Align Butyrate--acetoacetate CoA-transferase subunit A; Short=Coat A; EC 2.8.3.9 (characterized, see rationale)
to candidate 6936329 Sama_0518 3-oxoacid CoA-transferase (RefSeq)
Query= uniprot:P33752 (218 letters) >FitnessBrowser__SB2B:6936329 Length = 253 Score = 169 bits (427), Expect = 6e-47 Identities = 81/215 (37%), Positives = 131/215 (60%) Query: 1 MNSKIIRFENLRSFFKDGMTIMIGGFLNCGTPTKLIDFLVNLNIKNLTIISNDTCYPNTG 60 +N + + + +DGMT++ GGF CG P LI + +NLT++SN+ G Sbjct: 20 LNKVVTSYAQALAGLEDGMTVIAGGFGLCGIPENLIKEIKRKGTRNLTVVSNNCGTTEYG 79 Query: 61 IGKLISNNQVKKLIASYIGSNPDTGKKLFNNELEVELSPQGTLVERIRAGGSGLGGVLTK 120 +G L+ + Q+KK++ASY+G N + ++ + ELEVEL+PQGTL E++RA G+G+ T Sbjct: 80 LGILLLDKQIKKMVASYVGENTNFEAQMMSGELEVELTPQGTLAEKMRAAGAGIPAFYTA 139 Query: 121 TGLGTLIEKGKKKISINGTEYLLELPLTADVALIKGSIVDEAGNTFYKGTTKNFNPYMAM 180 TG GT + GK+ NG +Y+LE + D AL+K D GN ++ T +NFNP AM Sbjct: 140 TGFGTEVAVGKEVKEFNGRQYILEESIKGDFALVKAWKADTYGNLVFRKTARNFNPLAAM 199 Query: 181 AAKTVIVEAENLVSCEKLEKEKAMTPGVLINYIVK 215 A K +VE E +V+ +L+ ++ TPG+ ++ +++ Sbjct: 200 AGKITVVEVEQIVAPGELDPDEIHTPGIYVDRLIQ 234 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: 159 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: 218 Length of database: 253 Length adjustment: 23 Effective length of query: 195 Effective length of database: 230 Effective search space: 44850 Effective search space used: 44850 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