Align Butyrate--acetoacetate CoA-transferase subunit B; Short=Coat B; EC 2.8.3.9 (characterized, see rationale)
to candidate RR42_RS35920 RR42_RS35920 3-oxoadipate CoA-transferase
Query= uniprot:P23673 (221 letters) >FitnessBrowser__Cup4G11:RR42_RS35920 Length = 215 Score = 177 bits (449), Expect = 1e-49 Identities = 89/209 (42%), Positives = 138/209 (66%), Gaps = 4/209 (1%) Query: 5 KNLAKEIIAKRVARELKNGQLVNLGVGLPTMVADYIPKNFKITFQSENGIVGMGASPKIN 64 + L ++ +A RVA+++ +G +VNLG+GLPT+V +++P + +I SENG++GMG +P Sbjct: 2 QRLTRDQMAARVAKDIPDGAVVNLGIGLPTLVGNHLPADREILLHSENGLLGMGKAPPAG 61 Query: 65 EADKDVVNAGGDYTTVLPDGTFFDSSVSFSLIRGGHVDVTVLGALQVDEKGNIANWI--V 122 E D D++NAG T+ P G++F + SF+++RGGH+D VLGA QV KG++ANW Sbjct: 62 EEDGDLINAGKQPVTIKPGGSYFHHADSFAMMRGGHLDFCVLGAFQVSVKGDLANWHTGA 121 Query: 123 PGKMLSGMGGAMDLVNGAKKVIIAMRH-TNKGQPKILKKCTLPLTAKSQANLIVTELGVI 181 PG + +GGAMDL GAK+V + M H T +G+ KI+ +CT PLT + I T+L I Sbjct: 122 PG-AIPAVGGAMDLAIGAKEVFVMMEHQTKQGESKIVAECTYPLTGMTCVTRIYTDLATI 180 Query: 182 EVINDGLLLTEINKNTTIDEIRSLTAADL 210 +V DGL+ ++ + + DE++ LT L Sbjct: 181 DVTPDGLVARDLVEGLSFDELQRLTGVPL 209 Lambda K H 0.316 0.136 0.376 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: 167 Number of extensions: 4 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: 221 Length of database: 215 Length adjustment: 22 Effective length of query: 199 Effective length of database: 193 Effective search space: 38407 Effective search space used: 38407 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: 45 (21.9 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