Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate RR42_RS28045 RR42_RS28045 3-oxoacyl-ACP reductase
Query= curated2:P37079 (267 letters) >FitnessBrowser__Cup4G11:RR42_RS28045 Length = 249 Score = 116 bits (290), Expect = 5e-31 Identities = 85/267 (31%), Positives = 133/267 (49%), Gaps = 29/267 (10%) Query: 5 LNLKDNVIIVTGGASGIGLAIVDELLSQGAHVQMIDI-------HGGDRHHNGDNYHFWS 57 L +K V IVTG A G+G A L +G V + DI +G H Sbjct: 3 LQIKGKVAIVTGSARGLGAATARHLAQEGVKVVITDILREQAEATAAALRADGLQAHCIV 62 Query: 58 TDISSATEVQQTIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVN 117 DI+ +VQ+ +D I + + LVNNAG + LV ++ E ++ ++ Sbjct: 63 ADITRGADVQRLVDETIAHFGGVHILVNNAGFPRDKYLV---------KMTEEDWDLVME 113 Query: 118 INQKGVFFMSQAVARQMVKQRAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKE 177 + KG F ++AV ++++Q G ++N+SS + G+ Q+ YAA KA L ++ + E Sbjct: 114 VMLKGAFLATKAVMPRLIEQGWGRVINISSRAHF-GNPTQANYAAAKAGLIGMAKALALE 172 Query: 178 LGKYGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYTKNAIPIGRAGKLSE 237 G+YG+ V VAPG +E E +AL T E ++E A PI R G+ + Sbjct: 173 QGRYGVTVNCVAPGFMET------EMVQALP-----TYETIKERAVA-AQPIKRVGRPGD 220 Query: 238 VADFVCYLLSARASYITGVTTNIAGGK 264 +AD V +L S RAS+ITG ++ GG+ Sbjct: 221 IADAVAFLASERASFITGEVLHVTGGR 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: 171 Number of extensions: 12 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