Align Putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase; HMG aldolase; EC 4.1.3.17; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.1.112; Regulator of ribonuclease activity homolog; RraA-like protein (uncharacterized)
to candidate Ac3H11_143 Demethylmenaquinone methyltransferase
Query= curated2:Q9KBI9 (210 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_143 Length = 228 Score = 144 bits (362), Expect = 2e-39 Identities = 79/187 (42%), Positives = 109/187 (58%) Query: 7 DFITQFRTIPTTCISDALDGLTNLTSTIKPLNENDQVVGPARTVQVASGDNLAVLKAMYE 66 D +++ T ++D + + P++++ +V GPA TV+V GDNL + A+ Sbjct: 17 DVVSKAATYQAAILADVAGRRGTMHGRVAPVHQSMKVAGPAFTVEVRPGDNLMIHAAIAL 76 Query: 67 ASPGDVIVIDAKGDCTRAIAGDFVLGMAKTLGIAGFVVDGAIRDIRASKALNFPIFCRGT 126 A PGDV+VID KGD T A+ G +L K G+AG +VD AIRD L+FP+F G Sbjct: 77 AQPGDVLVIDGKGDQTAALMGTLMLSACKKRGLAGVIVDAAIRDKLEILELDFPVFSAGF 136 Query: 127 TIAASKKTGIGNINVPISCGGVPIRPGDLIVGDADGVTVIPKGQEENVLQKAKKKQADDE 186 A K G IN PIS GG + PGDL+VGDADGV VI + + ++L A KK AD+ Sbjct: 137 NPAGPTKYVPGRINHPISAGGATVNPGDLVVGDADGVVVIEREKAPSMLALADKKVADEA 196 Query: 187 ARERAIS 193 AR AI+ Sbjct: 197 ARIEAIA 203 Lambda K H 0.318 0.136 0.384 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: 159 Number of extensions: 4 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: 210 Length of database: 228 Length adjustment: 22 Effective length of query: 188 Effective length of database: 206 Effective search space: 38728 Effective search space used: 38728 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: 45 (21.9 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