Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_011813740.1 HHAL_RS04800 aspartate carbamoyltransferase catalytic subunit
Query= curated2:Q2LT98 (302 letters) >NCBI__GCF_000015585.1:WP_011813740.1 Length = 328 Score = 94.4 bits (233), Expect = 3e-24 Identities = 89/293 (30%), Positives = 134/293 (45%), Gaps = 17/293 (5%) Query: 19 IFEKARHLKSVHEQGVAYTPL-KGKTLGMIFDKSSTRTRISFEVGMYQLGGLALFLSNRD 77 I + A V + V PL +G+T+ +F + STRTR +FE+ +L L + Sbjct: 28 ILDTAESFSGVLGKSVKKVPLLRGRTIINLFFEPSTRTRTTFELAAQRLSADVLNIDVAT 87 Query: 78 TQLGRGETVADSAR-IMSRYLNGIMIRTFSHLIIEEFAAHAT--IPVIN-GLTDLLHPCQ 133 + +GE++ D R + + + ++R E A H + VIN G HP Q Sbjct: 88 SSTSKGESLLDMLRNLEAMQCDAFVVRHADSGAAEFIARHVAPGVAVINAGDGRHAHPTQ 147 Query: 134 ILSDLFTIIEKKGSYERLKIVYVGDGNNIANSWINAAARLPFHLALSCPEGYDPDSG--- 190 L D FTI +KG E L I VGD I +S + AR H L G G Sbjct: 148 ALLDAFTIRREKGPLEPLTIAIVGD---ILHSRV---ARSQIHALLGLGAGEVRVIGPRT 201 Query: 191 ILDRGVKEAKEGVSLMRDPYEAVRNADV-VYTDVWASMGQEAEQEARARVFRPYQINEAL 249 +L R ++ GV + D + ADV + + + A + + F Y + E Sbjct: 202 LLPRDIQRL--GVRVYEDMDAGLDGADVLIMLRLQRERMRGALLPSESEYFSRYGLTEQR 259 Query: 250 LSPAKKDAIVMHCLPAHRGEEITAAVLDGPRSVIIDQAENRLHVQKAILEILI 302 L +AIVMH P +RG E+ V DGPRSVI+ Q N + V+ A++ I++ Sbjct: 260 LERTHPEAIVMHPGPVNRGVELDPQVADGPRSVILRQVTNGIAVRMAVMSIVL 312 Lambda K H 0.321 0.137 0.394 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: 237 Number of extensions: 9 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: 302 Length of database: 328 Length adjustment: 27 Effective length of query: 275 Effective length of database: 301 Effective search space: 82775 Effective search space used: 82775 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 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