Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_037570777.1 BS73_RS08450 aspartate carbamoyltransferase catalytic subunit
Query= curated2:A9ERU2 (311 letters) >NCBI__GCF_000744815.1:WP_037570777.1 Length = 326 Score = 106 bits (265), Expect = 7e-28 Identities = 96/299 (32%), Positives = 139/299 (46%), Gaps = 33/299 (11%) Query: 25 ARLKEEPKGRRTTMLAGRAIAVVLEKASTRTRVSFEVGIAQLGAQPVVLSTQGSQLARGE 84 A L + P + T L GR + + + STRTR SFEV +L A + S +GS +++GE Sbjct: 27 AALSDRPIKKLPT-LRGRTVVNLFFEDSTRTRTSFEVAEKRLSADVINFSAKGSSVSKGE 85 Query: 85 PIRDTARVL-ARYCDAIAFRTSSTARLLEMAEAS---VPVINALSDDG---HPVQVLSDI 137 ++DTA L A DA+ R S++ +AE+ VINA DG HP Q L D Sbjct: 86 SLKDTALTLQAMGADAVVIRHSASGAPQRLAESDWLHGSVINA--GDGTHEHPTQALLDA 143 Query: 138 FTIQEALAASGDRTGIAGRRVAFLGDCA-SNMARSWLEAAQLFDFHLVLAGPEGYMPPAD 196 FT++ L A G +AGRRVA +GD S +ARS + + L P +P Sbjct: 144 FTLRRHLNA-GAGNDLAGRRVAVVGDILHSRVARSNVHLLHTLGAEVTLVSPPTLLP--- 199 Query: 197 EVERARKTGHVTITHDPREGAAGADVVNTDVWASMGHEAEAEKRRAAF--------AGWT 248 + + + P + D V A M + E+ AAF + Sbjct: 200 ----------IGVENWPCSVSYDLDAVLPKSDAVMMLRVQRERMNAAFFPTEREYSRRYG 249 Query: 249 VDAKVMARAAQHSIVLHCLPAHRGEEIDDETLEGPRSRVWDQAENRLHVQKALMLWLLG 307 +D MA +H++VLH P RG EI E + PR +Q N + V+ A++ LLG Sbjct: 250 LDGLRMAALPEHAVVLHPGPMVRGMEITAEVADSPRCTAVEQVANGVSVRMAVLYLLLG 308 Lambda K H 0.319 0.131 0.382 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: 191 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: 311 Length of database: 326 Length adjustment: 27 Effective length of query: 284 Effective length of database: 299 Effective search space: 84916 Effective search space used: 84916 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 09 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