Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_011446700.1 SARO_RS15545 aspartate carbamoyltransferase
Query= curated2:Q8DJW4 (310 letters) >NCBI__GCF_000013325.1:WP_011446700.1 Length = 341 Score = 110 bits (275), Expect = 5e-29 Identities = 102/316 (32%), Positives = 154/316 (48%), Gaps = 33/316 (10%) Query: 13 RDLLSIADLSRAEAEYLLDLAAQ-MKIGKVAPQCPKVLGLL-----FQKASTRTRVSFTV 66 RDL I L+R E YLLD A Q +++ + + + +L L F + STRT +SF + Sbjct: 22 RDLTGIGQLARHEILYLLDEAEQWVELNRQSQKTTDLLNGLTIINAFFENSTRTLLSFEI 81 Query: 67 AMYQLGGQVIDLNPQSTQVGRGEPLTDTARVLDRY-LDAVAIRTYGQAELQLFADYARIP 125 A +LG V++++ ++ V +GE L DTA L+ DA+ IR ++L A+ P Sbjct: 82 AGKRLGADVVNMHAATSSVKKGETLIDTAMTLNAMRADAIVIRHASSGAVRLIAEKVDCP 141 Query: 126 VINALT-DREHPCQILADLLTLRESF-----GTLAGLTLCYIGD--GNNVAHSLLLGCAL 177 V+NA EHP Q L D LT+R + L GL + GD + VA S +L Sbjct: 142 VLNAGDGQHEHPTQALLDALTMRHAMKLPAGSDLNGLKVTICGDILHSRVARSNILSLTA 201 Query: 178 LGVNIRVASPPQFAPLADIVAQAKALSGGKSEVAVLTDPQAAAKGAHALYTDVWASMGQE 237 LG +RV +PP P A+I A V D AA KGA+ + + + QE Sbjct: 202 LGAEVRVCAPPALMP-AEIEAMG---------VTPFHDFDAALKGANIV---MMLRLQQE 248 Query: 238 AEAGDRQPIFQPYQ----INDHLLALADPRAIVLHCLPAHRDEEITASVLEGP-QSRVWE 292 +G P + Y+ + LA A+ A V+H P +R EI ++V + P +S + Sbjct: 249 RMSGQFIPSPREYRHLYGLTPERLARAEADAFVMHPGPMNRGIEIDSTVADHPTRSLITR 308 Query: 293 QAENRLHVQKALLASL 308 Q E + ++ A L L Sbjct: 309 QVEMGVAIRMACLEVL 324 Lambda K H 0.321 0.135 0.392 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: 8 Number of successful extensions: 5 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: 310 Length of database: 341 Length adjustment: 28 Effective length of query: 282 Effective length of database: 313 Effective search space: 88266 Effective search space used: 88266 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