Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_014026891.1 PYRFU_RS06655 acetyl-CoA C-acyltransferase
Query= BRENDA::B1YB71 (392 letters) >NCBI__GCF_000223395.1:WP_014026891.1 Length = 401 Score = 410 bits (1053), Expect = e-119 Identities = 221/395 (55%), Positives = 277/395 (70%), Gaps = 5/395 (1%) Query: 3 VVVVGYVRTPIGKFGGAFKDVKPPHLAAFTIKKLLERTGVDGKLVEEVIFGSTLQGGVGQ 62 V +V VRTPIGKFGG F ++ P LAA I+ +ER G+ K V+ + G +QGGVGQ Sbjct: 7 VYIVSAVRTPIGKFGGVFANIPAPDLAAHAIRAAVERAGLAPKDVQAYVMGHVIQGGVGQ 66 Query: 63 NVARYAALLAGLPVDVSAFTVNRVCSSGMQAIIEAYREIALGDASVVIAGGVESMSTQPI 122 + AR AALLAG+P V+ F VN VCSSGM AI EA R I LG+ +V+AGG+ESMS PI Sbjct: 67 HSARRAALLAGIPEKVNGFVVNMVCSSGMLAIWEAVRMIKLGEYDIVLAGGMESMSRAPI 126 Query: 123 CVSHEARWGLRHSIGRRFELTDLMVFDGLTDPATGMLMGEEADMVAKEHKIAREELDKVA 182 + EARWGLRH I R +L DLM DGLTD +MG EAD VA E+ REELD +A Sbjct: 127 ALPPEARWGLRHLITREAKLIDLMAHDGLTDSWNWKMMGVEADEVAWENNAPREELDMIA 186 Query: 183 YESHMRAWRATENKWF-DDMEPVEGEF---GGVKLDRDEGIRPDTSLEKLAKLKPAFKPD 238 YESHMRA +AT+ WF +++ PVE E G V ++ DEGIR DTS EKLA+L PAF P Sbjct: 187 YESHMRAAKATDEGWFREEIVPVEVEIPKKGRVTVESDEGIRRDTSPEKLARLPPAFTPK 246 Query: 239 GLHTAGNSSQLSDGAAALLLMSEEKARELGVKPIARILGYSWHMLEPWRFTEAPVYAIQK 298 G HTAGNSSQLSDGAAAL+L S + +ELG+KP+A+++G++W + P +F V A + Sbjct: 247 GPHTAGNSSQLSDGAAALILASGKVVKELGLKPLAKVVGFAWVGIRPEKFVYGTVEAAKA 306 Query: 299 LLRKLGVSVDYFDYYEANEAFAVVNVLVNRVL-GVPYDRMNVFGGAIALGHPLGASGTRI 357 LL K+G + D++EANEAFA+ L R VP +R+N GGAIALGHPLG +G RI Sbjct: 307 LLDKIGWKPEDVDFWEANEAFAINIWLFYRAFPQVPKERVNPHGGAIALGHPLGCTGARI 366 Query: 358 VTTLISVLRRMGGRRGVAALCHGTGGGTAVALELI 392 V TLI LRR GG+RG+A LCHGTGGGTA+A+E++ Sbjct: 367 VVTLIHALRRHGGKRGIATLCHGTGGGTALAVEIV 401 Lambda K H 0.320 0.138 0.406 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: 486 Number of extensions: 20 Number of successful extensions: 3 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: 392 Length of database: 401 Length adjustment: 31 Effective length of query: 361 Effective length of database: 370 Effective search space: 133570 Effective search space used: 133570 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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