Align acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized)
to candidate WP_034997680.1 DL88_RS14830 CoA transferase subunit A
Query= reanno::psRCH2:GFF1045 (231 letters) >NCBI__GCF_000745425.1:WP_034997680.1 Length = 235 Score = 306 bits (785), Expect = 2e-88 Identities = 147/230 (63%), Positives = 181/230 (78%) Query: 1 MNKIYPSAAHALEGLVEDGMTIAVGGFGLCGIPEQLIAALRDSGKKDLTAISNNAGVDGF 60 MNK++P A AL +++DG T+ GGFGLCG+P+ LI A+++ G LT ISNNAGVDG Sbjct: 1 MNKVFPDARTALADILKDGQTLMAGGFGLCGVPQSLIDAIKELGATGLTVISNNAGVDGD 60 Query: 61 GLGLLLETRQISKMVSSYVGENKEFERQYLAGELALEFTPQGTLAEKLRAGGAGIPAFYT 120 GLG+LL TRQI KMVSSYVGENK FE QYL+GEL LEF PQGTLAE++RAGGAGIPAFYT Sbjct: 61 GLGILLATRQIKKMVSSYVGENKLFETQYLSGELELEFNPQGTLAERIRAGGAGIPAFYT 120 Query: 121 KTGYGTLVAEGKETRQFNGEWYVMEESLTADLALVKAWKADKAGNLLFRKTARNFNPLAA 180 +TG GTL+AEGKET++F+G Y+ME LTAD+++V A+K D GNL++R+TARNFNP+ A Sbjct: 121 RTGVGTLIAEGKETKEFDGVTYLMERGLTADISIVHAYKGDTEGNLVYRETARNFNPMMA 180 Query: 181 MAGEVCVVEVEEIVETGELDPDQIHLPGIYVHRIVHNPNPEKRIEKRTVR 230 AG + + EVE +V GE+DPD IH PGIYVHR+V K IEKRT R Sbjct: 181 TAGRITIAEVEHLVPAGEIDPDHIHTPGIYVHRLVARGPYVKPIEKRTTR 230 Lambda K H 0.316 0.135 0.391 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: 226 Number of extensions: 4 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: 231 Length of database: 235 Length adjustment: 23 Effective length of query: 208 Effective length of database: 212 Effective search space: 44096 Effective search space used: 44096 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: 41 (21.6 bits) S2: 46 (22.3 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