Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate Ac3H11_131 Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B (EC 2.8.3.5)
Query= reanno::psRCH2:GFF1044 (209 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_131 Length = 212 Score = 315 bits (806), Expect = 5e-91 Identities = 162/208 (77%), Positives = 180/208 (86%), Gaps = 5/208 (2%) Query: 1 MAWTREQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEE 60 M WT++QMA RAAQEL+DGFYVNLGIG+PTLVAN+ + +VWLQSENG+LGIGPFPTE+ Sbjct: 1 MPWTQDQMAARAAQELEDGFYVNLGIGIPTLVANFTGD-KEVWLQSENGMLGIGPFPTED 59 Query: 61 EIDPDLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPG 120 ++DPDLINAGKQTVT + GSS F + QSFAMIRGG INL+ILGAMQVSEKGDLANWMIPG Sbjct: 60 KVDPDLINAGKQTVTTIKGSSIFGSDQSFAMIRGGKINLSILGAMQVSEKGDLANWMIPG 119 Query: 121 KMVKGMGGAMDLVAGVKRVVVLMEHTA--KGGAH--KILPACDLPLTGLGVVDRIITDLG 176 KMVKGMGGAMDLVAGVKRV+VLMEH A K G KILPAC LPLTG+GVVDRIITDL Sbjct: 120 KMVKGMGGAMDLVAGVKRVIVLMEHVAKKKDGTEDLKILPACTLPLTGVGVVDRIITDLA 179 Query: 177 VLDVTEQGLKLVELAEGVSFDELQEATG 204 VLDVT GLKLVELA GV+F+ LQ TG Sbjct: 180 VLDVTPHGLKLVELAPGVTFEALQAKTG 207 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: 258 Number of extensions: 7 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: 209 Length of database: 212 Length adjustment: 21 Effective length of query: 188 Effective length of database: 191 Effective search space: 35908 Effective search space used: 35908 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