Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate WP_012172547.1 AZC_RS20655 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >NCBI__GCF_000010525.1:WP_012172547.1 Length = 309 Score = 140 bits (353), Expect = 4e-38 Identities = 110/337 (32%), Positives = 162/337 (48%), Gaps = 49/337 (14%) Query: 3 LKHFLNTQDWSRAELDALLTQAALFK-RNKLGSE---LKGKSIALVFFNPSMRTRTSFEL 58 ++HFL+ D +L +L + K + K G+E L GKS+A+VF PS RTR SF+L Sbjct: 6 VRHFLDLTDLEAVDLRGVLELSKQLKAKRKAGTEEKPLAGKSLAMVFDKPSTRTRVSFDL 65 Query: 59 GAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFV 118 QLGG ++L G M E IA+ ARVL R+VD I +R Sbjct: 66 AMRQLGGETIMLT------------GAEMQLGRGESIADTARVLSRFVDAIMIRIL---- 109 Query: 119 DWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTW 177 ED L AK++ VPVIN + ++HPCQ +A L +EH G+ + R + W Sbjct: 110 ----SHED--LLELAKFATVPVINGLTRVSHPCQVMADVLTFEEHKGSIEGRS----VAW 159 Query: 178 TYHPKPLNTAVANSALT--IATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQV 235 T AN+ L + D T+ TP + + + + V + ++ Sbjct: 160 T--------GDANNVLASWVHAAAQFDFTINVATPKELSPRQALK---EFVKRTQAKVRF 208 Query: 236 SHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMA-LTNNGVFSHC 294 D + A G D V +W ++ G+ E E+ + + + V+ + MA + +F HC Sbjct: 209 MRDPEEAVEGVDCVITDTWVSM---GDKEAERR-HNLLKPYQVNAKLMARAAPDAIFMHC 264 Query: 295 LPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMA 331 LP R + TD VMD P + DEAENRLH QK I+A Sbjct: 265 LPAHRGEEVTDEVMDGPQSVVFDEAENRLHAQKGILA 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: 252 Number of extensions: 11 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: 309 Length adjustment: 28 Effective length of query: 311 Effective length of database: 281 Effective search space: 87391 Effective search space used: 87391 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