Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate RR42_RS22965 RR42_RS22965 3-oxoadipate CoA-transferase
Query= reanno::psRCH2:GFF1044 (209 letters) >FitnessBrowser__Cup4G11:RR42_RS22965 Length = 211 Score = 207 bits (528), Expect = 9e-59 Identities = 108/202 (53%), Positives = 139/202 (68%), Gaps = 1/202 (0%) Query: 3 WTREQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEEEI 62 W REQ+A+ AAQ+++ G YVNLGIGLPTLV + +P +V+L SENG+L +GP P Sbjct: 4 WNREQIARHAAQDIRPGAYVNLGIGLPTLVGDMLPREREVFLHSENGILHLGPRPPLGHE 63 Query: 63 DPDLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMI-PGK 121 +PDLINA KQ VT PG++ FD+A SFAM+RGGH++LAILGA +V+E GDLANW Sbjct: 64 NPDLINASKQPVTLQPGAAIFDSALSFAMMRGGHLDLAILGAYEVAENGDLANWSRGDPN 123 Query: 122 MVKGMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDVT 181 +GGAM+L G + V VLMEHT + ++L C LPLT GVV RI TDL V+ VT Sbjct: 124 TPPAVGGAMELAFGAREVWVLMEHTTRDARPRLLHRCTLPLTASGVVSRIYTDLAVMHVT 183 Query: 182 EQGLKLVELAEGVSFDELQEAT 203 GL + +AEG++ ELQ T Sbjct: 184 PDGLLVEAMAEGMTLGELQALT 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: 157 Number of extensions: 5 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: 211 Length adjustment: 21 Effective length of query: 188 Effective length of database: 190 Effective search space: 35720 Effective search space used: 35720 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