Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate WP_011032099.1 MM_RS00775 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >NCBI__GCF_000007065.1:WP_011032099.1 Length = 302 Score = 126 bits (317), Expect = 6e-34 Identities = 105/336 (31%), Positives = 153/336 (45%), Gaps = 48/336 (14%) Query: 7 LNTQDWSRAELDALLTQAALFKRNKLGSE----LKGKSIALVFFNPSMRTRTSFELGAFQ 62 L+ D SR E+ LL AA K+ + E LK KS+ ++F S RTR SFE+ Sbjct: 6 LSITDLSREEIYELLESAADLKKKRKAGEPTEYLKHKSLGMIFEKSSTRTRVSFEVAMSD 65 Query: 63 LGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVDWSK 122 GGHA+ L ++ I+ G E I + AR L Y+ I R Sbjct: 66 FGGHALYL----NSRDIQVGRG--------ETIEDTARTLSGYLHGIMARVM-------- 105 Query: 123 DREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTWTYHP 181 ++ A++S +PVIN + HPCQ L + + E+ G K+ W Sbjct: 106 --SHDTVEKLARFSTIPVINALSDREHPCQILGDFMTIMEYKNR--FEGLKFA--WIGD- 158 Query: 182 KPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAA--QNVAESGGSLQVSHDI 239 V NSAL + MGM+ + CP E Y A + GG ++ D Sbjct: 159 ---GNNVCNSALLGSAIMGMEFVIACP-------EGYEPGAEFLEKAKALGGKFSITDDP 208 Query: 240 DSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTNNGVF-SHCLPLR 298 +A AD++Y W ++ E EK ++D + F V+ + + V HCLP R Sbjct: 209 KTAAKDADIIYTDVWVSMG--DEAEQEKRLKD-FGSFQVNTELLGVAKPDVIVMHCLPAR 265 Query: 299 RNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334 R ++ TD VMD PN + +EAENRLH QKA++ L+ Sbjct: 266 RGLEITDEVMDGPNSVIFEEAENRLHAQKALILKLM 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: 212 Number of extensions: 9 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: 302 Length adjustment: 28 Effective length of query: 311 Effective length of database: 274 Effective search space: 85214 Effective search space used: 85214 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 10 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