Align Butyrate--acetoacetate CoA-transferase subunit A; Short=Coat A; EC 2.8.3.9 (characterized, see rationale)
to candidate Echvi_3272 Echvi_3272 3-oxoacid CoA-transferase, A subunit
Query= uniprot:P33752 (218 letters) >FitnessBrowser__Cola:Echvi_3272 Length = 230 Score = 162 bits (410), Expect = 5e-45 Identities = 85/193 (44%), Positives = 115/193 (59%) Query: 21 IMIGGFLNCGTPTKLIDFLVNLNIKNLTIISNDTCYPNTGIGKLISNNQVKKLIASYIGS 80 +M+GGF CG P ID L+ I LT ISN+ + GIG ++ VKK+I+SY+G Sbjct: 22 LMLGGFGLCGIPENCIDALLKKPISGLTCISNNAGVDDFGIGLMLKKRMVKKMISSYVGE 81 Query: 81 NPDTGKKLFNNELEVELSPQGTLVERIRAGGSGLGGVLTKTGLGTLIEKGKKKISINGTE 140 N + ++L + ELEVEL PQG+L ER RAGG+G+ T G+GT + +GK+ +G Sbjct: 82 NAEFERQLLSGELEVELIPQGSLAERTRAGGAGIPAFFTPAGVGTEVAEGKEMREFDGKL 141 Query: 141 YLLELPLTADVALIKGSIVDEAGNTFYKGTTKNFNPYMAMAAKTVIVEAENLVSCEKLEK 200 Y+LE L AD +L+K D AGN YKGT +NFNP MA A I E E LV L+ Sbjct: 142 YILERWLKADFSLVKAWKGDTAGNLIYKGTARNFNPMMATAGTITIAEVEELVPAGTLDP 201 Query: 201 EKAMTPGVLINYI 213 + TPG+ + I Sbjct: 202 NQIHTPGIFVQRI 214 Lambda K H 0.315 0.136 0.380 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: 137 Number of extensions: 5 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: 218 Length of database: 230 Length adjustment: 22 Effective length of query: 196 Effective length of database: 208 Effective search space: 40768 Effective search space used: 40768 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: 42 (22.0 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