Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate SMc02041 SMc02041 short chain dehydrogenase
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__Smeli:SMc02041 Length = 254 Score = 116 bits (290), Expect = 5e-31 Identities = 84/270 (31%), Positives = 129/270 (47%), Gaps = 34/270 (12%) Query: 3 DWLNIAGKTVIVTGASSGIGKAIVDELLSLKVKVANFD--------LTDNGEKHENLLFQ 54 D L+ +GKTV+VTGA++GIG+A+ + + + +VA D G H + Sbjct: 9 DLLDFSGKTVVVTGAATGIGRAVAEAFATKRARVALLDRDAAVSDVAVSLGTGH---IAH 65 Query: 55 KVDVTSREQVEASVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKIT 114 DVT + VE +V +V E FG +D ++NNAGI P P Y A +++ Sbjct: 66 VADVTDEQGVERAVKSVTEAFGRIDILINNAGIG-------PLAPAESYPT--AEWDRTL 116 Query: 115 MINQKGLYLVSQAVGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAK 174 +N KG +L+++A+ ++ + G I+NMAS+A + G EG AY +KA + T A Sbjct: 117 AVNLKGAFLMARAIAPGMLEQGSGRIVNMASQAAIIGIEGHVAYCASKAGIIGMTNCMAL 176 Query: 175 ELGKYGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKL 234 E G GV V ++P ++E E L G+ E RA P R K Sbjct: 177 EWGPRGVTVNAVSPTVVET--------ELGLTGWAGEKGERARA------AIPTRRFAKP 222 Query: 235 SEVADLVAYYISDRSSYITGITTNVAGGKT 264 E+A V Y ++ + G + GG T Sbjct: 223 WEIAASVLYLAGGAAAMVNGANLMIDGGYT 252 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: 168 Number of extensions: 8 Number of successful extensions: 3 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: 254 Length adjustment: 24 Effective length of query: 242 Effective length of database: 230 Effective search space: 55660 Effective search space used: 55660 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