Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate RR42_RS15860 RR42_RS15860 aspartate carbamoyltransferase catalytic subunit
Query= curated2:Q2G3J8 (311 letters) >FitnessBrowser__Cup4G11:RR42_RS15860 Length = 323 Score = 108 bits (270), Expect = 2e-28 Identities = 96/318 (30%), Positives = 152/318 (47%), Gaps = 26/318 (8%) Query: 5 LKHFLNLTDAGGDAIAAMLNDALDRKSARAGQPKGKADADAPL-GGRVLAMVFEKNSTRT 63 LKH L++ + +A +L+ A S + K PL G+ + +F +NSTRT Sbjct: 16 LKHLLSIEGLSREMVAHILDTASQFVSLSDSDREVKK---VPLLRGKSVFNLFFENSTRT 72 Query: 64 RVSFDIAMRQLGGSALILDAGTTQLGRGETIADTARVLSRM-ADAIMLRTDDHAKVEELA 122 R +F+IA ++L L L+ + +GE++ DT LS M AD ++R +A Sbjct: 73 RTTFEIAAKRLSADVLNLNINASSTSKGESLLDTINNLSAMSADMFVVRHASSGAPYLIA 132 Query: 123 RHAT--VPVIN-GLTDLSHPCQIMADLLTVIEHGKALPGLEVAWLGDGNNVLNSIVEAAG 179 H V VIN G +HP Q + D+ T+ + K L VA +GD +L+S V + Sbjct: 133 EHVAPHVHVINAGDGRHAHPTQGLLDMYTIRHYKKDFTNLTVAIVGD---ILHSRVARSD 189 Query: 180 LMKFNVRIGVPEGYESDAGMIEAAVLAGAGIRVIRDPVEAVRGADVVVTDTWISMGQAHA 239 + +GVPE + + L G+RV + E ++G DVV+ M + Sbjct: 190 IHALTT-LGVPEVRAIGPRTLLPSGLEQMGVRVFHNMEEGMKGVDVVI------MLRLQN 242 Query: 240 EAKLAAMAP--------YQVNDALMAHAKPDAVFLHCLPAHRGEEVTDAVIDGPRSVVWD 291 E A+ P Y + +A AKPDA+ +H P +RG E+ AV DGP+SV+ + Sbjct: 243 ERMSGALLPSAQEYFKAYGLTPERLALAKPDAIVMHPGPMNRGVEIDSAVADGPQSVILN 302 Query: 292 EAENRIHAQKSVLRWVFG 309 + I + +V+ V G Sbjct: 303 QVTFGIAVRMAVMGIVAG 320 Lambda K H 0.319 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: 226 Number of extensions: 19 Number of successful extensions: 4 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: 311 Length of database: 323 Length adjustment: 27 Effective length of query: 284 Effective length of database: 296 Effective search space: 84064 Effective search space used: 84064 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)
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