Align 4-hydroxy-2-oxovalerate aldolase; HOA; EC 4.1.3.39 (uncharacterized)
to candidate WP_011612358.1 TERY_RS13550 aldolase
Query= curated2:O86013 (262 letters) >NCBI__GCF_000014265.1:WP_011612358.1 Length = 254 Score = 131 bits (329), Expect = 2e-35 Identities = 77/243 (31%), Positives = 132/243 (54%), Gaps = 3/243 (1%) Query: 4 PVNSFKAALREGPVQLGFWLALAHPDIAEICAGQGYDWLLIDGEHGPQTLPGIVAQLRAV 63 P N K L+ G V LG ++ A+P EIC G+D+++ID EHGP + RA Sbjct: 2 PKNQLKQKLKNGEVVLGPFMNCAYPAFVEICGLAGFDFVVIDLEHGPLNILVAEDLCRAA 61 Query: 64 EATPPCSAIVRVPGHDSVTIKQVLDLGAQTLMVPMVETAEQAKAIVTASRYPPAGERGLG 123 + + +VRV +D I++ LD+G+ + VP +ET A+ +V +++Y P G RGL Sbjct: 62 DCVG-IAPVVRVSKNDPAQIQRALDIGSTGVQVPQIETISDAEIVVQSAKYNPIGCRGLS 120 Query: 124 -GARASRWGGYPAYVA-EANAQVCIIAQIETATAVDNIEAIAAVDGIDALFLGPADLAAT 181 G RA + + + + NA+ ++ +E ++N+E I V ID +FLGP DL+ + Sbjct: 121 FGTRAGLYTSAGSNITNKLNAESLVVVHVEGTKGIENMEEIVKVPEIDVIFLGPYDLSQS 180 Query: 182 EGLLGASSFDALFKLTGEALARIVATGKPAGILSRDERLVQQFLDGGARFIANGIDSFTF 241 G+ G + + +L +A+ I ++GK G + + ++++D G ++I GID F Sbjct: 181 LGIPGQVNDIRVVELMQKAVEIIRSSGKVVGTFTNNSEAAKKWIDCGVQYIGLGIDVSIF 240 Query: 242 AKG 244 +G Sbjct: 241 LQG 243 Lambda K H 0.320 0.136 0.406 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: 139 Number of extensions: 7 Number of successful extensions: 3 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: 262 Length of database: 254 Length adjustment: 24 Effective length of query: 238 Effective length of database: 230 Effective search space: 54740 Effective search space used: 54740 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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