Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate PfGW456L13_4129 Oxidoreductase, short chain dehydrogenase/reductase family
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4129 Length = 248 Score = 112 bits (279), Expect = 1e-29 Identities = 88/273 (32%), Positives = 133/273 (48%), Gaps = 41/273 (15%) Query: 3 TWLNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQS--------SGNYN 54 T NL K+ + GG+ GIG AIV L A+GA V + K + G Sbjct: 2 TTQNLSGKVALIQGGSRGIGAAIVKRLAAEGATVAFTYVSSTAKAEELQDSITAKGGKAL 61 Query: 55 FWPTDISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEK 114 D + A + V ++ FGR+D LVNNAGV L V AP ++L + F++ Sbjct: 62 AIKADSADADAIRSAVSATVEAFGRLDILVNNAGV----LAV---APLAEFKLED--FDQ 112 Query: 115 MVNINQKGVFLMSQAVARQMVKQRSGVIVNV-SSESGLEGSEGQSCYAATKAALNSFTRS 173 + IN + VF+ +QA AR M + G I+N+ S+ + G YA +K+AL T+ Sbjct: 113 TLAINVRSVFIATQAAARHMTE--GGRIINIGSTNADRMPFAGGGPYAMSKSALVGLTKG 170 Query: 174 WSKELGKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPL---G 230 +++LG GI + V PG ++ T + E + ++++ IPL G Sbjct: 171 LARDLGPQGITINNVQPGPVD-TDMNPAEGD-----------------FAESLIPLMAVG 212 Query: 231 RSGRLTEVADFVCYLLSERASYMTGVTTNIAGG 263 R G+ E+A FV YL+S A Y+TG + I GG Sbjct: 213 RYGKAEEIASFVAYLVSPEAGYITGASLTIDGG 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: 10 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: 248 Length adjustment: 24 Effective length of query: 243 Effective length of database: 224 Effective search space: 54432 Effective search space used: 54432 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 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