Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate Ac3H11_2994 3-ketoacyl-CoA thiolase (EC 2.3.1.16)
Query= reanno::acidovorax_3H11:Ac3H11_2994 (397 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2994 Length = 397 Score = 778 bits (2008), Expect = 0.0 Identities = 397/397 (100%), Positives = 397/397 (100%) Query: 1 MSTTIQDPIVIVGAARTPMGSLQGDFSSLAAHDLGGAAIKAAIERAGVSPDAVGEVLFGN 60 MSTTIQDPIVIVGAARTPMGSLQGDFSSLAAHDLGGAAIKAAIERAGVSPDAVGEVLFGN Sbjct: 1 MSTTIQDPIVIVGAARTPMGSLQGDFSSLAAHDLGGAAIKAAIERAGVSPDAVGEVLFGN 60 Query: 61 CLMAGQGQAPARQAAFKGGLPKGAGAVTLSKMCGSGMKAAMMAHDMLLAGSHDVMVAGGM 120 CLMAGQGQAPARQAAFKGGLPKGAGAVTLSKMCGSGMKAAMMAHDMLLAGSHDVMVAGGM Sbjct: 61 CLMAGQGQAPARQAAFKGGLPKGAGAVTLSKMCGSGMKAAMMAHDMLLAGSHDVMVAGGM 120 Query: 121 ESMTNAPYLLQKGRGGYRLGHDRIFDHMMLDGLEDAYEAGRSMGTFGEDCAAKYSFTREQ 180 ESMTNAPYLLQKGRGGYRLGHDRIFDHMMLDGLEDAYEAGRSMGTFGEDCAAKYSFTREQ Sbjct: 121 ESMTNAPYLLQKGRGGYRLGHDRIFDHMMLDGLEDAYEAGRSMGTFGEDCAAKYSFTREQ 180 Query: 181 QDAFATASVQRAKAATESGAFAAEIVPVTVKTRAGETVVSVDEGPGKVKLEKIATLKPAF 240 QDAFATASVQRAKAATESGAFAAEIVPVTVKTRAGETVVSVDEGPGKVKLEKIATLKPAF Sbjct: 181 QDAFATASVQRAKAATESGAFAAEIVPVTVKTRAGETVVSVDEGPGKVKLEKIATLKPAF 240 Query: 241 KKDGTITAASSSSINDGAAALVMMRESTAKKLGAKPLARIVSHATHAQEPEWFATAPLGA 300 KKDGTITAASSSSINDGAAALVMMRESTAKKLGAKPLARIVSHATHAQEPEWFATAPLGA Sbjct: 241 KKDGTITAASSSSINDGAAALVMMRESTAKKLGAKPLARIVSHATHAQEPEWFATAPLGA 300 Query: 301 TQKALAKAGWQVGDVQLWEINEAFAVVPMALMKELDLPHDKVNVNGGACALGHPIGASGA 360 TQKALAKAGWQVGDVQLWEINEAFAVVPMALMKELDLPHDKVNVNGGACALGHPIGASGA Sbjct: 301 TQKALAKAGWQVGDVQLWEINEAFAVVPMALMKELDLPHDKVNVNGGACALGHPIGASGA 360 Query: 361 RIMVTLIHALKARGLTKGLATLCIGGGEATAVALELV 397 RIMVTLIHALKARGLTKGLATLCIGGGEATAVALELV Sbjct: 361 RIMVTLIHALKARGLTKGLATLCIGGGEATAVALELV 397 Lambda K H 0.317 0.131 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: 740 Number of extensions: 16 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: 397 Length of database: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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