Align acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized)
to candidate 3607727 Dshi_1136 3-oxoacid CoA-transferase, A subunit (RefSeq)
Query= reanno::psRCH2:GFF1045 (231 letters) >FitnessBrowser__Dino:3607727 Length = 231 Score = 328 bits (841), Expect = 5e-95 Identities = 163/231 (70%), Positives = 190/231 (82%), Gaps = 1/231 (0%) Query: 1 MNKIYPSAAHALEGLVEDGMTIAVGGFGLCGIPEQLIAALRDSGKKDLTAISNNAGVDGF 60 M KIY SAA ALEGL+ D M IA GGFGLCGIPE LI A++ SG K LT SNNAGVD F Sbjct: 1 MQKIYGSAAEALEGLLFDDMLIAAGGFGLCGIPELLIEAVQKSGVKRLTIASNNAGVDDF 60 Query: 61 GLGLLLETRQISKMVSSYVGENKEFERQYLAGELALEFTPQGTLAEKLRAGGAGIPAFYT 120 GLGLLL+T+Q+ KM+SSYVGEN F +QYL+GEL +EF PQGTLAE++RAGG GIP FYT Sbjct: 61 GLGLLLQTKQVKKMMSSYVGENDLFMQQYLSGELEIEFNPQGTLAERMRAGGCGIPGFYT 120 Query: 121 KTGYGTLVAEGKETRQFNGEWYVMEESLTADLALVKAWKADKAGNLLFRKTARNFNPLAA 180 KTG GT++AEGKE + FNGE Y++EE + ADL++VKAWKAD+ GNL+FRKTARNFNP AA Sbjct: 121 KTGVGTVIAEGKEHKDFNGETYILEEGIFADLSIVKAWKADETGNLVFRKTARNFNPPAA 180 Query: 181 MAGEVCVVEVEEIVETGELDPDQIHLPGIYVHRIVHNPNPEKRIEKRTVRS 231 M G+VCV EVEEIV TG LDPD IHLPGIYVHR+V + EKRIE+RT R+ Sbjct: 181 MCGKVCVAEVEEIVPTGTLDPDTIHLPGIYVHRLVQGEH-EKRIEQRTTRA 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: 5 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: 231 Length adjustment: 23 Effective length of query: 208 Effective length of database: 208 Effective search space: 43264 Effective search space used: 43264 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