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 GFF4101 PS417_21010 ribonuclease activity regulator protein RraA
Query= curated2:Q9S4U0 (163 letters) >FitnessBrowser__WCS417:GFF4101 Length = 163 Score = 321 bits (823), Expect = 3e-93 Identities = 155/163 (95%), Positives = 160/163 (98%) Query: 1 MIHYVTPDLCDAYPELVQVVEPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQADQPGAGK 60 M HYVTPDLCDAYP+LVQV+EPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQADQPGAGK Sbjct: 1 MNHYVTPDLCDAYPDLVQVLEPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQADQPGAGK 60 Query: 61 VLVVDGGGSLRRALLGDMIAEKAAKNGWEGLVIYGCVRDVDVLAQTDLGVQALAPHPMKT 120 VLVVDGGGSLRRALLGDMIAEKAAKNGWEGLVIYGC+RDVDV+AQTDLGVQALA HPMKT Sbjct: 61 VLVVDGGGSLRRALLGDMIAEKAAKNGWEGLVIYGCIRDVDVIAQTDLGVQALASHPMKT 120 Query: 121 DKRGIGDLNVVVTFASVTFRPGEYVYADNNGVIVSPSPLKMPE 163 DKRGIGDLNVVVTFA VTFRPGEY+YADNNGVIVSPSPLKMPE Sbjct: 121 DKRGIGDLNVVVTFAGVTFRPGEYIYADNNGVIVSPSPLKMPE 163 Lambda K H 0.319 0.140 0.418 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: 218 Number of extensions: 1 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: 163 Length of database: 163 Length adjustment: 18 Effective length of query: 145 Effective length of database: 145 Effective search space: 21025 Effective search space used: 21025 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 (21.7 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