Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_012046883.1 BBTA_RS33130 acetyl-CoA C-acyltransferase
Query= BRENDA::Q8VCH0 (424 letters) >NCBI__GCF_000015165.1:WP_012046883.1 Length = 395 Score = 293 bits (751), Expect = 5e-84 Identities = 172/394 (43%), Positives = 248/394 (62%), Gaps = 12/394 (3%) Query: 36 SDVVVVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDVKLKPEQLGDISVGNVLQPG 95 +D V+V RTPIG+A RG T LL + ++ K+ P ++ D+ +G LQ G Sbjct: 2 TDAVIVSTARTPIGKAYRGALNATGGATLLGHAIGEAVKRAKVDPAEVEDVVMGAALQQG 61 Query: 96 A-GAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMT 154 + G +AR A +G+P +V +T++RQC+SGLQA+A A + +I + G ES++ Sbjct: 62 STGGNIARKALLRAGLPVSVGGTTIDRQCASGLQAIALAARSVIFDGVEIAVGGGGESIS 121 Query: 155 LSQRGNHGNISSR---LLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAA 211 L Q + LLE + D +PM T+E V++R+G+SR+KQD +AL SQ++ A Sbjct: 122 LVQNDKMNAFQATDPALLEIKG--DVYMPMIDTAEIVSKRYGISREKQDEYALESQRRTA 179 Query: 212 SAQSRGCFHAEIVPVTTTV-LNDKGDK----KTITVSQDEGVRPSTTMQGLAKLKPAFKD 266 +AQ G F+ E+ P+TT + + DK K IT+SQDEG RP TT +GLA LK D Sbjct: 180 AAQQGGKFNDELAPITTKMAVTDKATGNVSFKDITLSQDEGPRPETTAEGLAGLKAVRGD 239 Query: 267 GGSTTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIP 326 G + TAGN+SQ+SDGA+A ++ + A + GL LG+ R + G PD MGIGP +A+P Sbjct: 240 GFTITAGNASQLSDGASACVIMSDATAAKRGLQPLGIFRGFVAHGCEPDEMGIGPVFAVP 299 Query: 327 AALQKAGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQ 386 L++ GLTV+DI ++E+NEAFA Q +YC +KLGI +K+N GGAI++GHP G +GAR Sbjct: 300 RLLKRHGLTVDDIGLWELNEAFAVQVLYCRDKLGIDPDKINVNGGAISVGHPYGMSGARL 359 Query: 387 VVTLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420 L E +RR + Y VV+MC+G GMGAA +FE Sbjct: 360 TGHALIEGRRR-KAKYAVVTMCVGGGMGAAGLFE 392 Lambda K H 0.317 0.133 0.377 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: 487 Number of extensions: 26 Number of successful extensions: 6 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: 424 Length of database: 395 Length adjustment: 31 Effective length of query: 393 Effective length of database: 364 Effective search space: 143052 Effective search space used: 143052 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: 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