Align Butyrate--acetoacetate CoA-transferase subunit B; Short=Coat B; EC 2.8.3.9 (characterized, see rationale)
to candidate WP_061533759.1 CAter10_RS13185 CoA transferase subunit B
Query= uniprot:P23673 (221 letters) >NCBI__GCF_001584165.1:WP_061533759.1 Length = 217 Score = 187 bits (476), Expect = 1e-52 Identities = 90/210 (42%), Positives = 140/210 (66%), Gaps = 5/210 (2%) Query: 9 KEIIAKRVARELKNGQLVNLGVGLPTMVADYIPKNFKITFQSENGIVGMGASPKINEADK 68 ++ +A R A+EL++G VNLG+GLPT+VA+++P+ ++ QSENG++G+G P + D Sbjct: 5 RDEMAARAAKELQDGFYVNLGIGLPTLVANHVPQEIEVWLQSENGLLGIGPFPTDDAVDP 64 Query: 69 DVVNAGGDYTTVLPDGTFFDSSVSFSLIRGGHVDVTVLGALQVDEKGNIANWIVPGKMLS 128 D++NAG T LP ++F S+ SF++IRGG +++ +LGA+QV + G++ANW++PGKM+ Sbjct: 65 DLINAGKQTVTSLPGSSYFSSADSFAMIRGGKINIAILGAMQVSKNGDLANWMIPGKMVK 124 Query: 129 GMGGAMDLVNGAKKVIIAMRHTNKGQP-----KILKKCTLPLTAKSQANLIVTELGVIEV 183 GMGGAMDLV G +V++ M H K + KIL C+LPLT N I+T+LGV++V Sbjct: 125 GMGGAMDLVAGVGRVVVLMEHVAKAKDGSTSHKILDACSLPLTGVGVVNRIITDLGVLDV 184 Query: 184 INDGLLLTEINKNTTIDEIRSLTAADLLIS 213 GL + E+ + +I T L +S Sbjct: 185 TPQGLKVIELAPGVSQQDIIEQTGTPLDVS 214 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: 178 Number of extensions: 9 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: 217 Length adjustment: 22 Effective length of query: 199 Effective length of database: 195 Effective search space: 38805 Effective search space used: 38805 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 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