Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate RR42_RS36320 RR42_RS36320 acetyl-CoA acetyltransferase
Query= BRENDA::Q0K368 (391 letters) >FitnessBrowser__Cup4G11:RR42_RS36320 Length = 392 Score = 650 bits (1676), Expect = 0.0 Identities = 324/392 (82%), Positives = 360/392 (91%), Gaps = 1/392 (0%) Query: 1 MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60 MAEAYIVAA RTAGGRKGGKL+GWHPADLAAQVL+ALV R+GADPAL++DVIMGCV Q G Sbjct: 1 MAEAYIVAAARTAGGRKGGKLAGWHPADLAAQVLNALVARSGADPALIDDVIMGCVGQAG 60 Query: 61 EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120 EQAGNVARNA+LAS+LP+SVPGTSVDRQCGSSQQALHFAAQAVMSG MDIVIAAGVESMT Sbjct: 61 EQAGNVARNAVLASKLPQSVPGTSVDRQCGSSQQALHFAAQAVMSGTMDIVIAAGVESMT 120 Query: 121 RVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180 RVPMGL S LP KNGFG SP ++ RYPGV+FSQFTGAEM++RKY L+R+ LD YAL+S Sbjct: 121 RVPMGLPSTLPFKNGFGSSMSPAMQERYPGVKFSQFTGAEMMSRKYGLTRDDLDRYALES 180 Query: 181 HQRAIAATKSGRFTAEILPVEVRTADG-ANGEMHTTDEGVRYDATLESIGSVKLIAEGGR 239 H+RAIAAT++GRF EI+PV VR ADG ANGE+HT DEG+R++A+LESI SVKLI EGG Sbjct: 181 HRRAIAATQAGRFKDEIVPVAVRAADGSANGELHTVDEGIRFEASLESISSVKLIEEGGT 240 Query: 240 VTAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVAL 299 VTAASASQICDGAAGLMVVNEAGLKKLGVKPLAR+H M+V+GHDPV+MLEAPLPAT AL Sbjct: 241 VTAASASQICDGAAGLMVVNEAGLKKLGVKPLARIHHMSVLGHDPVIMLEAPLPATLRAL 300 Query: 300 KKAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMTT 359 KAG++IGDIDLFE+NEAFAPVPLAWL+ TGADPAR+NV+GGAIALGHPLGGSGAKLMTT Sbjct: 301 DKAGMKIGDIDLFEINEAFAPVPLAWLQTTGADPARMNVNGGAIALGHPLGGSGAKLMTT 360 Query: 360 LVHALHTHGKRYGLQTMCEGGGLANVTIVERL 391 LVHALH GKRYGLQTMCEGGG+ANVTIVERL Sbjct: 361 LVHALHAQGKRYGLQTMCEGGGMANVTIVERL 392 Lambda K H 0.317 0.132 0.379 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: 652 Number of extensions: 28 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: 391 Length of database: 392 Length adjustment: 31 Effective length of query: 360 Effective length of database: 361 Effective search space: 129960 Effective search space used: 129960 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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