Align Galactose-6-phosphate isomerase subunit LacA; EC 5.3.1.26 (characterized)
to candidate SMc01613 SMc01613 ribose-5-phosphate isomerase B
Query= SwissProt::P23494 (141 letters) >FitnessBrowser__Smeli:SMc01613 Length = 145 Score = 72.0 bits (175), Expect = 3e-18 Identities = 46/142 (32%), Positives = 76/142 (53%), Gaps = 3/142 (2%) Query: 1 MAIVVGADLKGTRLKDVVKNFLVEEG-FEVIDVTKDGQDFVDVTLAVASEVNKDEQNLGI 59 M I +GAD G L DV+ L + EV D+++ G + D++ +A + E GI Sbjct: 1 MKIAIGADSAGKPLLDVIAAHLAKRSDLEVKDLSQTGY-YADLSRDLAQTITAGENERGI 59 Query: 60 VIDAYGAGPFMVATKIKGMVAAEVSDERSAYMTRGHNNARMITVGAEIVGDELAKNIAKA 119 +I G G + A K+ G+ AA D SA NNA++IT+GA ++G ELAK+I Sbjct: 60 LICGTGIGVCISANKVPGIRAALTHDTYSAERAAKSNNAQIITMGARVIGPELAKSIVDT 119 Query: 120 FVNGKYD-GGRHQVRVDMLNKM 140 ++ ++D G V+ ++++ Sbjct: 120 WLASEFDPNGPSAANVEAIDRL 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: 52 Number of extensions: 2 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: 145 Length adjustment: 16 Effective length of query: 125 Effective length of database: 129 Effective search space: 16125 Effective search space used: 16125 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 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