Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate WP_061532100.1 CAter10_RS02130 CoA transferase subunit B
Query= reanno::psRCH2:GFF1044 (209 letters) >NCBI__GCF_001584165.1:WP_061532100.1 Length = 213 Score = 236 bits (601), Expect = 3e-67 Identities = 115/206 (55%), Positives = 150/206 (72%), Gaps = 1/206 (0%) Query: 3 WTREQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEEEI 62 +TR+QMA R AQ++ +G YVNLGIGLPT VANY+P+ +++L SENGLLG+GP P E Sbjct: 4 FTRDQMAARVAQDIPEGAYVNLGIGLPTKVANYLPQEREIFLHSENGLLGMGPAPAPGEE 63 Query: 63 DPDLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMI-PGK 121 D DLINAGKQ VT L G ++F + SFAM+RGGH+++ +LGA QVS GDLANW Sbjct: 64 DEDLINAGKQPVTLLTGGAYFHHGDSFAMMRGGHLDICVLGAFQVSAGGDLANWHTGAAD 123 Query: 122 MVKGMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDVT 181 + +GGAMDL G K+V V+MEH K G KI+ C PLTG+ V+RI TDL VLDVT Sbjct: 124 AIPAVGGAMDLAIGAKQVFVMMEHQTKSGESKIVAHCTYPLTGIACVNRIYTDLAVLDVT 183 Query: 182 EQGLKLVELAEGVSFDELQEATGSPI 207 GL+++E+ EG++FDELQ+ T +P+ Sbjct: 184 PAGLRVLEMVEGLAFDELQKVTAAPL 209 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: 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: 213 Length adjustment: 21 Effective length of query: 188 Effective length of database: 192 Effective search space: 36096 Effective search space used: 36096 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