Align 3-oxoadipate CoA-transferase subunit B; 3-oxoadipate:succinyl-CoA transferase subunit B; Beta-ketoadipate:succinyl-CoA transferase subunit B; EC 2.8.3.6 (characterized)
to candidate WP_011912436.1 PST_RS06385 CoA-transferase subunit beta
Query= SwissProt::Q8VPF2 (260 letters) >NCBI__GCF_000013785.1:WP_011912436.1 Length = 260 Score = 472 bits (1214), Expect = e-138 Identities = 235/260 (90%), Positives = 249/260 (95%) Query: 1 MSAYSTNEMMTVAAARRLKNGAVCFVGIGLPSKAANLARLTSSPDVVLIYESGPIGAKPT 60 MSAYSTNEMMTVAAARRL NG+VCFVGIGLPSKAANLARLT +P+VVLIYESGPIGAKP+ Sbjct: 1 MSAYSTNEMMTVAAARRLGNGSVCFVGIGLPSKAANLARLTHAPEVVLIYESGPIGAKPS 60 Query: 61 VLPLSIGDGELAETADTVVPTGEIFRYWLQGGRIDVGFLGAAQVDRFGNINTTVIGDYNK 120 VLPLSIGDGELAETADTVVPTGEIFRYWLQGGRIDVGFLGAAQVD++GNINTTVIGDY+K Sbjct: 61 VLPLSIGDGELAETADTVVPTGEIFRYWLQGGRIDVGFLGAAQVDKYGNINTTVIGDYHK 120 Query: 121 PKVRLPGAGGAPEIAGSAKEVLIILKQSHRTFVDKLAFITSVGHGEGGDHRKQLGLPGKG 180 PKVRLPGAGGAPEIAGSAKEVLIILKQSHRTFVDKLAFITSVG GEGG+HRKQLGLPGKG Sbjct: 121 PKVRLPGAGGAPEIAGSAKEVLIILKQSHRTFVDKLAFITSVGFGEGGEHRKQLGLPGKG 180 Query: 181 PVAIITDLCIMEPEAGSNEFIVTSLHPGVTREQVIENTGWAIRFAEQVKETAAPTEVELE 240 PVAIITDLCIMEPE G++EF+VT+LHPGVTREQV+ENTGWAIRFAEQV T AP EL+ Sbjct: 181 PVAIITDLCIMEPEVGTHEFVVTALHPGVTREQVVENTGWAIRFAEQVTTTEAPRAEELQ 240 Query: 241 ALRALEARTAAAHGQQGGEE 260 ALRALEARTAAAHGQ GGEE Sbjct: 241 ALRALEARTAAAHGQPGGEE 260 Lambda K H 0.316 0.135 0.389 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: 382 Number of extensions: 11 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: 260 Length of database: 260 Length adjustment: 24 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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: 47 (22.7 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