Align acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized)
to candidate WP_042453492.1 C1M55_RS06025 CoA transferase subunit A
Query= reanno::psRCH2:GFF1045 (231 letters) >NCBI__GCF_002893965.1:WP_042453492.1 Length = 251 Score = 256 bits (653), Expect = 4e-73 Identities = 135/244 (55%), Positives = 166/244 (68%), Gaps = 19/244 (7%) Query: 4 IYPSAAHALEGLVEDGMTIAVGGFGLCGIPEQLIAALRDSGKKDLTAISNNAGVDGFGLG 63 +Y SAA A+ +V DG T+AVGGFGLCGIP+ LI A+ + L SNN GVD GLG Sbjct: 1 MYESAAEAVADIV-DGATLAVGGFGLCGIPDVLIDAIAATSATHLEVFSNNCGVDDHGLG 59 Query: 64 LLLETRQISKMVSSYVGENKEFERQYLAGELALEFTPQGTLAEKLRAGGAGIPAFYTKTG 123 +LL +I ++ +SYVGENKEF RQYLAGEL +E TPQGTLAE+LRAGG GIPAF+T G Sbjct: 60 ILLSAGRIRRVTASYVGENKEFARQYLAGELEVELTPQGTLAERLRAGGTGIPAFFTPAG 119 Query: 124 YGTLVAEG------------------KETRQFNGEWYVMEESLTADLALVKAWKADKAGN 165 G+ +++G KETR F + YVMEE++ AD ALV A D GN Sbjct: 120 VGSPISDGGMPWRYDADGSIAIASPPKETRVFGTKRYVMEEAINADYALVHAVLGDTDGN 179 Query: 166 LLFRKTARNFNPLAAMAGEVCVVEVEEIVETGELDPDQIHLPGIYVHRIVHNPNPEKRIE 225 L+F KTA NFNPLAAMAG V + +VE +VE GE+DP +HLPG++V R+VH KRIE Sbjct: 180 LVFDKTAMNFNPLAAMAGRVTIAQVERLVEPGEIDPASVHLPGVFVQRVVHTGPQNKRIE 239 Query: 226 KRTV 229 KRTV Sbjct: 240 KRTV 243 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: 196 Number of extensions: 8 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: 231 Length of database: 251 Length adjustment: 23 Effective length of query: 208 Effective length of database: 228 Effective search space: 47424 Effective search space used: 47424 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