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 Dsui_0010 Dsui_0010 RraA family protein
Query= curated2:Q5P203 (159 letters) >FitnessBrowser__PS:Dsui_0010 Length = 163 Score = 223 bits (568), Expect = 1e-63 Identities = 110/163 (67%), Positives = 128/163 (78%), Gaps = 4/163 (2%) Query: 1 MEFQTADLCDANESRV----KIVSPMFRSYGGRGAFCGRITTLKVFEDNSLVRTALEGPG 56 M F T DLCDANE+ + ++V+PMF++YGGR FCGRI TLK+FEDNSLVR AL PG Sbjct: 1 MSFTTPDLCDANEAAIGHTLRVVTPMFKAYGGRARFCGRIHTLKIFEDNSLVREALGQPG 60 Query: 57 QGKVLVVDGGGSMRCALVGDQLALLGVKNQWAGVIVYGCIRDSKAIGTMELGVFALGSHP 116 QGKVLVVDGGGS+RCALVGDQLA+L KN W G++VYGCIRDS I +LGV AL +HP Sbjct: 61 QGKVLVVDGGGSLRCALVGDQLAVLAQKNGWEGIVVYGCIRDSAEINRTDLGVRALDTHP 120 Query: 117 LKSIKKGAGDVDIAVTFGGVTFTPGHFIYADEDGVVVSESSLL 159 KSIKKG GD +I VTFGGVTF P +IY DEDGV+VS + LL Sbjct: 121 QKSIKKGVGDQNIDVTFGGVTFKPEEWIYVDEDGVIVSATPLL 163 Lambda K H 0.321 0.140 0.416 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: 142 Number of extensions: 4 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: 159 Length of database: 163 Length adjustment: 17 Effective length of query: 142 Effective length of database: 146 Effective search space: 20732 Effective search space used: 20732 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