Align Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit A (characterized)
to candidate CA265_RS06305 CA265_RS06305 succinyl-CoA--3-ketoacid-CoA transferase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2111 (232 letters) >FitnessBrowser__Pedo557:CA265_RS06305 Length = 234 Score = 289 bits (740), Expect = 3e-83 Identities = 141/229 (61%), Positives = 178/229 (77%), Gaps = 1/229 (0%) Query: 5 DKRVSSYEEALEGLKDGMTVIAGGFGLCGIPENLIAEIKRKGIRDLTVVSNNCGVDGFGL 64 +K VS EEA++ + DG+T++ GGFGLCGIPEN I + K +++LT +SNN GVD FG+ Sbjct: 3 NKVVSGAEEAIKDISDGVTLMLGGFGLCGIPENCIKALVNKQVKNLTCISNNAGVDDFGI 62 Query: 65 GVLLEDRQIRKVVASYVGENALFEQQLLSGEIEVVLTPQGTLAEKMRAGGAGIPAFFTAT 124 G++L+ RQ++K+++SYVGENA FE+QLLSGE+EV L PQGTLA + A G G+PA FT Sbjct: 63 GLMLKQRQVKKMISSYVGENAEFERQLLSGELEVDLIPQGTLATRCLAAGYGMPAIFTPA 122 Query: 125 GVGTPVAEGKEVREFHGRQYLMEESITGDFAIVKGWKADHFGNVIYRHTAQNFNPLAATA 184 GVGT VAEGKE+R F G+ YLME + DFAIVK WK D GN+I+R T++NFNP+ A A Sbjct: 123 GVGTEVAEGKEIRNFDGKDYLMEYAFDADFAIVKAWKGDTAGNLIFRSTSRNFNPVMAMA 182 Query: 185 GKITVVEVEEIVEPGELDPTQIHTPGIYVDRVICG-TFEKRIEQRTVRK 232 GKIT+ EVEE+VE GELDP IHTPGIYV R+ G +EKRIEQRTVRK Sbjct: 183 GKITIAEVEELVEAGELDPDYIHTPGIYVHRIFQGKDYEKRIEQRTVRK 231 Lambda K H 0.319 0.139 0.403 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: 226 Number of extensions: 4 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: 232 Length of database: 234 Length adjustment: 23 Effective length of query: 209 Effective length of database: 211 Effective search space: 44099 Effective search space used: 44099 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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