Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate WP_047006347.1 AAW01_RS06205 SDR family NAD(P)-dependent oxidoreductase
Query= metacyc::MONOMER-13092 (266 letters) >NCBI__GCF_001010925.1:WP_047006347.1 Length = 261 Score = 85.1 bits (209), Expect = 1e-21 Identities = 82/263 (31%), Positives = 118/263 (44%), Gaps = 32/263 (12%) Query: 13 IVTGASSGIGKAIVDELLSLKVKVANFDLTDNGEKHENL------LFQKVDVTSREQVEA 66 IVTG +SG+G+A L + KVA FDL N E+ E + +F KVDV+ +EA Sbjct: 10 IVTGGASGLGEATARALAAKGAKVALFDL--NEERGEAVAAEIGGVFCKVDVSDEASIEA 67 Query: 67 SVAAVVEHFGTVDAVVNNAGI-NIPRLLVDPKDPHGQYELDDATFEKITMINQKGLY--L 123 A E G +VN AGI + + ++ L A FEK IN G + + Sbjct: 68 GFARAREAHGQERVLVNCAGIATVGKTTKRDRETGAISHLPLAAFEKTIRINLMGTFNCM 127 Query: 124 VSQAVGRLLVAK-----KKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAKELGK 178 A G + + ++GVIIN AS A +G GQ AYA +KA V T A++L Sbjct: 128 AKAAAGMITLDTVGEYGERGVIINTASVAAEDGQIGQVAYATSKAGVKGMTLPAARDLMG 187 Query: 179 YGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKLSEVA 238 G+RV I PGI + L E+ + A++ P R G+ E A Sbjct: 188 EGIRVNAILPGIFHTPMMDGLP-------------EKAQVALAASVPFP-KRLGRPEEYA 233 Query: 239 DLVAYYISDRSSYITGITTNVAG 261 L + + + Y+ T + G Sbjct: 234 KLACFMV--ETEYMNAETVRLDG 254 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: 136 Number of extensions: 5 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: 261 Length adjustment: 25 Effective length of query: 241 Effective length of database: 236 Effective search space: 56876 Effective search space used: 56876 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 24 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