Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_066917917.1 ACG33_RS00745 acetyl-CoA C-acyltransferase
Query= BRENDA::Q8VCH0 (424 letters) >NCBI__GCF_001579945.1:WP_066917917.1 Length = 400 Score = 301 bits (770), Expect = 3e-86 Identities = 181/401 (45%), Positives = 251/401 (62%), Gaps = 22/401 (5%) Query: 37 DVVVVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDVKLKPEQLGDISVGNVLQPGA 96 + V+V RTPIG+A RG F +T EL+ V+ +Q + P ++ D+ VG LQ G+ Sbjct: 3 EAVIVSVARTPIGKAYRGAFNNTQGQELMGHVIAQAVQRAAIDPAEVDDVVVGCALQQGS 62 Query: 97 -GAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMTL 155 G+ +AR +G+P TVP T++R+CSSGL A+A A I I + GVES++L Sbjct: 63 TGSNVARQGLLRAGLPVTVPGMTIDRKCSSGLMAIATAAKQITQDGMLITIGGGVESISL 122 Query: 156 SQRGNHGNISSR---LLENEKARDCLIPMGI--TSENVAERFGVSRQKQDAFALASQQKA 210 Q + + L+E I MG+ T+E VAER+ +SR++QD +AL SQQ+ Sbjct: 123 VQNDKMNSFRANDPWLVEQIPQ----IYMGMLETAEIVAERYDISREEQDQYALQSQQRT 178 Query: 211 ASAQSRGCFHAEIVPVTTT-VLNDKGD----KKTITVSQDEGVRPSTTMQGLAKLKPAFK 265 A AQ+ G + AEIVP+T+T ++ DK +K I + +DEG RP TT+ L L+P FK Sbjct: 179 AQAQTEGRYDAEIVPLTSTMIVTDKATGATTEKQIILERDEGNRPKTTLAELQALQPVFK 238 Query: 266 DGGST------TAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGI 319 +G TAGN+SQ+SDGAAA++L +AE+ GL LG R AV G PD MGI Sbjct: 239 NGQRIAAGRFITAGNASQLSDGAAALVLMEAKEAEKRGLEPLGAYRGMAVAGCDPDEMGI 298 Query: 320 GPAYAIPAALQKAGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPL 379 GP +A+P LQ GL ++DI ++E+NEAFASQ +Y +KLGIP + +N GGAI++GHP Sbjct: 299 GPVFAVPKLLQTQGLKMDDIGLWELNEAFASQVLYIRDKLGIPNDLLNVSGGAISIGHPY 358 Query: 380 GCTGARQVVTLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420 G +GAR LL E +RR + YGVV+MCIG GMGAA +FE Sbjct: 359 GMSGARMTGHLLIEGRRR-KAKYGVVTMCIGGGMGAAGLFE 398 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: 449 Number of extensions: 16 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: 400 Length adjustment: 31 Effective length of query: 393 Effective length of database: 369 Effective search space: 145017 Effective search space used: 145017 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