Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate AO353_22325 AO353_22325 short-chain dehydrogenase
Query= curated2:P37079 (267 letters) >FitnessBrowser__pseudo3_N2E3:AO353_22325 Length = 249 Score = 94.4 bits (233), Expect = 2e-24 Identities = 79/265 (29%), Positives = 115/265 (43%), Gaps = 29/265 (10%) Query: 7 LKDNVIIVTGGASGIGLAIVDELLSQGAHV--------QMIDIHGGDRHHNGDNYHFWST 58 L + +VTG + GIG AI +L GA V + D G + Sbjct: 4 LHRKIALVTGSSKGIGAAIARQLAKDGATVIVNYTRSREDADRVVSQILETGARAYAIRA 63 Query: 59 DISSATEVQQTIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNI 118 D+S+A EV+ AI+ ID LVNNAGV A E+ E F + N+ Sbjct: 64 DVSNALEVKALFKAIVHEHGHIDILVNNAGVY---------ATGALAEITEQEFNRQFNL 114 Query: 119 NQKGVFFMSQAVARQMVKQRAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKEL 178 N G+ +Q A + + G I+N+SS + Y A+K A+++ T++ + EL Sbjct: 115 NVLGLIQCTQE-AVAVFNPKGGSIINISSSVTSFTPANSTVYTASKGAVDAITKTLANEL 173 Query: 179 GKYGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYTKNAIPIGRAGKLSEV 238 G IRV V PG++ G+ + E Q E T P+GR G ++ Sbjct: 174 GPKNIRVNSVNPGLVVTEGVHASGFFED-------AFRQKIEAIT----PLGRIGSPEDI 222 Query: 239 ADFVCYLLSARASYITGVTTNIAGG 263 A V +L S A +ITG I GG Sbjct: 223 APAVAFLASDDAGWITGEILVIGGG 247 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: 156 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: 249 Length adjustment: 24 Effective length of query: 243 Effective length of database: 225 Effective search space: 54675 Effective search space used: 54675 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 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