Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate WP_082679266.1 V473_RS20815 CoA transferase subunit A
Query= CharProtDB::CH_021928 (231 letters) >NCBI__GCF_001046645.1:WP_082679266.1 Length = 239 Score = 206 bits (524), Expect = 3e-58 Identities = 108/215 (50%), Positives = 144/215 (66%), Gaps = 3/215 (1%) Query: 4 KTYESIASAVEGIT-DGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEIGL 62 K + +A+ G+ DG TIM GGFG +G P LI GL+ + R+LTIISNN G GL Sbjct: 5 KIFPDAGAALSGVLFDGMTIMSGGFGLSGNPEHLIAGLLHSAVRELTIISNNCGADGFGL 64 Query: 63 AALLMAGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAFFS 122 LL G +RK+V S+ ++ +F ELY AGK++LE+ PQG LAERI A G+GI AF++ Sbjct: 65 WTLLNNGQIRKMVSSYI--GENKLFAELYLAGKLDLELNPQGTLAERIRAGGAGIPAFYT 122 Query: 123 PTGYGTLLAEGKETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPIMA 182 TG GT++AEGK E +G +YV E L AD +++KA K D GNL YRK ARNF P MA Sbjct: 123 KTGVGTVVAEGKPVEEFEGALYVRETWLRADLSIVKAWKADPEGNLVYRKTARNFNPNMA 182 Query: 183 MAAKTAIAQVDQVVELGELDPEHIITPGIFVQRVV 217 A K IA+V+++V G LDP+ + TPGI+V R++ Sbjct: 183 TAGKITIAEVEEIVPAGALDPDQVHTPGIYVDRII 217 Lambda K H 0.318 0.135 0.381 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: 155 Number of extensions: 8 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: 231 Length of database: 239 Length adjustment: 23 Effective length of query: 208 Effective length of database: 216 Effective search space: 44928 Effective search space used: 44928 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 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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