Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate WP_110206713.1 DNK54_RS09440 3-oxoacid CoA-transferase subunit B
Query= reanno::psRCH2:GFF1044 (209 letters) >NCBI__GCF_003194585.1:WP_110206713.1 Length = 236 Score = 184 bits (468), Expect = 9e-52 Identities = 93/206 (45%), Positives = 140/206 (67%), Gaps = 4/206 (1%) Query: 4 TREQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEEEID 63 T +++A+ A+++ +G ++NLGIG PT +A+++P + V L +ENG+LG+GP ++ID Sbjct: 29 TMDELAEVIARDIPEGSFLNLGIGQPTKIADHLPAELGVILHTENGMLGMGPAADGDQID 88 Query: 64 PDLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPGK-- 121 PDL NAGK VT LPG+S+F +A SFAM+RGGH+++ +LGA QV+ GDLANW GK Sbjct: 89 PDLTNAGKVPVTELPGASYFHHADSFAMMRGGHLDVCVLGAYQVAANGDLANWH-TGKPD 147 Query: 122 MVKGMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDVT 181 + +GGAMDL G K V+V+M K G K++ +C PLTG+G V R+ TD G+ +V Sbjct: 148 AIPAVGGAMDLAIGAKDVLVMMTLFGKDGTPKLVRSCSYPLTGVGCVSRVYTDHGIFEVG 207 Query: 182 EQGLKLVELAEGVSFDELQEATGSPI 207 + + +V G+S +L+E G P+ Sbjct: 208 GESV-VVRATWGISVADLEERLGMPL 232 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: 182 Number of extensions: 12 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: 236 Length adjustment: 22 Effective length of query: 187 Effective length of database: 214 Effective search space: 40018 Effective search space used: 40018 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