Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate 3607382 Dshi_0796 ornithine carbamoyltransferase (RefSeq)
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__Dino:3607382 Length = 308 Score = 146 bits (369), Expect = 6e-40 Identities = 116/347 (33%), Positives = 164/347 (47%), Gaps = 54/347 (15%) Query: 3 LKHFLNTQDWSRAELDALLTQAALFKRNKLG---------SELKGKSIALVFFNPSMRTR 53 + HFL+ A+L A+L + K + G L G +AL+F PS RTR Sbjct: 1 MTHFLDIHTTDPADLRAMLDRGRAMKTARAGRPKGASDDDQPLAGHMVALIFEKPSTRTR 60 Query: 54 TSFELGAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRA 113 SF+LG Q+GG +VL G M E IA+ ARVL RYVDLI +R Sbjct: 61 VSFDLGVRQMGGQTMVLS------------GADMQLGHGETIADTARVLSRYVDLIMIRT 108 Query: 114 FPKFVDWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKK 172 F E+ L A+++ VPVIN + THPCQ +A + +EH G + GKK Sbjct: 109 F----------EETTLLEMAEHASVPVINGLTNRTHPCQIMADVMTYEEHRGP--IAGKK 156 Query: 173 YVLTWTYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAES--- 229 V W V S L A + G D+T P +D A+ VA + Sbjct: 157 VV--WCGD----GNNVCASFLHAAGQFGFDMTFTGPPT--------LDPEAEFVAGARAK 202 Query: 230 GGSLQVSHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTN-N 288 G ++++ D A GAD+V A +W ++ + ++ +Q + + VD M + Sbjct: 203 GVTVEIERDPAVAVQGADLVVADTWVSM--HDSQTTKERRHNQLRPYQVDRALMEKAKPD 260 Query: 289 GVFSHCLPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALVG 335 +F HCLP R + T VMD P+ + DEAENRLH QKA+M +G Sbjct: 261 ALFMHCLPAHRGEEVTSEVMDGPHSVIFDEAENRLHAQKAVMRWCLG 307 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: 227 Number of extensions: 13 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: 308 Length adjustment: 28 Effective length of query: 311 Effective length of database: 280 Effective search space: 87080 Effective search space used: 87080 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