Align acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized)
to candidate WP_041380313.1 SWIT_RS26985 CoA transferase subunit A
Query= reanno::psRCH2:GFF1045 (231 letters) >NCBI__GCF_000016765.1:WP_041380313.1 Length = 236 Score = 302 bits (774), Expect = 3e-87 Identities = 157/229 (68%), Positives = 177/229 (77%) Query: 2 NKIYPSAAHALEGLVEDGMTIAVGGFGLCGIPEQLIAALRDSGKKDLTAISNNAGVDGFG 61 +KIY S A AL GL+ DGMTI GGFGL G PE LI +R SG K+LT ISNNAG DGFG Sbjct: 3 SKIYDSPASALSGLLFDGMTIMSGGFGLSGNPESLIPQVRASGVKELTVISNNAGADGFG 62 Query: 62 LGLLLETRQISKMVSSYVGENKEFERQYLAGELALEFTPQGTLAEKLRAGGAGIPAFYTK 121 L LLE+RQ+ KM+SSYVGENK FE QYL+GEL LE PQGTLAE++RAGGAGIPAFYTK Sbjct: 63 LWTLLESRQVRKMISSYVGENKLFESQYLSGELELELNPQGTLAERIRAGGAGIPAFYTK 122 Query: 122 TGYGTLVAEGKETRQFNGEWYVMEESLTADLALVKAWKADKAGNLLFRKTARNFNPLAAM 181 TG GT+VAEGK F GE Y+ E L ADL+++KAW+AD AGNL+FRKTARNFNP A Sbjct: 123 TGVGTVVAEGKPVETFEGEDYIRETWLRADLSIIKAWRADPAGNLMFRKTARNFNPNMAT 182 Query: 182 AGEVCVVEVEEIVETGELDPDQIHLPGIYVHRIVHNPNPEKRIEKRTVR 230 AG V VVEVEEIV G LDPD +H PGIYV RIV + EKRIE+ TVR Sbjct: 183 AGMVTVVEVEEIVAEGSLDPDCVHTPGIYVDRIVLSTINEKRIEQLTVR 231 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: 206 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: 236 Length adjustment: 23 Effective length of query: 208 Effective length of database: 213 Effective search space: 44304 Effective search space used: 44304 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