Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_026595792.1 A3OQ_RS0112905 aspartate carbamoyltransferase catalytic subunit
Query= curated2:Q7V8G9 (318 letters) >NCBI__GCF_000385335.1:WP_026595792.1 Length = 316 Score = 118 bits (296), Expect = 2e-31 Identities = 106/312 (33%), Positives = 163/312 (52%), Gaps = 29/312 (9%) Query: 15 LKGRDFLSCADFTAEQTVA--LLELSRQLKSGDRRIDLGNRVLGLIFTKASTRTRVSFQV 72 L G + LS D A +A +E+SRQ++ +R+ L R L +F +ASTRT+ SF++ Sbjct: 15 LLGIEGLSPLDINALLDLAEDAVEVSRQVEK--KRMTLRGRTLINLFFEASTRTQSSFEL 72 Query: 73 AMARLGGQTVDLNPQVTQLGRGEPLEDTARVLSRFC-DVMAVRTFAQQELLDYAHWASIP 131 A RLG ++++ + + +GE L DTA L+ D++ VR + A Sbjct: 73 AGKRLGADVMNMSVATSSVKKGETLIDTAMTLNAMRPDIIVVRHAQAGAVHLLAKKVDCA 132 Query: 132 VLNALTDL-EHPCQAMADFLTIQEALGSLTGQTLAYVGD--GNNVSHSLMLCGALLGVNV 188 V+NA EHP QA+ D LTI+ GS++G T+A GD + V+ S +L A LG V Sbjct: 133 VVNAGDGAHEHPTQALLDALTIRRNKGSISGLTVAICGDILHSRVARSNILLLACLGARV 192 Query: 189 RIGCPQGFEPLPEVIDQARNLAVADARIEVMTDPVDAVRGAQALYTDVWASMGQEQEQSQ 248 R+ P LP I++ +EV TD ++GA D+ + ++E+ Sbjct: 193 RVIGPSTL--LPPGIERMG--------VEVFTDMRKGLKGA-----DIVMMLRLQRERMS 237 Query: 249 ------REEAFRGFCLNEDLLAHADPNAIVLHCLPAHRGEEISSGVMEGEASRIFDQAEN 302 +E FR F L+E+ LA A P+A+V+H P +RG EI S V +G S I +Q E Sbjct: 238 GGFVPSSKEYFRFFGLDEEKLALAKPDALVMHPGPMNRGVEIDSAVADGPQSLIREQVEM 297 Query: 303 RLHVQQALLAAV 314 + V+ A+L A+ Sbjct: 298 GVAVRMAVLEAL 309 Lambda K H 0.321 0.135 0.391 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: 202 Number of extensions: 11 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: 318 Length of database: 316 Length adjustment: 27 Effective length of query: 291 Effective length of database: 289 Effective search space: 84099 Effective search space used: 84099 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)
This GapMind analysis is from Apr 10 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