Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate WP_058929519.1 AU252_RS03415 CoA transferase subunit A
Query= CharProtDB::CH_021928 (231 letters) >NCBI__GCF_001484605.1:WP_058929519.1 Length = 264 Score = 187 bits (476), Expect = 1e-52 Identities = 104/237 (43%), Positives = 139/237 (58%), Gaps = 20/237 (8%) Query: 1 MINKTYESIASAVEGITDGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEI 60 MINK S A+ I DG+++ VGGFG G+P LID L G +DL +SNN G + Sbjct: 1 MINKVVASAEEAIADIPDGASLAVGGFGLCGIPVALIDALHRHGTKDLETVSNNCGVDDW 60 Query: 61 GLAALLMAGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAF 120 GL LL G +R+ V S+ ++ F Y +G++E+ + PQG LAE++ A G+GI AF Sbjct: 61 GLGVLLRDGRIRRTVSSYVGENKE--FARQYLSGELEVVLTPQGTLAEKLRAGGAGIPAF 118 Query: 121 FSPTGYGTLLAEG------------------KETREIDGRMYVLEMPLHADFALIKAHKG 162 ++ G GT +++G KE R YVLE L D+ L+ A KG Sbjct: 119 YTKAGVGTQVSDGGLPQKYDAHGGIAIASSPKEVRTFHDVDYVLEESLTPDYGLVHAWKG 178 Query: 163 DRWGNLTYRKAARNFGPIMAMAAKTAIAQVDQVVELGELDPEHIITPGIFVQRVVAV 219 DR GNL + A NF P+ AMA K IA+V+++VE GELDPEH+ TPGIFVQRVV V Sbjct: 179 DRHGNLVFHATAMNFNPLCAMAGKITIAEVEELVEPGELDPEHVHTPGIFVQRVVVV 235 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: 148 Number of extensions: 9 Number of successful extensions: 3 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: 264 Length adjustment: 24 Effective length of query: 207 Effective length of database: 240 Effective search space: 49680 Effective search space used: 49680 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 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