Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate WP_012541879.1 KVAR_RS13985 CoA transferase subunit B
Query= reanno::psRCH2:GFF1044 (209 letters) >NCBI__GCF_000025465.1:WP_012541879.1 Length = 218 Score = 217 bits (553), Expect = 1e-61 Identities = 105/201 (52%), Positives = 143/201 (71%), Gaps = 1/201 (0%) Query: 4 TREQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEEEID 63 TR++MAQR A+++ +G YVNLGIGLPT +ANY+P +V+L SENGLLG+GP P E D Sbjct: 5 TRDEMAQRVARDIPEGAYVNLGIGLPTRIANYLPADKEVFLHSENGLLGMGPKPQPGEED 64 Query: 64 PDLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPG-KM 122 P+LINAGK+ VT L G +F + SFAM+RGGH+++ +LGA QVS GDLANW Sbjct: 65 PELINAGKEYVTLLQGGCYFHHGDSFAMMRGGHLDICVLGAYQVSASGDLANWSTGAPDA 124 Query: 123 VKGMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDVTE 182 + +GGAMDL G ++V V+M+H + G K++ C PLTG+G V RI TDL V+D+T+ Sbjct: 125 IPAVGGAMDLAIGARQVFVMMDHLTRDGECKLVAQCSYPLTGVGCVSRIYTDLAVIDITD 184 Query: 183 QGLKLVELAEGVSFDELQEAT 203 +G + E+ G+SF+ELQ T Sbjct: 185 RGPVVREIFNGLSFEELQRIT 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: 177 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: 218 Length adjustment: 22 Effective length of query: 187 Effective length of database: 196 Effective search space: 36652 Effective search space used: 36652 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 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