Align acyl CoA carboxylase biotin carboxyl carrier protein subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate WP_050656086.1 C1M55_RS09265 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13596 (167 letters) >NCBI__GCF_002893965.1:WP_050656086.1 Length = 679 Score = 55.8 bits (133), Expect = 1e-12 Identities = 27/60 (45%), Positives = 41/60 (68%), Gaps = 1/60 (1%) Query: 98 EGEVISPLQGRIVTIRVNEGDAVNKGQPLLSVEAMKSETIISAPIAGIVEKIIVKPGQGV 157 + E+ SP+ G ++ + V G AV+ GQPL+ VEAMK E +++PI GIVE ++V+ G V Sbjct: 590 DAEIASPMPGAVIAVNVENGAAVSAGQPLVVVEAMKMEHSLTSPIDGIVE-VLVRQGDQV 648 Lambda K H 0.313 0.136 0.368 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: 235 Number of extensions: 9 Number of successful extensions: 1 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: 167 Length of database: 679 Length adjustment: 28 Effective length of query: 139 Effective length of database: 651 Effective search space: 90489 Effective search space used: 90489 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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