Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate 8500677 DvMF_1425 aspartate carbamoyltransferase catalytic subunit (RefSeq)
Query= curated2:Q8DJW4 (310 letters) >FitnessBrowser__Miya:8500677 Length = 325 Score = 95.5 bits (236), Expect = 1e-24 Identities = 89/305 (29%), Positives = 134/305 (43%), Gaps = 22/305 (7%) Query: 13 RDLLSIADLSRAEAEYLLDLAAQMK------IGKVAPQCPKVLGLLFQKASTRTRVSFTV 66 +DLL + L+RAE +LLD AAQ + KV K + L F + STRT+ SF V Sbjct: 12 KDLLDVTQLTRAELFHLLDTAAQFHDINRRPVKKVPTLKGKSVVLFFAEPSTRTKTSFDV 71 Query: 67 AMYQLGGQVIDLNPQSTQVGRGEPLTDTARVLDRYL-DAVAIRTYGQAELQLFADYARIP 125 A +L L + + +GE L DTA L D + IR Q A+ Sbjct: 72 AGKRLSADTFSLAKSGSSLSKGESLKDTALTLQAMTPDIIVIRHSSSGAAQFLAERLDCS 131 Query: 126 VINALTD-REHPCQILADLLTLRESFG-TLAGLTLCYIGD--GNNVAHSLLLGCALLGVN 181 V+NA HP Q L D +LR+ +G T G TL +GD + VA S + + LGV Sbjct: 132 VVNAGDGWHAHPTQALLDCYSLRQVWGDTFEGRTLLILGDIAHSRVARSNVHLLSSLGVK 191 Query: 182 IRVASPPQFAPLADIVAQAKALSGGKSEVAVLTDPQAAAKGAHALYT-DVWASMGQEAEA 240 +R+ +P P V + A +G A+ + Q Sbjct: 192 VRLCAPRTLLPAGV----------HNWPVTIFNRLDDAVQGVDAVMCLRLQLERQQAGLL 241 Query: 241 GDRQPIFQPYQINDHLLALADPRAIVLHCLPAHRDEEITASVLEGPQSRVWEQAENRLHV 300 D + Q + ++ L +A P A VLH P +R EI++ + + P+S + +Q + Sbjct: 242 PDLREYAQRFCLSPRHLTMAAPSARVLHPGPMNRGLEISSVLADAPESLILDQVAAGVAT 301 Query: 301 QKALL 305 + A+L Sbjct: 302 RMAIL 306 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: 200 Number of extensions: 8 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 310 Length of database: 325 Length adjustment: 27 Effective length of query: 283 Effective length of database: 298 Effective search space: 84334 Effective search space used: 84334 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