Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate CA265_RS18520 CA265_RS18520 acetylornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__Pedo557:CA265_RS18520 Length = 324 Score = 182 bits (461), Expect = 1e-50 Identities = 113/338 (33%), Positives = 174/338 (51%), Gaps = 34/338 (10%) Query: 2 SLKHFLNTQDWSRAELDALLTQAALFKRNKLGSELKGKSIALVFFNPSMRTRTSFELGAF 61 S+K F+N DAL +A + LG K K++ LVF NPS+RTR S + A Sbjct: 12 SIKQFVN---------DALALKANPYAHQDLG---KNKTLGLVFMNPSLRTRLSTQKAAL 59 Query: 62 QLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVDWS 121 LG + +V+ K+ W +E G VM+G T EHI E A V+G+Y D++G+R+FPK + Sbjct: 60 NLGMNVMVMNLDKEGWALETQDGVVMNGSTVEHIREAAAVMGQYCDILGLRSFPKLNNRE 119 Query: 122 KDREDQVLKSFAKYSPVPVINMETIT-HPCQELAHALALQEHF-GTPDLRGKKYVLTWTY 179 +D + F KY VPV+++E+ T HP Q A + + E + PD R K VL W Sbjct: 120 EDYSEDFFNKFVKYCAVPVVSLESATRHPLQSFADIITIHETWTKKPDGRKPKVVLAWAP 179 Query: 180 HPKPLNTAVANSA---LTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVS 236 H K L AV NS + A GM + Y L E + A + Sbjct: 180 HVKALPQAVPNSFAEWMCKAQAEGMIDFTIAQPEGYELSEDFTPDA-----------NIQ 228 Query: 237 HDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTNNGVFSHCLP 296 ++++ A AGAD VY K+W + +G + ++++ K+ TN+ HCLP Sbjct: 229 YNLEEALAGADYVYVKNWSSYKEYGK------VLTYPDGWMMNNEKLKFTNDAKVMHCLP 282 Query: 297 LRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334 +RR+++ + ++D PN + I EA NRL +A++ A++ Sbjct: 283 VRRDLELSSEILDGPNSLVIHEAGNRLWAAQAVIKAML 320 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: 286 Number of extensions: 9 Number of successful extensions: 4 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: 324 Length adjustment: 28 Effective length of query: 311 Effective length of database: 296 Effective search space: 92056 Effective search space used: 92056 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: 49 (23.5 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