Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate 3608297 Dshi_1700 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__Dino:3608297 Length = 251 Score = 96.7 bits (239), Expect = 4e-25 Identities = 82/268 (30%), Positives = 121/268 (45%), Gaps = 33/268 (12%) Query: 5 LNIAGKTVIVTGASSGIGKAIVDELLSLKVKVANFDLTDNGEKHE-----NLLFQKVDVT 59 + ++ ++VTG +SG+G+A V L + VA D D H+ LF + DVT Sbjct: 1 MQVSDHAILVTGGASGLGEATVRHLRAKGAAVAVLD-RDATRGHQLAAESGALFFETDVT 59 Query: 60 SREQVEASVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKITMINQK 119 EASV A G + A V AG+ + + PHG LD F++ IN Sbjct: 60 DDVSAEASVTAAATALGRITACVTCAGVATSAKTLGREGPHG---LD--AFQRTIDINLV 114 Query: 120 GLYLVSQAVGRLLVAKK------KGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWA 173 G + +++ + +GVI+ AS A +G +GQ+AYA +KA V + A Sbjct: 115 GTFNIARLAAAEMARNAPDADGARGVIVTTASIAAFDGQKGQAAYAASKAGVTGLSLPMA 174 Query: 174 KELGKYGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGK 233 ++L + G+RV+ IAPGI L L EEI A+ T P R G Sbjct: 175 RDLAREGIRVMSIAPGIFRTPMLIGLG-------------EEIMEALAADVTFP-KRLGD 220 Query: 234 LSEVADLVAYYISDRSSYITGITTNVAG 261 E A LVA+ + Y+ G T + G Sbjct: 221 PVEYARLVAFIL--ECGYLNGTTIRLDG 246 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: 156 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: 251 Length adjustment: 24 Effective length of query: 242 Effective length of database: 227 Effective search space: 54934 Effective search space used: 54934 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