Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate BWI76_RS03010 BWI76_RS03010 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__Koxy:BWI76_RS03010 Length = 334 Score = 137 bits (344), Expect = 5e-37 Identities = 114/359 (31%), Positives = 164/359 (45%), Gaps = 57/359 (15%) Query: 4 KHFLNTQDWSRAELDALLTQAALFKRNKLGS----ELKGKSIALVFFNPSMRTRTSFELG 59 KHFL D++ AE+ ALL AA K +K + L GK+IAL+F S RTR SFE+ Sbjct: 7 KHFLKLLDFTPAEITALLELAARLKADKKNNIEIQHLTGKNIALIFEKDSTRTRCSFEVA 66 Query: 60 AFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVD 119 AF G L P +G +E I + ARVLGR D I R Sbjct: 67 AFDQGARVTYLGPSGS------QIG------HKESIKDTARVLGRMYDGIQYRG------ 108 Query: 120 WSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTWT 178 +V+++ A+Y+ VPV N + HP Q LA L +QEH L GK + Sbjct: 109 ----HGQEVVETLAEYAGVPVWNGLTNEFHPTQLLADLLTMQEH-----LPGKAFNQMTL 159 Query: 179 YHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHD 238 + + NS L A G+D+ L+ PT + +E+ ++ ++GG++ ++ D Sbjct: 160 VYAGDARNNMGNSMLEAAALTGLDLRLVAPTACW-PEEKLVEQCRALAQKNGGNITLTED 218 Query: 239 IDSAYAGADVVYAKSWGAL-PFFGNWEPEKPIRDQYQHFIVDERKMALTNNG--VFSHCL 295 I + GAD +Y W ++ W + YQ V+ MALT N F HCL Sbjct: 219 IAAGVKGADFIYTDVWVSMGEAKEKWAERIALLRAYQ---VNSEMMALTGNPQVKFLHCL 275 Query: 296 P------------------LRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALVGQ 336 P L ++ TD V +S I D+AENR+H KA+M A +G+ Sbjct: 276 PAFHDDQTTLGKQMAAEYGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATLGK 334 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: 232 Number of extensions: 17 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: 334 Length adjustment: 28 Effective length of query: 311 Effective length of database: 306 Effective search space: 95166 Effective search space used: 95166 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