Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate WP_003472283.1 J416_RS11750 SDR family oxidoreductase
Query= curated2:P37079 (267 letters) >NCBI__GCF_000359605.1:WP_003472283.1 Length = 253 Score = 127 bits (318), Expect = 3e-34 Identities = 90/275 (32%), Positives = 139/275 (50%), Gaps = 42/275 (15%) Query: 5 LNLKDNVIIVTGGAS--GIGLAIVDELLSQGAHVQMIDIHGGDRHHN---------GDNY 53 +N KD V I+TG S GIG +L GA V + DI D H + G + Sbjct: 1 MNFKDQVAIITGAGSENGIGRETARQLSKGGATVVLTDID--DTHLDDAVKEMKNLGGHA 58 Query: 54 HFWSTDISSATEVQQTIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFE 113 D+S+ + + + ++ ++D LVNNAG++ P ++D + E ++ Sbjct: 59 ISMKVDVSNQEQAANCVKETVNQFGKVDILVNNAGISRPSSILD---------ITEKEWD 109 Query: 114 KMVNINQKGVFFMSQAVARQMVKQRAGVIVNVSSESGLEGSE--GQSCYAATKAALNSFT 171 + N+N KGVFF++QAV M ++ G I+N+SS SG G G S Y+A KA + F+ Sbjct: 110 LVFNVNMKGVFFLTQAVLPYMKEKNYGRILNLSSVSGKRGGGIFGGSHYSAAKAGVTGFS 169 Query: 172 RSWSKELGKYGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYTKN---AIP 228 ++ ++E G YGI VAPG++ T IT +QL + K IP Sbjct: 170 KAVAREFGPYGITCNTVAPGLIGGT---------------EITGDQLTDEKKKQIIAGIP 214 Query: 229 IGRAGKLSEVADFVCYLLSARASYITGVTTNIAGG 263 +GR G++ +VA + +L+S A YITG +I GG Sbjct: 215 LGRVGEVKDVAHSITFLVSEPAGYITGEELDINGG 249 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: 196 Number of extensions: 9 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: 253 Length adjustment: 24 Effective length of query: 243 Effective length of database: 229 Effective search space: 55647 Effective search space used: 55647 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 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