Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate WP_058929518.1 AU252_RS03410 CoA transferase subunit B
Query= reanno::psRCH2:GFF1044 (209 letters) >NCBI__GCF_001484605.1:WP_058929518.1 Length = 255 Score = 265 bits (678), Expect = 4e-76 Identities = 127/209 (60%), Positives = 164/209 (78%), Gaps = 4/209 (1%) Query: 3 WTREQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEEEI 62 WTR ++A R A+EL +G YVNLGIG+PTL+ NYIP ++V L SENG+LG+GP+P+E+ + Sbjct: 38 WTRNELAARVARELSNGQYVNLGIGMPTLIPNYIPASVEVVLHSENGILGVGPYPSEDAV 97 Query: 63 DPDLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPGKM 122 DPDLINAGK+TVT G++FFD+A SF MIRGGH+++A+LGAM+V++ GDLANWMIPGKM Sbjct: 98 DPDLINAGKETVTVNKGAAFFDSASSFGMIRGGHVDVAVLGAMEVAQNGDLANWMIPGKM 157 Query: 123 VKGMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDVTE 182 VKGMGGAMDLV G K+V+V+MEH + G KI+ C LPLTG VDRIITDL V+DV Sbjct: 158 VKGMGGAMDLVFGAKKVIVMMEHVDRNGNPKIVEHCSLPLTGKACVDRIITDLAVIDVVT 217 Query: 183 QG----LKLVELAEGVSFDELQEATGSPI 207 +G L L ELA VS +++ ATG+ + Sbjct: 218 EGGRSRLVLRELAPNVSVEDVAAATGAEL 246 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: 222 Number of extensions: 6 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: 255 Length adjustment: 23 Effective length of query: 186 Effective length of database: 232 Effective search space: 43152 Effective search space used: 43152 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: 46 (22.3 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