Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate N515DRAFT_1736 N515DRAFT_1736 3-oxoacid CoA-transferase
Query= reanno::psRCH2:GFF1044 (209 letters) >FitnessBrowser__Dyella79:N515DRAFT_1736 Length = 451 Score = 289 bits (740), Expect = 5e-83 Identities = 146/201 (72%), Positives = 171/201 (85%), Gaps = 1/201 (0%) Query: 5 REQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEEEIDP 64 R MAQRAA+EL+DGFYVNLGIG+PTLVAN+IP G+DV LQSENGLLGIGPFP + +DP Sbjct: 241 RTAMAQRAAKELRDGFYVNLGIGIPTLVANFIPAGIDVTLQSENGLLGIGPFPDDAHVDP 300 Query: 65 DLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPGKMVK 124 DLINAGKQT+T LPGSSFF +A+SFAMIRGGHI+L+ILG ++VS GDLANWM+PGKMVK Sbjct: 301 DLINAGKQTITTLPGSSFFSSAESFAMIRGGHIDLSILGGLEVSCTGDLANWMVPGKMVK 360 Query: 125 GMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDVTE-Q 183 G GGAMDLV+GVKRVVVLMEHTAK G+ KI CDLPLTG VVD IITDL V +V + + Sbjct: 361 GPGGAMDLVSGVKRVVVLMEHTAKDGSPKIKNQCDLPLTGQQVVDLIITDLCVFEVEKGK 420 Query: 184 GLKLVELAEGVSFDELQEATG 204 GL L+EL EGV+ +E++ TG Sbjct: 421 GLTLIELQEGVTVEEVKAKTG 441 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: 357 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: 209 Length of database: 451 Length adjustment: 27 Effective length of query: 182 Effective length of database: 424 Effective search space: 77168 Effective search space used: 77168 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: 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