Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate Ga0059261_3206 Ga0059261_3206 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__Korea:Ga0059261_3206 Length = 307 Score = 117 bits (292), Expect = 5e-31 Identities = 111/346 (32%), Positives = 154/346 (44%), Gaps = 51/346 (14%) Query: 1 MSLKHFLNTQDWSRAELDALLTQAALFKRNKLG---------SELKGKSIALVFFNPSMR 51 M+ ++FL+ D + A+L A KR + G + L G+++A+VF S R Sbjct: 1 MTYRNFLSLSDAGADGIAAMLADAIDRKRARAGQPKGAVDADAPLAGRTLAMVFEKNSTR 60 Query: 52 TRTSFELGAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGV 111 TR SFE+ QLGG AVVL DA + G E +A+ ARVL Y D I V Sbjct: 61 TRVSFEMAIRQLGGSAVVL----DAATSQLGRG--------ETVADTARVLSGYCDAIMV 108 Query: 112 RAFPKFVDWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRG 170 R D +K L A+Y+ VPVIN + +HPCQ +A + E L G Sbjct: 109 RTD----DHAK------LLEMAQYATVPVINGLTDDSHPCQIMADLQTILE--SGKALPG 156 Query: 171 KKYVLTWTYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESG 230 K + W V S + A M DV CP + L E M A Sbjct: 157 LK--VAWLGD----GNNVLASIVEAAGLMHFDVVAACPQ-SFALPEEAM-------ALGK 202 Query: 231 GSLQVSHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTNNGV 290 G + +D A AGADVV +W ++ G + + + + + + + Sbjct: 203 GRARTVNDPVEAVAGADVVVTDTWISM---GQAHADVKLAALAPYQVTEALMAQASPDAK 259 Query: 291 FSHCLPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALVGQ 336 F HCLP R + TDAV+D P + EAENRLH QKA++ GQ Sbjct: 260 FLHCLPAHRGEEVTDAVIDGPQSLIWPEAENRLHAQKAVLRWCFGQ 305 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: 218 Number of extensions: 7 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: 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