Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate WP_092345283.1 BLU87_RS04910 succinyl-CoA--3-ketoacid-CoA transferase
Query= reanno::psRCH2:GFF1044 (209 letters) >NCBI__GCF_900107645.1:WP_092345283.1 Length = 452 Score = 265 bits (677), Expect = 1e-75 Identities = 126/203 (62%), Positives = 163/203 (80%), Gaps = 1/203 (0%) Query: 5 REQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEEEIDP 64 RE A+R ++E ++G Y NLGIG+PTLVANYIPE + V L +ENGLLG+GPFP E+ ID Sbjct: 242 REWQAKRISKEFKNGMYANLGIGMPTLVANYIPEEITVTLHAENGLLGVGPFPDEDSIDA 301 Query: 65 DLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPGKMVK 124 DLINAGKQT+T LPG++FFD+++SFAM+RGGHI+L++LGAMQVS+ GDLANWMIPG MVK Sbjct: 302 DLINAGKQTITWLPGAAFFDSSESFAMVRGGHIDLSVLGAMQVSQFGDLANWMIPGSMVK 361 Query: 125 GMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDV-TEQ 183 G GGAMDLV+GVK+++++M+H AK G K++ C LPLTG VVD ++TDL V V E+ Sbjct: 362 GPGGAMDLVSGVKKIIIMMDHCAKDGTSKLMEQCTLPLTGKNVVDMVVTDLAVFKVDAEK 421 Query: 184 GLKLVELAEGVSFDELQEATGSP 206 GL L ELA G + + ++E TG P Sbjct: 422 GLTLTELAPGSTLEMVKEKTGCP 444 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: 339 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: 209 Length of database: 452 Length adjustment: 27 Effective length of query: 182 Effective length of database: 425 Effective search space: 77350 Effective search space used: 77350 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 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