Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate WP_018232268.1 THITHI_RS0106510 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >NCBI__GCF_000378965.1:WP_018232268.1 Length = 300 Score = 141 bits (355), Expect = 2e-38 Identities = 111/340 (32%), Positives = 166/340 (48%), Gaps = 47/340 (13%) Query: 1 MSLKHFLNTQDWSRAELDALLTQAALFKR-NKLGSE---LKGKSIALVFFNPSMRTRTSF 56 M+++HFL+ D S EL L+ +A KR ++ G+E L+GK + ++F S RTR SF Sbjct: 1 MTVRHFLSLLDLSTEELRGLIARAIELKRLHRSGTEHESLRGKVLGMIFEKSSTRTRVSF 60 Query: 57 ELGAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPK 116 E+G QLGG A+ L P + LG E I + ARVL R VD + +R + Sbjct: 61 EVGMIQLGGQALFLSPR------DTQLGR------GEPIEDTARVLSRMVDGVMIRTY-- 106 Query: 117 FVDWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVL 175 E + ++ FA +S VPVIN + + HPCQ LA EH G D+ G+ V+ Sbjct: 107 --------EHEKIERFAAHSRVPVINGLTDLEHPCQLLADLQTWFEHRG--DITGR--VV 154 Query: 176 TWTYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQV 235 T+ + NS + A +G + CP E Y D + V +G ++ V Sbjct: 155 TYVGD----GNNMCNSYINAAQLLGFTLRAACP-------EGY-DPDPELVRAAGDAVSV 202 Query: 236 SHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTN-NGVFSHC 294 D A AD+V W ++ G + + R + ++VD M N +F HC Sbjct: 203 VRDPAEAVRNADLVVTDVWASM---GQEDEQTARRQAFTDYVVDSALMKRANPEALFMHC 259 Query: 295 LPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334 LP R + + V++ P + DEAENRLH QKA++ L+ Sbjct: 260 LPAHREEEVSTEVLEGPQSVVWDEAENRLHAQKALLEFLL 299 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: 13 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: 300 Length adjustment: 28 Effective length of query: 311 Effective length of database: 272 Effective search space: 84592 Effective search space used: 84592 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