Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate Ac3H11_1333 Ornithine carbamoyltransferase (EC 2.1.3.3)
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1333 Length = 328 Score = 124 bits (311), Expect = 3e-33 Identities = 109/345 (31%), Positives = 155/345 (44%), Gaps = 45/345 (13%) Query: 2 SLKHFLNTQDWSRAELDALLTQAALFKRNKLGSE----LKGKSIALVFFNPSMRTRTSFE 57 +LKH+L D + E L +AAL K+ + L +++A++F S RTR SFE Sbjct: 12 TLKHYLQFTDLNADEYAYLFERAALIKKKFKAYDKHHPLVDRTLAMIFEKASTRTRVSFE 71 Query: 58 LGAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKF 117 G +QLGG V L G + LG E I + A+V+ R DL+ +R + Sbjct: 72 AGMYQLGGSVVHLTTG------DSQLGRA------EPIEDSAKVISRMTDLVMIRTY--- 116 Query: 118 VDWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRG------ 170 E ++ FA S VPVIN + HPCQ LA EH G D G Sbjct: 117 -------EQAKIERFAANSRVPVINGLTNEYHPCQILADIFTFIEHRGPKDGTGNLTDCL 169 Query: 171 KKYVLTWTYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESG 230 K + W +AN+ + A+ +G V + P Y +DE+ AA S Sbjct: 170 KGKTVAWVGD----GNNMANTWVQAASLLGFKVHVSTPR-GYEIDEKL---AAGAHGISA 221 Query: 231 GSLQVSHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTN-NG 289 S Q + A GAD+V W ++ + E K + + VD MA + Sbjct: 222 DSYQFFSNPMEACRGADLVTTDVWTSMGYEAENEARKKA---FADWCVDTEMMAAAQPDA 278 Query: 290 VFSHCLPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334 +F HCLP R + V+D P + DEAENR+HVQKA+M L+ Sbjct: 279 LFMHCLPAHRGEEVEADVIDGPQSVVWDEAENRMHVQKALMEYLL 323 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: 256 Number of extensions: 8 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: 328 Length adjustment: 28 Effective length of query: 311 Effective length of database: 300 Effective search space: 93300 Effective search space used: 93300 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