Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_046007579.1 OLEAN_RS00415 aspartate carbamoyltransferase catalytic subunit
Query= BRENDA::Q51742 (315 letters) >NCBI__GCF_000967895.1:WP_046007579.1 Length = 336 Score = 97.4 bits (241), Expect = 4e-25 Identities = 91/298 (30%), Positives = 136/298 (45%), Gaps = 20/298 (6%) Query: 24 ILETAKMF-KIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEVAMAHLGGHALYLNAQD 82 IL+ A F ++ K LL GKT+ +F + STRTR +FE+A L L L+ Sbjct: 35 ILDLADSFISTQERAVKKVPLLRGKTVVNLFFENSTRTRSTFELAAKRLSADILNLDIAS 94 Query: 83 LQLRRGETIADTA-RVLSRYVDAIMARVYDHKDVEDLAKYAT--VPVIN-GLSDFSHPCQ 138 +GET+ DT + + Y D + R D +A+ T V +IN G +HP Q Sbjct: 95 SATSKGETLMDTLWNLEAMYSDMFVVRHADSGAAHFIAEQVTPGVAIINAGDGRHAHPTQ 154 Query: 139 ALADYMTIWEKKGTIKGVKVVYVGD--GNNVAHSLMIAGTKLGA-DVVVATPEGYEPDEK 195 A+ D +TI KG I+G V VGD + VA S + A LGA ++ V P P E Sbjct: 155 AMLDMLTIRRHKGAIEGQTVAIVGDILHSRVARSQIHALKTLGAKEIRVIGPATLIPKEM 214 Query: 196 VIKWAEQNAAESGGSFELLHDPVKAVKDADV-IYTDVWASMGQEAEAEERRKIFRPFQVN 254 A + D + + D DV I + +A + F+ + + Sbjct: 215 KDLGA-----------NIYFDMEQGLADVDVIIMLRLQKERMSDALLPSEGEYFKLYGLT 263 Query: 255 KDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWDQAENRLHAQKAVLALVMGG 312 + + AKPD + MH P +RG E+ V D SV+ +Q + + AV+A+ M G Sbjct: 264 EAKLALAKPDAIVMHPGPINRGVEIDSAVADGAQSVILNQVSYGIAVRMAVMAMAMSG 321 Lambda K H 0.319 0.134 0.400 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: 222 Number of extensions: 12 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: 315 Length of database: 336 Length adjustment: 28 Effective length of query: 287 Effective length of database: 308 Effective search space: 88396 Effective search space used: 88396 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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