Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate 3609683 Dshi_3066 acetyl-CoA acetyltransferase (RefSeq)
Query= reanno::Phaeo:GFF329 (391 letters) >FitnessBrowser__Dino:3609683 Length = 391 Score = 714 bits (1842), Expect = 0.0 Identities = 355/391 (90%), Positives = 372/391 (95%) Query: 1 MTNVVIASAARTAVGSFGGAFAKTPAHDLGAAVLQAVVERAGIDKSEVSETILGQVLTAA 60 MTNVVIASAARTAVGSFGG+FA TPAHDLG+AVL+A+V RAGI+K EVSETILGQVLT Sbjct: 1 MTNVVIASAARTAVGSFGGSFANTPAHDLGSAVLEALVARAGIEKGEVSETILGQVLTGG 60 Query: 61 QGQNPARQAHINAGLPQESAAWSLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENMTL 120 QGQNPARQAHINAGLPQESAAW LNQVCGSGLRAVAL AQHIQLGDA IVCAGGQENMTL Sbjct: 61 QGQNPARQAHINAGLPQESAAWGLNQVCGSGLRAVALGAQHIQLGDAEIVCAGGQENMTL 120 Query: 121 SPHAANLRAGHKMGDMSYIDTMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA 180 SPH ANLRAG KMGDM +ID+MIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA Sbjct: 121 SPHVANLRAGQKMGDMKFIDSMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA 180 Query: 181 SQNKAEAAQKAGKFADEIAAFTVKTRKGDIIVDQDEYIRHGATIEAMQKLRPAFAKDGSV 240 SQNKAEAAQKAGKF DE+ AFT+KTRKGDI+VD+DEYIRHGAT+EAMQKLRPAF KDGSV Sbjct: 181 SQNKAEAAQKAGKFDDEVVAFTIKTRKGDIVVDKDEYIRHGATMEAMQKLRPAFTKDGSV 240 Query: 241 TAANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMGVGPIYASRKALE 300 TAANASGLNDGAA LLMSA++AEKRGI P+ARIASYATAGLDPSIMGVGPIYASRKALE Sbjct: 241 TAANASGLNDGAAGVLLMSAENAEKRGITPMARIASYATAGLDPSIMGVGPIYASRKALE 300 Query: 301 KAGWSVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASGCRVLNTL 360 KAGW VDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASG RVLNTL Sbjct: 301 KAGWKVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASGARVLNTL 360 Query: 361 LFEMKRRDAKKGLATLCIGGGMGVAMCVERP 391 LFEM+RRDAKKGLATLCIGGGMGVA+CVERP Sbjct: 361 LFEMQRRDAKKGLATLCIGGGMGVALCVERP 391 Lambda K H 0.316 0.130 0.376 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: 620 Number of extensions: 12 Number of successful extensions: 1 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: 391 Length adjustment: 31 Effective length of query: 360 Effective length of database: 360 Effective search space: 129600 Effective search space used: 129600 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