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 BPHYT_RS30330 BPHYT_RS30330 hypothetical protein
Query= curated2:Q9KBI9 (210 letters) >FitnessBrowser__BFirm:BPHYT_RS30330 Length = 222 Score = 134 bits (337), Expect = 1e-36 Identities = 68/192 (35%), Positives = 111/192 (57%), Gaps = 1/192 (0%) Query: 3 QAEIDFITQFRTIPTTCISDALDGLTNLTSTIKPLNENDQVVGPARTVQVASGDNLAVLK 62 QA+ + R + + +SD + + + ++P ++ + G A TV GDNLA+ + Sbjct: 14 QADAATLETLRELAVSLLSDNMARASGMVG-LRPYHQPRPMAGTAVTVHTRPGDNLAIHR 72 Query: 63 AMYEASPGDVIVIDAKGDCTRAIAGDFVLGMAKTLGIAGFVVDGAIRDIRASKALNFPIF 122 A PGDV+VID GD T+A+ G+ + A++LG+ G V+DGAIRD+ + FP++ Sbjct: 73 AFDFCRPGDVLVIDGAGDLTQALMGEIMASFAESLGVQGLVIDGAIRDVGSLCQREFPVY 132 Query: 123 CRGTTIAASKKTGIGNINVPISCGGVPIRPGDLIVGDADGVTVIPKGQEENVLQKAKKKQ 182 RG T K G G INVP++ GG + PGD+IVGD DG+ I V++ A+++ Sbjct: 133 ARGVTHRGPYKNGPGEINVPVTVGGTVVHPGDIIVGDEDGLLAITPADVAAVIEGARRQH 192 Query: 183 ADDEARERAISD 194 A + A ++I++ Sbjct: 193 AKETAALKSIAE 204 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: 179 Number of extensions: 12 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: 222 Length adjustment: 22 Effective length of query: 188 Effective length of database: 200 Effective search space: 37600 Effective search space used: 37600 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