Align Butyrate--acetoacetate CoA-transferase subunit A; Short=Coat A; EC 2.8.3.9 (characterized, see rationale)
to candidate WP_058929519.1 AU252_RS03415 CoA transferase subunit A
Query= uniprot:P33752 (218 letters) >NCBI__GCF_001484605.1:WP_058929519.1 Length = 264 Score = 145 bits (366), Expect = 7e-40 Identities = 80/236 (33%), Positives = 123/236 (52%), Gaps = 18/236 (7%) Query: 1 MNSKIIRFENLRSFFKDGMTIMIGGFLNCGTPTKLIDFLVNLNIKNLTIISNDTCYPNTG 60 +N + E + DG ++ +GGF CG P LID L K+L +SN+ + G Sbjct: 2 INKVVASAEEAIADIPDGASLAVGGFGLCGIPVALIDALHRHGTKDLETVSNNCGVDDWG 61 Query: 61 IGKLISNNQVKKLIASYIGSNPDTGKKLFNNELEVELSPQGTLVERIRAGGSGLGGVLTK 120 +G L+ + ++++ ++SY+G N + ++ + ELEV L+PQGTL E++RAGG+G+ TK Sbjct: 62 LGVLLRDGRIRRTVSSYVGENKEFARQYLSGELEVVLTPQGTLAEKLRAGGAGIPAFYTK 121 Query: 121 TGLGTLIEKG------------------KKKISINGTEYLLELPLTADVALIKGSIVDEA 162 G+GT + G K+ + + +Y+LE LT D L+ D Sbjct: 122 AGVGTQVSDGGLPQKYDAHGGIAIASSPKEVRTFHDVDYVLEESLTPDYGLVHAWKGDRH 181 Query: 163 GNTFYKGTTKNFNPYMAMAAKTVIVEAENLVSCEKLEKEKAMTPGVLINYIVKEPA 218 GN + T NFNP AMA K I E E LV +L+ E TPG+ + +V PA Sbjct: 182 GNLVFHATAMNFNPLCAMAGKITIAEVEELVEPGELDPEHVHTPGIFVQRVVVVPA 237 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: 139 Number of extensions: 9 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: 264 Length adjustment: 23 Effective length of query: 195 Effective length of database: 241 Effective search space: 46995 Effective search space used: 46995 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 Apr 09 2024. 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