Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate WP_011382764.1 AMB_RS01610 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >NCBI__GCF_000009985.1:WP_011382764.1 Length = 305 Score = 140 bits (354), Expect = 3e-38 Identities = 114/331 (34%), Positives = 166/331 (50%), Gaps = 45/331 (13%) Query: 4 KHFLNTQDWSRAELDALLTQAALFKRNK-LGSELKGKSIALVFFNPSMRTRTSFELGAFQ 62 +HFL+ + A L +L +K+ K + L GK +A++F PS RTR SFE+G Q Sbjct: 11 RHFLDLDGFDTATLRHILDLGLAYKQGKGPKAPLAGKMLAMIFEKPSTRTRVSFEVGMKQ 70 Query: 63 LGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVDWSK 122 LGG ++L G + LG G+T IA+ ARVL R+VD + +R Sbjct: 71 LGGDVIMLAAG------DTQLGR---GET---IADTARVLSRFVDAVMIRT--------- 109 Query: 123 DREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTWTYHP 181 + L AKY+ VPVIN + +HPCQ +A + +EH G+ L+GK V+ W Sbjct: 110 -NLPEKLTELAKYADVPVINGLTDQSHPCQVMADVMTFEEHRGS--LKGK--VVAWVGD- 163 Query: 182 KPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERY-MDWAAQNVAESGGSLQVSHDID 240 VA S + A G ++ L CP D ++ R +DWA G S+ ++ Sbjct: 164 ---GNNVAASWIHAAGHFGCEIRLACP--DSLMPSRAAVDWARAK----GASVVLTTHPA 214 Query: 241 SAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMA-LTNNGVFSHCLPLRR 299 A AGA +V +W ++ + E + + YQ V+E MA + +F HCLP R Sbjct: 215 EAVAGAHLVLTDTWVSMGCQDSNRHE--LLEPYQ---VNEALMAKAAPDALFMHCLPAHR 269 Query: 300 NVKATDAVMDSPNCIAIDEAENRLHVQKAIM 330 + TD VMD + DEAENR+HVQK I+ Sbjct: 270 GEEVTDPVMDGIQSVVWDEAENRMHVQKGIL 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: 259 Number of extensions: 11 Number of successful extensions: 5 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: 305 Length adjustment: 28 Effective length of query: 311 Effective length of database: 277 Effective search space: 86147 Effective search space used: 86147 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