Align Galactose-6-phosphate isomerase subunit LacA; EC 5.3.1.26 (characterized)
to candidate WP_103234702.1 C1634_RS02900 ribose 5-phosphate isomerase B
Query= SwissProt::P23494 (141 letters) >NCBI__GCF_002899945.2:WP_103234702.1 Length = 144 Score = 74.3 bits (181), Expect = 7e-19 Identities = 49/138 (35%), Positives = 71/138 (51%), Gaps = 4/138 (2%) Query: 3 IVVGADLKGTRLKDVVKNFLVEEGFEVIDV---TKDGQDFVDVTLAVASEVNKDEQNLGI 59 I + AD G K++VKN+L E FEV D + + D+ D A+ V E LGI Sbjct: 5 IAIAADHAGYEYKEIVKNYLSER-FEVQDFGTFSTNSVDYPDFVHPAATSVENGENELGI 63 Query: 60 VIDAYGAGPFMVATKIKGMVAAEVSDERSAYMTRGHNNARMITVGAEIVGDELAKNIAKA 119 +I G G + A K + + A A + R HN+A MI++ A + ELA I Sbjct: 64 LICGSGNGVQITANKHQKIRCALCWMPEIATLARLHNDANMISMPARFISKELALEIVDK 123 Query: 120 FVNGKYDGGRHQVRVDML 137 F++ ++GGRHQ RVD + Sbjct: 124 FLSTDFEGGRHQNRVDKI 141 Lambda K H 0.318 0.136 0.374 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: 47 Number of extensions: 3 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: 141 Length of database: 144 Length adjustment: 16 Effective length of query: 125 Effective length of database: 128 Effective search space: 16000 Effective search space used: 16000 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: 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