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_2834 Ribonuclease E inhibitor RraA
Query= curated2:Q21X23 (173 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2834 Length = 170 Score = 248 bits (632), Expect = 5e-71 Identities = 122/170 (71%), Positives = 138/170 (81%), Gaps = 8/170 (4%) Query: 3 PSFATCDLCDAHKNDVSGAFRVLPPVFRDFGGVRQFCGPVVTVKCFEDNSSVKAAVESVG 62 P F+TCD CD HK DVSGAFRVLPPVF+ +GG R F GPV TVKC EDNS VKAAVES G Sbjct: 7 PPFSTCDFCDVHKADVSGAFRVLPPVFQSYGGKRVFAGPVTTVKCHEDNSLVKAAVESPG 66 Query: 63 YQETPAGRVGKVLVVDGGGSLRRALLGGNLGAAAARNGWAGVVIDGCVRDVSELAAVGLG 122 G+VLVVDGGGSLRRAL+GGNL AAAA NGWAGVV+DGCVRDV+EL A +G Sbjct: 67 E--------GRVLVVDGGGSLRRALVGGNLAAAAAHNGWAGVVVDGCVRDVAELNAAAVG 118 Query: 123 IRALASMPLPTEKRGEGQSDLALQIQGVWVRPGDWLYADEDGMVLAAGRL 172 IRALA +PLPTE+RGEGQ D+A+ +QGVWVRPGDWLYAD DG+V++A L Sbjct: 119 IRALALIPLPTERRGEGQRDVAVLMQGVWVRPGDWLYADADGIVVSAQAL 168 Lambda K H 0.321 0.139 0.430 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: 136 Number of extensions: 2 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: 173 Length of database: 170 Length adjustment: 18 Effective length of query: 155 Effective length of database: 152 Effective search space: 23560 Effective search space used: 23560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 43 (21.2 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