Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_012592798.1 MSIL_RS19540 aspartate carbamoyltransferase catalytic subunit
Query= curated2:Q7V8G9 (318 letters) >NCBI__GCF_000021745.1:WP_012592798.1 Length = 316 Score = 111 bits (278), Expect = 2e-29 Identities = 99/316 (31%), Positives = 152/316 (48%), Gaps = 30/316 (9%) Query: 18 RDFLSCADFTAEQTVALLELSRQLKSGDRRID-----LGNRVLGLIFTKASTRTRVSFQV 72 R L + + LL+LS R+++ L R L +F +ASTRT+ SF++ Sbjct: 13 RHLLGIEGLSPQDIDVLLDLSEHAIEVSRQVEKKLSTLRGRTLINLFFEASTRTQSSFEL 72 Query: 73 AMARLGGQTVDLNPQVTQLGRGEPLEDTARVLSRFC-DVMAVRTFAQQELLDYAHWASIP 131 A RLG ++++ + + +GE L DTA L+ D++ VR + A Sbjct: 73 AGKRLGADVMNMSVASSSVKKGETLLDTAMTLNAMRPDIIVVRHAQAGAVHLLARKVDCS 132 Query: 132 VLNALTDL-EHPCQAMADFLTIQEALGSLTGQTLAYVGD--GNNVSHSLMLCGALLGVNV 188 V+NA EHP QA+ D LTI+ G + G +A GD + V+ S +L LG V Sbjct: 133 VVNAGDGAHEHPTQALLDALTIRRNRGRIAGLIVAICGDILHSRVARSNILLLTALGARV 192 Query: 189 RIGCPQGFEPLPEVIDQARNLAVADARIEVMTDPVDAVRGAQALYTDVWASMGQEQEQSQ 248 R+ P P +A +EV TD ++ A D+ + ++E+ Q Sbjct: 193 RVIGPSTLLPA----------GIARMGVEVFTDMKQGLQDA-----DIVMMLRLQRERMQ 237 Query: 249 R------EEAFRGFCLNEDLLAHADPNAIVLHCLPAHRGEEISSGVMEGEASRIFDQAEN 302 +E FR F L+E+ L +A P+A+VLH P +RG EI S V +G SRI +Q E Sbjct: 238 GGFIPSPKEFFRFFGLDEEKLGYARPDALVLHPGPMNRGVEIDSAVADGGQSRIREQVEM 297 Query: 303 RLHVQQALLAAVLGGL 318 + V+ A+L A+ L Sbjct: 298 GVAVRIAVLGALAAHL 313 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: 213 Number of extensions: 15 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 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