Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate Dsui_3249 Dsui_3249 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__PS:Dsui_3249 Length = 307 Score = 120 bits (301), Expect = 4e-32 Identities = 103/339 (30%), Positives = 157/339 (46%), Gaps = 46/339 (13%) Query: 2 SLKHFLNTQDWSRAELDALLTQAAL----FKRNKLGSELKGKSIALVFFNPSMRTRTSFE 57 S+KHFL +D++R E D L + FK K L +++ ++F S RTR SFE Sbjct: 3 SIKHFLQFKDFTREEFDYLFARTRWIKDQFKNYKQYWPLTDRTLVMIFEKASTRTRLSFE 62 Query: 58 LGAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKF 117 G QLGG A+ L + LG E + + A+V+ R D++ +R F Sbjct: 63 AGMQQLGGSAIYLNTR------DSQLGR------GEPVEDAAQVISRMSDIVMIRTF--- 107 Query: 118 VDWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLT 176 E ++++ FA S VPVIN + HPCQ +A EH G ++GK + Sbjct: 108 -------EQEIIERFAANSRVPVINGLTNEYHPCQIMADIFTYIEHRGP--IQGK--TVA 156 Query: 177 WTYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVS 236 W + V N+ L A + +V + P + ER + N + ++ Sbjct: 157 WIGD----SNNVCNTWLQAAEVLDFNVHVSTPPGYEVEAERAGLYGTANFEQFSDPME-- 210 Query: 237 HDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALT-NNGVFSHCL 295 A GAD+V W ++ F E E+ ++D + + VD M + ++ +F HCL Sbjct: 211 -----AAKGADIVTTDVWTSMGFEA--ENEERLKD-FADWQVDGDMMRIAKSDAIFLHCL 262 Query: 296 PLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334 P R + T V+D P DEAENRLH QKA+M L+ Sbjct: 263 PAHRGEEVTAEVIDGPQSAVWDEAENRLHTQKALMEYLL 301 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: 238 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: 307 Length adjustment: 28 Effective length of query: 311 Effective length of database: 279 Effective search space: 86769 Effective search space used: 86769 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