Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_010530471.1 ON01_RS07805 aspartate carbamoyltransferase catalytic subunit
Query= curated2:Q7V0J3 (308 letters) >NCBI__GCF_000224785.1:WP_010530471.1 Length = 307 Score = 118 bits (295), Expect = 2e-31 Identities = 93/307 (30%), Positives = 149/307 (48%), Gaps = 29/307 (9%) Query: 10 KNFLSSLDITTDEVFHILDLSKKFKNKKLNINLHNKVLGLIFDKSSTRTRVSFQVAMSRL 69 + FLS+ ++++D ++ IL+ ++ + K +I L F+ S TRT+ SFQVA RL Sbjct: 2 REFLSTRELSSDSIYSILETAEAMRKKPESIRSERFAANLFFEVS-TRTKTSFQVAEKRL 60 Query: 70 GGTTIDLNPTTSQIERGEPIKDTARVLSRY-CDVIAIRTFNHADLEEYARWSTKPVINAL 128 G T+D +S + +GE + DT R D++ +R +E A + P+INA Sbjct: 61 GMETLDFQMESSSMTKGESLYDTVRTYEAIGADLLIVRHAYDHWYDELAGRISVPIINAG 120 Query: 129 TDL-EHPCQALADFLTIYEEFLDFKDVVLTFIGD--GNNVANSLILCGALLGVEVRIACP 185 EHP Q++ D LTIY+EF F+ + + GD + VA S LG V A Sbjct: 121 AGKGEHPTQSMLDLLTIYQEFGSFEGLNVVIAGDIKHSRVARSNAYALTTLGANVSFAAA 180 Query: 186 KGYEPNSMVI-----NKAYEIYKNRNLLKITNDPDTAVLGANVLYTDVWSSMGEENQKAE 240 G+E +S I ++A ++ LL+I ++ A V Y S +G+ E Sbjct: 181 PGFEDDSFDIPYVSMDEACDMCDVLMLLRIQHERH-----AQVSYRTT-SYLGDYGLTME 234 Query: 241 KDKVFNGFTIDNDLVSKADKEAIILHCLPAYRSKEITDEVFESKKNRIFDQAENRMHVQQ 300 +++ + AI+LH P R EI + E ++RIF Q EN +H + Sbjct: 235 RER-------------RMRDHAIVLHPAPVNRGVEIDTRLVECDRSRIFKQMENGVHTRM 281 Query: 301 ALLSCLL 307 A++S LL Sbjct: 282 AIISILL 288 Lambda K H 0.319 0.135 0.389 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: 185 Number of extensions: 7 Number of successful extensions: 3 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: 308 Length of database: 307 Length adjustment: 27 Effective length of query: 281 Effective length of database: 280 Effective search space: 78680 Effective search space used: 78680 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 Jul 26 2024. The underlying query database was built on Jul 25 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