Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate CCNA_00207 CCNA_00207 succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B
Query= reanno::psRCH2:GFF1044 (209 letters) >FitnessBrowser__Caulo:CCNA_00207 Length = 213 Score = 291 bits (744), Expect = 8e-84 Identities = 145/205 (70%), Positives = 171/205 (83%), Gaps = 2/205 (0%) Query: 1 MAWTREQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEE 60 MAWTR+++A RAA+ELQDGFYVNLGIG+PTLVAN+IPEGM V LQSENG+LG+GPFP E Sbjct: 1 MAWTRDEVAARAAKELQDGFYVNLGIGIPTLVANHIPEGMHVTLQSENGMLGMGPFPYEG 60 Query: 61 EIDPDLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPG 120 E D DLINAGKQT+T L SS+F +A SFAMIRGGHI L+ILG MQVSE GDLANWM+PG Sbjct: 61 EEDADLINAGKQTITELDSSSYFSSADSFAMIRGGHIALSILGGMQVSENGDLANWMVPG 120 Query: 121 KMVKGMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDV 180 KMVKGMGGAMDLVAGVKRVVV+M+H K GA K+L C LPLTG GVVD +IT+LGV ++ Sbjct: 121 KMVKGMGGAMDLVAGVKRVVVVMDHCEKSGAPKLLKQCSLPLTGAGVVDLLITELGVFEI 180 Query: 181 T--EQGLKLVELAEGVSFDELQEAT 203 + +KL+ELA GV+ DE++ T Sbjct: 181 NRGKTPVKLIELAPGVTVDEVKAKT 205 Lambda K H 0.318 0.138 0.404 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: 235 Number of extensions: 7 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: 209 Length of database: 213 Length adjustment: 21 Effective length of query: 188 Effective length of database: 192 Effective search space: 36096 Effective search space used: 36096 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 (21.7 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