Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate GFF1678 Psest_1716 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__psRCH2:GFF1678 Length = 253 Score = 107 bits (267), Expect = 2e-28 Identities = 80/269 (29%), Positives = 128/269 (47%), Gaps = 29/269 (10%) Query: 5 LNIAGKTVIVTGASSGIGKAIVDELLSLKVKVANFDLTDNGEKHE---------NLLFQK 55 + +G+ +VTGA++GIG+A +KV D+ + G + + + Sbjct: 3 MTFSGQVALVTGAAAGIGRATAQAFAEQGLKVVLADIDEAGIRDGAESIRAAGGEAIAVR 62 Query: 56 VDVTSREQVEASVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKITM 115 DVT +V+A + V+ FG +D NNAGI I + + E +A F+ I Sbjct: 63 CDVTRDAEVKALIEQVLAQFGRLDYAFNNAGIEIEQGRLA--------EGSEAEFDAIMG 114 Query: 116 INQKGLYLVSQAVGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAKE 175 +N KG++L + +++A+ G I+N AS AGL + S YA +K AV T+S A E Sbjct: 115 VNVKGVWLCMKHQLPVMLAQGGGAIVNTASVAGLGAAPKMSIYAASKHAVIGLTKSAAIE 174 Query: 176 LGKYGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKLS 235 K +RV + P +++ T + AYE + R + P+GR GK+ Sbjct: 175 YAKKKIRVNAVCPAVID-TDMFRRAYE-----------ADPRKAEFAAAMHPVGRIGKVE 222 Query: 236 EVADLVAYYISDRSSYITGITTNVAGGKT 264 E+A V Y D +++ TG V GG T Sbjct: 223 EIAAAVLYLCCDGAAFTTGQALAVDGGAT 251 Lambda K H 0.313 0.131 0.361 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: 151 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: 266 Length of database: 253 Length adjustment: 24 Effective length of query: 242 Effective length of database: 229 Effective search space: 55418 Effective search space used: 55418 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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