Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_053767828.1 BVI061214_RS07270 aspartate carbamoyltransferase catalytic subunit
Query= BRENDA::Q5SJ15 (301 letters) >NCBI__GCF_001280255.1:WP_053767828.1 Length = 301 Score = 92.4 bits (228), Expect = 1e-23 Identities = 96/310 (30%), Positives = 137/310 (44%), Gaps = 34/310 (10%) Query: 10 KDLLDFSGYGPKELQALLDLA----EQLKRERYRGEDLKGKVLALLFEKPSLRTRTTLEV 65 + LLDF G+ +L+++LD A E L+R + L+G +A +F +PS RTRT+ E+ Sbjct: 2 RHLLDFEGWSRADLESVLDTARVMREVLERPVKKVPALQGFTVATVFFEPSTRTRTSFEL 61 Query: 66 AMVHLGGHAVYLDQKQVGIGEREPVRDVAKNLERFVEGIAARVFRHETV---EALARHAK 122 A + V + + + E +D LE G+ A V R + R K Sbjct: 62 AARRMSADVVSFAAQSSSLQKGESYKDTLLTLEAM--GVDAYVIRADAAGVPHQATRWVK 119 Query: 123 VPVVNALS-DRAHPLQALADLLTLKEVFGGLAGLEVAWVGD--GNNVLNSLLEVAPLAGL 179 VVN RAHP QAL D TL E G L G ++A VGD + V S E+ L G Sbjct: 120 GVVVNGGDGQRAHPTQALLDAYTLLEALGSLEGKKIAIVGDILHSRVARSGAELFSLLGA 179 Query: 180 KVRVATPKGYEPDPGLLKRA--NAFFTHDPKEAALGAHALYTDVWTSMGQEAEREK---- 233 +V A P P LL ++ A T +EA A A+ M ++E+ Sbjct: 180 EVWCAGP------PSLLPQSLPGARLTPSLEEALEEADAV-------MALRLQKERMEAG 226 Query: 234 --RLRDF-QGFQVNGELLKLLRPEGVFLHCLPAHYGEETTEEAVHGPRSRVFDQAENRLH 290 L D+ +Q+ L L +P+ LH P + E PRS V Q +N + Sbjct: 227 LVNLEDYIARYQITERRLGLAKPQAPLLHPGPMNRDVELEGTLADSPRSLVNRQVQNGVA 286 Query: 291 TAKAVLLTLL 300 AVL LL Sbjct: 287 VRMAVLYHLL 296 Lambda K H 0.319 0.137 0.396 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: 1 Number of HSP's successfully gapped: 1 Length of query: 301 Length of database: 301 Length adjustment: 27 Effective length of query: 274 Effective length of database: 274 Effective search space: 75076 Effective search space used: 75076 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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