Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate WP_053767952.1 BVI061214_RS08055 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >NCBI__GCF_001280255.1:WP_053767952.1 Length = 301 Score = 118 bits (296), Expect = 2e-31 Identities = 101/334 (30%), Positives = 157/334 (47%), Gaps = 46/334 (13%) Query: 4 KHFLNTQDWSRAELDALLTQAALFKRNKL-GSELKGKSIALVFFNPSMRTRTSFELGAFQ 62 K L+ +++ L LL A KR + G +LKGKS+AL+F PS+RTRT+ E+ Sbjct: 10 KDLLDFSGYTKEALKRLLDLAEALKRERYRGEDLKGKSLALLFEKPSLRTRTTLEVAMVH 69 Query: 63 LGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVDWSK 122 LGGHA+ L + +G E + ++A+ L R+V+ I R + Sbjct: 70 LGGHALYLDQK------QVGIG------EREPVRDIAKNLERFVEGIAARVY-------- 109 Query: 123 DREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTWTYHP 181 + ++ A+++ +PVIN + HP Q LA L L+E FG L G + + W Sbjct: 110 --RHRTVEELARHARIPVINALSDRAHPLQALADLLTLKEAFG--GLEGLE--VAWVGD- 162 Query: 182 KPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHDIDS 241 V S L +A +G+ V + P R + A +A +G L +HD Sbjct: 163 ---GNNVLASLLEVAPLVGLKVRVATP--------RGYEPEAALLARAGAFL--THDPKE 209 Query: 242 AYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTN-NGVFSHCLPLRRN 300 A GA +Y W ++ E EK +RD +Q F + + L + G+F HCLP Sbjct: 210 AVLGAHALYTDVWTSMG--QEAEREKRLRD-FQGFQANGPLLDLLHPEGIFLHCLPAHYG 266 Query: 301 VKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334 + T+ + P D+AENRLH KA++ L+ Sbjct: 267 EETTEEAVFGPRSRVFDQAENRLHTAKAVLLTLL 300 Lambda K H 0.320 0.134 0.412 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: 230 Number of extensions: 13 Number of successful extensions: 2 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: 339 Length of database: 301 Length adjustment: 28 Effective length of query: 311 Effective length of database: 273 Effective search space: 84903 Effective search space used: 84903 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 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