Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate H281DRAFT_04119 H281DRAFT_04119 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__Burk376:H281DRAFT_04119 Length = 309 Score = 137 bits (344), Expect = 5e-37 Identities = 111/338 (32%), Positives = 162/338 (47%), Gaps = 46/338 (13%) Query: 3 LKHFLNTQDWSRAELDALLTQAALFKRNKLGSE----LKGKSIALVFFNPSMRTRTSFEL 58 ++H+L +D+S + + +L +A + KR E L +++A++F S RTR SFE Sbjct: 6 IRHYLQFKDFSLDDYEYVLERARILKRKFKNYETYHPLHDRTLAMIFEKNSTRTRLSFEA 65 Query: 59 GAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFV 118 G FQLGGHAV + + LG E I + A+V+ R VD+I +R F + Sbjct: 66 GIFQLGGHAVFMSTR------DTQLGR------GEPIEDAAQVISRMVDIIMIRTFGQ-- 111 Query: 119 DWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTW 177 +++ FA+ S VPVIN + HPCQ LA EH G +RGK + W Sbjct: 112 --------DIIQRFAENSRVPVINGLTNEYHPCQVLADIFTYFEHRGP--IRGK--TVAW 159 Query: 178 TYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSH 237 + + + A +G + L P P Y LD + AES Q Sbjct: 160 VGDANNM----LYTWIEAAQILGFKLRLSTP-PGYKLDRALV------AAESAPFFQEFD 208 Query: 238 DIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTN-NGVFSHCLP 296 D + A AGAD+V W ++ F E K + + VD M+ N + +F HCLP Sbjct: 209 DPNEACAGADLVTTDVWTSMGFEAENEARKKA---FADWCVDAEMMSRANADALFMHCLP 265 Query: 297 LRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334 R + + V+D P + DEAENRLHVQKA+M L+ Sbjct: 266 AHRGEEVSAEVIDGPQSVVWDEAENRLHVQKALMEYLL 303 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: 258 Number of extensions: 13 Number of successful extensions: 7 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: 309 Length adjustment: 28 Effective length of query: 311 Effective length of database: 281 Effective search space: 87391 Effective search space used: 87391 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