Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate Echvi_2940 Echvi_2940 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= curated2:P37079 (267 letters) >FitnessBrowser__Cola:Echvi_2940 Length = 251 Score = 113 bits (282), Expect = 5e-30 Identities = 88/266 (33%), Positives = 134/266 (50%), Gaps = 30/266 (11%) Query: 7 LKDNVIIVTGGASGIGLAIVDELLSQGAHVQMIDIH-------GGDRHHNGDNYHFWSTD 59 +K+ I++TGGASGIGLA+ +G +V ID + G F D Sbjct: 1 MKNKTILITGGASGIGLAMTKRFAEEGGNVYFIDYDQKTGEKVAEELTSKGHRVTFLQGD 60 Query: 60 ISSATEVQQTIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNIN 119 +S E++QTI +I ID LVNNAG++ L + E F+++ +N Sbjct: 61 VSQTEEMKQTISSIS---GSIDVLVNNAGISHVGNLENTA---------EEDFDRLYQVN 108 Query: 120 QKGVFFMSQAVARQMVKQRAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELG 179 KG++ S A +M K++ G I+N++S + G + Y+ TK A+ S T S +++ Sbjct: 109 VKGIYNCSLASLPKM-KEKGGSIINMASVASTMGLPDRFAYSMTKGAVFSMTLSMARDYV 167 Query: 180 KYGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYTKNAI--PIGRAGKLSE 237 +Y IRV +APG + TP + LA +N ++ +E + K A PIGR GK E Sbjct: 168 EYNIRVNSIAPG-----RVHTPFVDGFLA--KNYPGKE-KEMFDKLAATQPIGRMGKPEE 219 Query: 238 VADFVCYLLSARASYITGVTTNIAGG 263 +A YL S AS++TG I GG Sbjct: 220 IAAMAVYLSSDEASFLTGGNYPIDGG 245 Lambda K H 0.316 0.133 0.386 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: 134 Number of extensions: 8 Number of successful extensions: 5 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: 251 Length adjustment: 24 Effective length of query: 243 Effective length of database: 227 Effective search space: 55161 Effective search space used: 55161 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 (21.6 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