Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate WP_013819184.1 METME_RS12880 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >NCBI__GCF_000214665.1:WP_013819184.1 Length = 299 Score = 122 bits (306), Expect = 1e-32 Identities = 107/338 (31%), Positives = 152/338 (44%), Gaps = 45/338 (13%) Query: 1 MSLKHFLNTQDWSRAELDALLTQAALFK--RNKLGSELKGKSIALVFFNPSMRTRTSFEL 58 M +HF++ D S AEL L+ +A K R+ LKGK +A+VF S RTR SFE Sbjct: 1 MQPRHFISLLDLSGAELRNLIYRAIQLKTHRDPDFQPLKGKVLAMVFEKSSTRTRISFEA 60 Query: 59 GAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFV 118 G Q GG A+ L P + LG E + + A+V+ VD I +R Sbjct: 61 GMTQFGGSAIFLSPR------DTQLGR------GEPLEDSAKVISSMVDCIMLRT----- 103 Query: 119 DWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTW 177 E + +FAKYS VPVIN + + HPCQ LA EH G D+ GK + W Sbjct: 104 -----NEHDTVTTFAKYSRVPVINGLTDLLHPCQLLADMQTYFEHRG--DIAGK--TVAW 154 Query: 178 TYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSH 237 + +S + A + + + P DY + +D AA VA + + Sbjct: 155 IGD----GNNMCHSYINAARQFDFKLHIASPA-DYGPVQDIVDAAADKVAFFNSPVLAAQ 209 Query: 238 DIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTN-NGVFSHCLP 296 AD+V W ++ G +K ++ F V E M N + +F HCLP Sbjct: 210 Q-------ADLVVTDVWASM---GQESEQKKREYAFRDFQVTEEVMQAANPDALFMHCLP 259 Query: 297 LRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334 R + V+D + DEAENRLH QKA++ L+ Sbjct: 260 AHRGEEVAAEVIDGSQSVVFDEAENRLHAQKALLEFLI 297 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: 226 Number of extensions: 10 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: 299 Length adjustment: 27 Effective length of query: 312 Effective length of database: 272 Effective search space: 84864 Effective search space used: 84864 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