Align Succinyl-CoA:3-ketoacid coenzyme A transferase subunit A; Succinyl-CoA:3-oxoacid CoA-transferase; OXCT A; EC 2.8.3.5 (characterized)
to candidate Echvi_3272 Echvi_3272 3-oxoacid CoA-transferase, A subunit
Query= SwissProt::P56006 (232 letters) >FitnessBrowser__Cola:Echvi_3272 Length = 230 Score = 284 bits (726), Expect = 1e-81 Identities = 131/229 (57%), Positives = 178/229 (77%) Query: 1 MNKVITDLDKALSALKDGDTILVGGFGLCGIPEYAIDYIYKKGIKDLIVVSNNCGVDDFG 60 +NK ++ ++A+ + +++GGFGLCGIPE ID + KK I L +SNN GVDDFG Sbjct: 2 INKTVSGAEEAVEDIPSNSVLMLGGFGLCGIPENCIDALLKKPISGLTCISNNAGVDDFG 61 Query: 61 LGILLEKKQIKKIIASYVGENKIFESQMLNGEIEVVLTPQGTLAENLHAGGAGIPAYYTP 120 +G++L+K+ +KK+I+SYVGEN FE Q+L+GE+EV L PQG+LAE AGGAGIPA++TP Sbjct: 62 IGLMLKKRMVKKMISSYVGENAEFERQLLSGELEVELIPQGSLAERTRAGGAGIPAFFTP 121 Query: 121 TGVGTLIAQGKESREFNGKEYILERAITGDYGLIKAYKSDTLGNLVFRKTARNFNPLCAM 180 GVGT +A+GKE REF+GK YILER + D+ L+KA+K DT GNL+++ TARNFNP+ A Sbjct: 122 AGVGTEVAEGKEMREFDGKLYILERWLKADFSLVKAWKGDTAGNLIYKGTARNFNPMMAT 181 Query: 181 AAKICVAEVEEIVPAGELDPDEIHLPGIYVQHIYKGEKFEKRIEKITTR 229 A I +AEVEE+VPAG LDP++IH PGI+VQ I++G+ +EKRIEK T + Sbjct: 182 AGTITIAEVEELVPAGTLDPNQIHTPGIFVQRIFQGDHYEKRIEKRTVK 230 Lambda K H 0.317 0.140 0.400 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: 218 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: 232 Length of database: 230 Length adjustment: 23 Effective length of query: 209 Effective length of database: 207 Effective search space: 43263 Effective search space used: 43263 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: 41 (21.6 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