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_045585974.1 AL072_RS28295 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13596 (167 letters) >NCBI__GCF_001305595.1:WP_045585974.1 Length = 667 Score = 55.8 bits (133), Expect = 1e-12 Identities = 35/101 (34%), Positives = 53/101 (52%), Gaps = 7/101 (6%) Query: 66 ILLDNASVFRLERLTELPSKEGESIEEMIKGKEGEVISPLQGRIVTIRVNEGDAVNKGQP 125 +L+D A + RLT L + E+ +G G + +P+ G +V + V G +V G P Sbjct: 569 VLIDGA----VSRLT-LDDPSARAAEQ--EGGSGRLTAPMPGTVVRVLVEPGQSVEAGTP 621 Query: 126 LLSVEAMKSETIISAPIAGIVEKIIVKPGQGVKKGDTLLII 166 L+ +EAMK E I AP AG V + G V +G LL++ Sbjct: 622 LMLLEAMKMEHTIKAPAAGTVSAVNFSAGDQVSEGVDLLVL 662 Score = 31.6 bits (70), Expect = 3e-05 Identities = 11/30 (36%), Positives = 23/30 (76%) Query: 138 ISAPIAGIVEKIIVKPGQGVKKGDTLLIIK 167 ++AP+ G V +++V+PGQ V+ G L++++ Sbjct: 597 LTAPMPGTVVRVLVEPGQSVEAGTPLMLLE 626 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: 267 Number of extensions: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 167 Length of database: 667 Length adjustment: 28 Effective length of query: 139 Effective length of database: 639 Effective search space: 88821 Effective search space used: 88821 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: 48 (23.1 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