Align Butyrate--acetoacetate CoA-transferase subunit A; Short=Coat A; EC 2.8.3.9 (characterized, see rationale)
to candidate N515DRAFT_1736 N515DRAFT_1736 3-oxoacid CoA-transferase
Query= uniprot:P33752 (218 letters) >FitnessBrowser__Dyella79:N515DRAFT_1736 Length = 451 Score = 160 bits (405), Expect = 4e-44 Identities = 80/202 (39%), Positives = 121/202 (59%) Query: 17 DGMTIMIGGFLNCGTPTKLIDFLVNLNIKNLTIISNDTCYPNTGIGKLISNNQVKKLIAS 76 D MTI GGF CG P LI L+ K LTI+ N+ + G+G L+ QVK++ AS Sbjct: 18 DDMTIAAGGFGLCGIPENLIAALLAAGTKGLTIVGNNAGVDDFGMGPLLKTRQVKRVYAS 77 Query: 77 YIGSNPDTGKKLFNNELEVELSPQGTLVERIRAGGSGLGGVLTKTGLGTLIEKGKKKISI 136 Y+G N + +++ ELE+ L PQGTL E++RAGG+G+ G T+T GT + +GK+ Sbjct: 78 YVGENKEFERQVLAGELELHLVPQGTLAEKLRAGGAGIPGFYTRTAFGTKLAEGKETKVF 137 Query: 137 NGTEYLLELPLTADVALIKGSIVDEAGNTFYKGTTKNFNPYMAMAAKTVIVEAENLVSCE 196 +G EY+LE + ADV+++K D GN ++ T +NFNP +A K + E E LV Sbjct: 138 DGKEYVLEEAIHADVSIVKAWKGDRLGNLVFRKTARNFNPMIATCGKLCVAEVEELVEVG 197 Query: 197 KLEKEKAMTPGVLINYIVKEPA 218 LE ++ PG+ ++ I++ P+ Sbjct: 198 TLEPDQVHVPGIYVDRIIQGPS 219 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: 237 Number of extensions: 13 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: 451 Length adjustment: 27 Effective length of query: 191 Effective length of database: 424 Effective search space: 80984 Effective search space used: 80984 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: 48 (23.1 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