Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_053936590.1 WG78_RS04575 3-oxoacyl-ACP reductase FabG
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >NCBI__GCF_001294205.1:WP_053936590.1 Length = 246 Score = 135 bits (340), Expect = 8e-37 Identities = 89/268 (33%), Positives = 146/268 (54%), Gaps = 30/268 (11%) Query: 5 LNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIH--GGDKHQSS-----GNYNFWP 57 + LK K+ +TG ASGIG A + + +GA V + D++ G D S G + Sbjct: 1 MKLKNKVAIITGAASGIGHATARKFVTEGARVVVCDVNRAGVDAVVSELIAQGGQALGFE 60 Query: 58 TDISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVN 117 D+++ +++ V Q+FGRID LVNNAG+ A + ++ E F+++++ Sbjct: 61 VDVTNKAQIAAMVAGTQQQFGRIDILVNNAGI---------VADAQLSKMTEDQFDRVID 111 Query: 118 INQKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKE 177 IN KGV+ ++AV M++Q+SGVI+N SS GL G+ GQ+ YAA K + ++W++E Sbjct: 112 INLKGVYNCTRAVVDIMIEQQSGVILNASSVVGLYGNFGQTNYAAAKFGVIGMVKTWARE 171 Query: 178 LGKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTE 237 LGK GIR V PG + TP ++ +++ +G + +PL R + E Sbjct: 172 LGKKGIRANAVCPGF-----VATPILKD--------MPDKVIQGMEER-VPLRRMAQPEE 217 Query: 238 VADFVCYLLSERASYMTGVTTNIAGGKT 265 +A+ +L S+ ASY++G + GG T Sbjct: 218 IANVYAFLASDEASYISGAAIEVTGGLT 245 Lambda K H 0.315 0.132 0.378 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: 156 Number of extensions: 9 Number of successful extensions: 4 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: 267 Length of database: 246 Length adjustment: 24 Effective length of query: 243 Effective length of database: 222 Effective search space: 53946 Effective search space used: 53946 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: 42 (22.0 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