Align acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized)
to candidate RR42_RS10005 RR42_RS10005 3-oxoadipate CoA-transferase
Query= reanno::psRCH2:GFF1045 (231 letters) >FitnessBrowser__Cup4G11:RR42_RS10005 Length = 217 Score = 201 bits (510), Expect = 1e-56 Identities = 106/217 (48%), Positives = 143/217 (65%), Gaps = 3/217 (1%) Query: 1 MNKIYPSAAHALEGLVEDGMTIAVGGFGLCGIPEQLIAALRDSGKKDLTAISNNAGVDGF 60 ++K+Y +A A+ V DG TIA+GGFG G+P++LI AL + G KDLT +SNNAG Sbjct: 2 IDKLYATAREAVAD-VADGATIAIGGFGGAGMPDELIDALIEQGAKDLTVVSNNAGNGDA 60 Query: 61 GLGLLLETRQISKMVSSYVGENKE--FERQYLAGELALEFTPQGTLAEKLRAGGAGIPAF 118 GL LL+ R++ +++ S+ + FE Y AGE+ LE PQGTLAE+LRA G GI F Sbjct: 61 GLAALLKARRVRRLMCSFPRQRDAYVFEALYRAGEIELEVIPQGTLAERLRAAGCGIGGF 120 Query: 119 YTKTGYGTLVAEGKETRQFNGEWYVMEESLTADLALVKAWKADKAGNLLFRKTARNFNPL 178 YT TG+GTL+A GKE R+ YV+E + D+AL+ A AD+ GNL++ KTARNF P+ Sbjct: 121 YTPTGHGTLLAAGKEARRIGARDYVLEYPIHVDVALINAAAADRWGNLVYNKTARNFAPV 180 Query: 179 AAMAGEVCVVEVEEIVETGELDPDQIHLPGIYVHRIV 215 AMA + V + E GELDP+ I PGI+V R+V Sbjct: 181 MAMAATTTIAAVTRVCELGELDPEAIVTPGIFVKRVV 217 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: 160 Number of extensions: 9 Number of successful extensions: 2 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: 217 Length adjustment: 22 Effective length of query: 209 Effective length of database: 195 Effective search space: 40755 Effective search space used: 40755 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 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