Align citrate lyase γ subunit (characterized)
to candidate BWI76_RS04440 BWI76_RS04440 citrate lyase ACP
Query= metacyc::MONOMER-17000 (97 letters) >FitnessBrowser__Koxy:BWI76_RS04440 Length = 97 Score = 171 bits (434), Expect = 1e-48 Identities = 90/97 (92%), Positives = 94/97 (96%) Query: 1 MEMKIDALAGTLESSDVMVRIGPAAQPGIQLEIDSIVKQQFGAAIEQVVRETLAQLGVKQ 60 MEM IDALAGTLESSDVMVRIGPA +PGIQLEIDSIVKQQFGAAIEQVVRETLAQLGV + Sbjct: 1 MEMMIDALAGTLESSDVMVRIGPANEPGIQLEIDSIVKQQFGAAIEQVVRETLAQLGVTR 60 Query: 61 ANVVVDDKGALECVLRARVQAAALRAAQQTQLQWSQL 97 ANVVVDDKGALECVL+ARVQAAALRAAQQ+QLQWSQL Sbjct: 61 ANVVVDDKGALECVLKARVQAAALRAAQQSQLQWSQL 97 Lambda K H 0.318 0.129 0.344 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: 75 Number of extensions: 1 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: 97 Length of database: 97 Length adjustment: 10 Effective length of query: 87 Effective length of database: 87 Effective search space: 7569 Effective search space used: 7569 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (20.8 bits) S2: 39 (19.6 bits)
This GapMind analysis is from Sep 17 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