Align galactose-6-phosphate isomerase lacA subunit (EC 5.3.1.26) (characterized)
to candidate WP_101444524.1 BD749_RS11805 ribose 5-phosphate isomerase B
Query= metacyc::MONOMER-2781 (142 letters) >NCBI__GCF_002846395.1:WP_101444524.1 Length = 145 Score = 77.4 bits (189), Expect = 8e-20 Identities = 45/138 (32%), Positives = 75/138 (54%), Gaps = 2/138 (1%) Query: 3 IIIGSDEAGKRLKEVIKSYLLDNKYDVVDVTEGQE--VDFVDATLAVAKDVQSQEGNLGI 60 I IG D AG K+++K L ++V D G + VD+ D +AK V S+E + G+ Sbjct: 5 IAIGGDHAGFTYKKLLKEQLEAAGHEVTDFGPGSDASVDYPDHVHPLAKAVVSKEADFGV 64 Query: 61 VIDAFGTGSFMVATKIKGMIAAEVSDERSGYMTRGHNNSRMITMGSEIVGDTLAKNVVKG 120 +I G G M A K + + AA ++R HNN+ ++ + + V +A ++ + Sbjct: 65 LICGSGNGVAMTANKYQEIRAALCWQTELAKLSREHNNANILCIPARFVSQEVASDMTRV 124 Query: 121 FVEGKYDGGRHQIRVDML 138 F+E +++GGRHQ RVD + Sbjct: 125 FLETEFEGGRHQNRVDKI 142 Lambda K H 0.317 0.135 0.370 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: 54 Number of extensions: 2 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: 142 Length of database: 145 Length adjustment: 16 Effective length of query: 126 Effective length of database: 129 Effective search space: 16254 Effective search space used: 16254 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 (21.6 bits) S2: 42 (20.8 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