Align Butyrate--acetoacetate CoA-transferase subunit B; Short=Coat B; EC 2.8.3.9 (characterized, see rationale)
to candidate N515DRAFT_1736 N515DRAFT_1736 3-oxoacid CoA-transferase
Query= uniprot:P23673 (221 letters) >FitnessBrowser__Dyella79:N515DRAFT_1736 Length = 451 Score = 206 bits (525), Expect = 4e-58 Identities = 98/207 (47%), Positives = 146/207 (70%), Gaps = 2/207 (0%) Query: 12 IAKRVARELKNGQLVNLGVGLPTMVADYIPKNFKITFQSENGIVGMGASPKINEADKDVV 71 +A+R A+EL++G VNLG+G+PT+VA++IP +T QSENG++G+G P D D++ Sbjct: 244 MAQRAAKELRDGFYVNLGIGIPTLVANFIPAGIDVTLQSENGLLGIGPFPDDAHVDPDLI 303 Query: 72 NAGGDYTTVLPDGTFFDSSVSFSLIRGGHVDVTVLGALQVDEKGNIANWIVPGKMLSGMG 131 NAG T LP +FF S+ SF++IRGGH+D+++LG L+V G++ANW+VPGKM+ G G Sbjct: 304 NAGKQTITTLPGSSFFSSAESFAMIRGGHIDLSILGGLEVSCTGDLANWMVPGKMVKGPG 363 Query: 132 GAMDLVNGAKKVIIAMRHTNK-GQPKILKKCTLPLTAKSQANLIVTELGVIEV-INDGLL 189 GAMDLV+G K+V++ M HT K G PKI +C LPLT + +LI+T+L V EV GL Sbjct: 364 GAMDLVSGVKRVVVLMEHTAKDGSPKIKNQCDLPLTGQQVVDLIITDLCVFEVEKGKGLT 423 Query: 190 LTEINKNTTIDEIRSLTAADLLISNEL 216 L E+ + T++E+++ T D +++ L Sbjct: 424 LIELQEGVTVEEVKAKTGCDFAVASTL 450 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: 260 Number of extensions: 11 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: 221 Length of database: 451 Length adjustment: 27 Effective length of query: 194 Effective length of database: 424 Effective search space: 82256 Effective search space used: 82256 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: 48 (23.1 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