Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate WP_015739792.1 ADEG_RS09240 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >NCBI__GCF_000024605.1:WP_015739792.1 Length = 312 Score = 130 bits (328), Expect = 3e-35 Identities = 109/336 (32%), Positives = 163/336 (48%), Gaps = 40/336 (11%) Query: 4 KHFLNTQDWSRAELDALLTQAALFKRNKLGSELK----GKSIALVFFNPSMRTRTSFELG 59 + FL+ D++ E+ LL+ AA K K E GKS+A++F PS RTR SFE+ Sbjct: 12 RDFLSIADFTSEEIMGLLSFAAELKEAKKRGETHTFCAGKSLAMIFQKPSTRTRVSFEVA 71 Query: 60 AFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVD 119 F LGG+A+ L +A ++ G E IA+ RVL RYVD +R F Sbjct: 72 MFDLGGYALYL----NAQDLQLGRG--------ESIADTGRVLSRYVDGCVIRTF----- 114 Query: 120 WSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTWT 178 R+++V + A+ + +PVIN + + HPCQ LA L + + G L G K Sbjct: 115 ----RQEEV-EELAEAATIPVINGLTSWEHPCQILADFLTILQSKGR--LAGLKLAYVGD 167 Query: 179 YHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHD 238 + +S L R+GM + + P P Y + A + A G + V+ D Sbjct: 168 ------GNNICHSLLLGCPRVGMSIYVATP-PQYAPHPTVVARAQE--AARGTEVVVTED 218 Query: 239 IDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTNNGVFSHCLPLR 298 A GADVV W ++ E +K + YQ + +E + +F HCLP Sbjct: 219 PVQAVKGADVVVTDVWVSMGQEEEAETKKKVFLPYQ--VNEELVSHAKPDFIFLHCLPAH 276 Query: 299 RNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334 R + T ++D P+ + +EAENRLHVQKA++A L+ Sbjct: 277 RGEEVTAEIIDGPHSLVWEEAENRLHVQKALLALLL 312 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: 241 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: 312 Length adjustment: 28 Effective length of query: 311 Effective length of database: 284 Effective search space: 88324 Effective search space used: 88324 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