Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate WP_012965238.1 FERP_RS03605 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >NCBI__GCF_000025505.1:WP_012965238.1 Length = 305 Score = 135 bits (339), Expect = 2e-36 Identities = 110/346 (31%), Positives = 160/346 (46%), Gaps = 55/346 (15%) Query: 3 LKHFLNTQDWSRAELDALLTQAALFKRNK----LGSELKGKSIALVFFNPSMRTRTSFEL 58 +KH L+ D + E+ +L A K + L LK K++ ++F PS RTR SFE+ Sbjct: 1 MKHVLSITDLKKEEIIEILDLADKLKEERRKGILKEYLKNKTLGMIFELPSTRTRVSFEV 60 Query: 59 GAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFV 118 GG+A+ + W + LG G+T IA+ AR L RYV + +R Sbjct: 61 AMNDCGGYAIYMN-----WN-DLQLGR---GET---IADTARTLSRYVHAVMMRV----- 103 Query: 119 DWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTW 177 R + L FAK+S VPVIN + + HPCQ LA ++E G+ +++ + W Sbjct: 104 -----RRHETLVEFAKFSSVPVINGLSNLEHPCQILADLQTIREKKGSLNVK-----VAW 153 Query: 178 TYHPKPLNTAVANSALTIATRMGMDVTLLCPT----PDYILDERYMDWAAQNVAESGGSL 233 V NS L + +G ++ L P PD IL + E GG Sbjct: 154 VGD----GNNVCNSLLLASAIIGFEMKLAIPEGFDPPDEIL---------KKAEELGGRF 200 Query: 234 QVSHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQ--HFIVDERKMALTNNGVF 291 ++ D A GADV+Y W ++ E I YQ +V E K + + Sbjct: 201 EILRDPKEAVRGADVIYTDVWASMGQEEERERRLKIFRPYQVNMELVGEAK----EDVIV 256 Query: 292 SHCLPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALVGQS 337 HCLP R + TD V+DS + D+AENRLH QKA++ L+G S Sbjct: 257 MHCLPAHRGEEITDEVIDSEYSVVFDQAENRLHAQKALLLKLIGGS 302 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: 236 Number of extensions: 18 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 10 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