Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate PfGW456L13_1016 Aspartate carbamoyltransferase (EC 2.1.3.2)
Query= curated2:Q2G3J8 (311 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1016 Length = 339 Score = 115 bits (288), Expect = 1e-30 Identities = 93/313 (29%), Positives = 149/313 (47%), Gaps = 28/313 (8%) Query: 5 LKHFLNLTDAGGDAIAAMLNDALDRKSARAGQPKGKADADAPL-GGRVLAMVFEKNSTRT 63 L+HFL+L + + +L+ A A +A PL G+ + VF +NSTRT Sbjct: 18 LRHFLSLDGLRRELLTEILDTADSFLEVGA-----RAVKKVPLLRGKTVCNVFFENSTRT 72 Query: 64 RVSFDIAMRQLGGSALILDAGTTQLGRGETIADTARVLSRM-ADAIMLRTDDHAKVEELA 122 R +F++A ++L + L+ T+ +GET+ DT R L M AD ++R D +A Sbjct: 73 RTTFELAAQRLSADVITLNVSTSSASKGETLLDTLRNLEAMAADMFVVRHGDSGAAHFIA 132 Query: 123 RHA--TVPVINGLTDL-SHPCQIMADLLTVIEHGKALPGLEVAWLGDGNNVLNSIVEAAG 179 H V +ING +HP Q M D+LT+ H L VA +GD +L+S V + Sbjct: 133 EHVCPQVAIINGGDGRHAHPTQGMLDMLTIRRHKGGFENLSVAIVGD---ILHSRVARSN 189 Query: 180 LMKFNVRIGVPEGYESDAGMIEAAVLAGAGIRVIRDPVEAVRGADVVVTDTWISMGQAHA 239 ++ +G P+ + + G++V D E ++ DVV+ M + Sbjct: 190 MLALKT-LGCPDIRVIAPKTLLPIGIEQYGVKVYTDMTEGLKDVDVVI------MLRLQR 242 Query: 240 EAKLAAMAP--------YQVNDALMAHAKPDAVFLHCLPAHRGEEVTDAVIDGPRSVVWD 291 E + P + + A +A AKPDA+ +H P +RG E+ AV DGP SV+ + Sbjct: 243 ERMTGGLLPSEGEFYRLFGLTTARLAGAKPDAIVMHPGPINRGVEIESAVADGPHSVILN 302 Query: 292 EAENRIHAQKSVL 304 + I + +VL Sbjct: 303 QVTYGIAIRMAVL 315 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: 234 Number of extensions: 18 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: 339 Length adjustment: 28 Effective length of query: 283 Effective length of database: 311 Effective search space: 88013 Effective search space used: 88013 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 Aug 03 2021. The underlying query database was built on Aug 03 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