Align acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized)
to candidate WP_108357971.1 B9Z44_RS03445 3-oxoacid CoA-transferase subunit A
Query= reanno::psRCH2:GFF1045 (231 letters) >NCBI__GCF_003063475.1:WP_108357971.1 Length = 242 Score = 193 bits (490), Expect = 3e-54 Identities = 108/229 (47%), Positives = 146/229 (63%), Gaps = 12/229 (5%) Query: 1 MNKIYPSAAHALEGLVEDGMTIAVGGFGLCGIPEQL----IAALRDSGKKDLTAISNNAG 56 +NK+ S A AL+GL DGMT+ VGGFG GIP +L I + D + LT ++NNAG Sbjct: 2 INKVADSMAQALQGLT-DGMTVMVGGFGTAGIPSELLDGLIEVIHDRQVRGLTVVNNNAG 60 Query: 57 VDGFGLGLLLETRQISKMVSSYV--GENKEFERQYLAGELALEFTPQGTLAEKLRAGGAG 114 GL LL+T + K++ S+ ++ F+ Y AG+L LE PQG L+E++RA GAG Sbjct: 61 NGDTGLAALLKTGCVRKIICSFPRQADSHVFDGLYRAGKLELELVPQGNLSERIRAAGAG 120 Query: 115 IPAFYTKTGYGTLVAE-----GKETRQFNGEWYVMEESLTADLALVKAWKADKAGNLLFR 169 I AF+T TGYGT +A+ KETR+ +G YV+E + ADLAL+KA K D+ GNL +R Sbjct: 121 IGAFFTPTGYGTDLAKYPDGSPKETREIHGRMYVLEYPIHADLALIKAEKGDRWGNLTYR 180 Query: 170 KTARNFNPLAAMAGEVCVVEVEEIVETGELDPDQIHLPGIYVHRIVHNP 218 K+ARNF P+ A A + V V E+V+ G LDP+ I PGIYV +V P Sbjct: 181 KSARNFGPVMAAAAKRTVASVHEVVDLGALDPESIVTPGIYVSHVVQVP 229 Lambda K H 0.316 0.135 0.391 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: 10 Number of successful extensions: 4 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: 231 Length of database: 242 Length adjustment: 23 Effective length of query: 208 Effective length of database: 219 Effective search space: 45552 Effective search space used: 45552 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 (21.6 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