Align Butyrate--acetoacetate CoA-transferase subunit A; Short=Coat A; EC 2.8.3.9 (characterized, see rationale)
to candidate PP_3951 PP_3951 3-oxoadipate CoA-transferase subunit A
Query= uniprot:P33752 (218 letters) >FitnessBrowser__Putida:PP_3951 Length = 231 Score = 155 bits (392), Expect = 6e-43 Identities = 84/200 (42%), Positives = 123/200 (61%), Gaps = 2/200 (1%) Query: 17 DGMTIMIGGFLNCGTPTKLIDFLVNLNIKNLTIISNDTCYPNTGIGKLISNNQVKKLIAS 76 DG TIM+GGF G P++LID L+ ++LTIISN+ G+ L+ V+K++ S Sbjct: 18 DGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEIGLAALLMAGSVRKVVCS 77 Query: 77 YIG-SNPDTGKKLFN-NELEVELSPQGTLVERIRAGGSGLGGVLTKTGLGTLIEKGKKKI 134 + S+ +L+ ++E+E+ PQG L ERIRA GSG+G + TG GTL+ +GK+ Sbjct: 78 FPRQSDSYVFDELYRAGKIELEVVPQGNLAERIRAAGSGIGAFFSPTGYGTLLAEGKETR 137 Query: 135 SINGTEYLLELPLTADVALIKGSIVDEAGNTFYKGTTKNFNPYMAMAAKTVIVEAENLVS 194 I+G Y+LE+PL AD ALIK D GN Y+ +NF P MAMAAKT I + + +V Sbjct: 138 EIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPIMAMAAKTAIAQVDQVVE 197 Query: 195 CEKLEKEKAMTPGVLINYIV 214 +L+ E +TPG+ + +V Sbjct: 198 LGELDPEHIITPGIFVQRVV 217 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: 111 Number of extensions: 3 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: 218 Length of database: 231 Length adjustment: 22 Effective length of query: 196 Effective length of database: 209 Effective search space: 40964 Effective search space used: 40964 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