Align Butyrate--acetoacetate CoA-transferase subunit B; Short=Coat B; EC 2.8.3.9 (characterized, see rationale)
to candidate Ac3H11_131 Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B (EC 2.8.3.5)
Query= uniprot:P23673 (221 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_131 Length = 212 Score = 179 bits (453), Expect = 5e-50 Identities = 89/205 (43%), Positives = 136/205 (66%), Gaps = 6/205 (2%) Query: 12 IAKRVARELKNGQLVNLGVGLPTMVADYIPKNFKITFQSENGIVGMGASPKINEADKDVV 71 +A R A+EL++G VNLG+G+PT+VA++ ++ QSENG++G+G P ++ D D++ Sbjct: 8 MAARAAQELEDGFYVNLGIGIPTLVANFTGDK-EVWLQSENGMLGIGPFPTEDKVDPDLI 66 Query: 72 NAGGDYTTVLPDGTFFDSSVSFSLIRGGHVDVTVLGALQVDEKGNIANWIVPGKMLSGMG 131 NAG T + + F S SF++IRGG +++++LGA+QV EKG++ANW++PGKM+ GMG Sbjct: 67 NAGKQTVTTIKGSSIFGSDQSFAMIRGGKINLSILGAMQVSEKGDLANWMIPGKMVKGMG 126 Query: 132 GAMDLVNGAKKVIIAMRHTNKGQP-----KILKKCTLPLTAKSQANLIVTELGVIEVIND 186 GAMDLV G K+VI+ M H K + KIL CTLPLT + I+T+L V++V Sbjct: 127 GAMDLVAGVKRVIVLMEHVAKKKDGTEDLKILPACTLPLTGVGVVDRIITDLAVLDVTPH 186 Query: 187 GLLLTEINKNTTIDEIRSLTAADLL 211 GL L E+ T + +++ T L+ Sbjct: 187 GLKLVELAPGVTFEALQAKTGVTLI 211 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: 172 Number of extensions: 6 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: 212 Length adjustment: 22 Effective length of query: 199 Effective length of database: 190 Effective search space: 37810 Effective search space used: 37810 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