPVINGLTDDTHPCQIMADIMTFEEHRGPV 150 ************************************************************************* PP TIGR00658 147 kevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadv 219 ++ ++++ GD+nnv +sl+ ++a +G +++a P g ep+ + +++a+ +ngg++ l ++ ++av++a+ NCBI__GCF_000018545.1:WP_012706739.1 151 QGKTIAWTGDGNNVLHSLIEGSARFGYRMNMAVPLGSEPQDKFLNWAR----NNGGEILLCHEAEQAVAGAHC 219 *********************************************995....6******************** PP TIGR00658 220 iytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRl 292 ++tD+wvsm +e+++ ++++pyqvn l+++a pe++f+hCLPa+rGeevtdev++g++s+vfd aenRl NCBI__GCF_000018545.1:WP_012706739.1 220 VVTDTWVSMNQEHRA-RGHNVFQPYQVNAALMKHAVPEAVFMHCLPAHRGEEVTDEVIDGPQSVVFDAAENRL 291 **********99887.5679***************************************************** PP TIGR00658 293 haqkavlkall 303 haqk++l+++l NCBI__GCF_000018545.1:WP_012706739.1 292 HAQKSILAWCL 302 *******9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (305 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 14.89 // [ok]
This GapMind analysis is from Apr 09 2024. 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