Align Galactose-6-phosphate isomerase subunit LacB; EC 5.3.1.26 (characterized)
to candidate GFF2367 PS417_12070 ribose 5-phosphate isomerase
Query= SwissProt::P23495 (171 letters) >FitnessBrowser__WCS417:GFF2367 Length = 153 Score = 96.7 bits (239), Expect = 2e-25 Identities = 50/149 (33%), Positives = 83/149 (55%), Gaps = 2/149 (1%) Query: 3 IAIGCDHIVTDVKMAVSEFLKSKGYEVLDFGTYDHVRTHYPIYGKKVGEAVVSGQADLGV 62 +AIGCD ++K + +++ GY V DFGT+ YP V A+ +GQ LGV Sbjct: 7 VAIGCDEAGFELKELLKRHIEALGYPVTDFGTHSTAPVLYPDIALAVANAINAGQQRLGV 66 Query: 63 CICGTGVGINNAVNKVPGVRSALVRDMTSALYAKEELNANVIGFGGMITGGLLMNDIIEA 122 +CGTG+G+ + NKV G+R+A D SA A++ +A ++ G + G L I+++ Sbjct: 67 LVCGTGIGMAISANKVLGIRAAQAHDTYSAERARKSNDAQILSIGARVIGAELAKSIVKS 126 Query: 123 FIEAEYKPTEENKKLIAKIEHVETHNAHQ 151 F+E+E++ K + +I +E + HQ Sbjct: 127 FLESEFESARSGAK-VERINAIE-RDGHQ 153 Lambda K H 0.318 0.137 0.405 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: 84 Number of extensions: 5 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: 171 Length of database: 153 Length adjustment: 17 Effective length of query: 154 Effective length of database: 136 Effective search space: 20944 Effective search space used: 20944 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 (21.7 bits) S2: 43 (21.2 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