Align NAD(P)H-dependent D-xylose reductase xyl1; XR; EC 1.1.1.307 (characterized)
to candidate CCNA_03541 CCNA_03541 2,5-diketo-D-gluconic acid reductase
Query= SwissProt::Q9P8R5 (319 letters) >FitnessBrowser__Caulo:CCNA_03541 Length = 279 Score = 153 bits (387), Expect = 4e-42 Identities = 97/290 (33%), Positives = 152/290 (52%), Gaps = 44/290 (15%) Query: 14 MPLVGFGLWKVNNDTCADQIYHAIKEGYRLFDGACDYGNEVEAGQGIARAIKDGLVKREE 73 MP +GFG W++ N T + A++ GYR D A YGNE + G AI++ VKR+E Sbjct: 15 MPALGFGTWQLENGTAVPLVEKALEIGYRHIDTAQIYGNERDVGA----AIRNSGVKRDE 70 Query: 74 LFIVSKLW-NSFHDGDRVEPICRKQLADWGIDYFDLYIVHFPISLKYVDPAVRYPPGWKS 132 +F+ +K+W + F DGD ++ K L G+D DL ++H+P Sbjct: 71 IFLTTKVWIDQFADGD-LQRSAEKSLEKLGVDQVDLLLLHWP------------------ 111 Query: 133 EKDELEFGNATIQETWTAMESLVDKKLARSIGISNFSAQLVMDLLRYARIRPATLQIEHH 192 K E+ + ET A+ ++ K R+IG+SNF + + + + + AT Q+E+H Sbjct: 112 -KPEVP-----LAETLKALNAVRAKGWTRAIGLSNFPSAQLEEAAKLSEAPIATDQVEYH 165 Query: 193 PYLTQTRLVEYAQKEGLTVTAYSSFGPLSFLELSVQNAVDSPPLFEHQLVKSIAEKHGRT 252 PYL+ L A + G+++TA+S L+ P L E I HG+T Sbjct: 166 PYLSLKTLKAKADQLGVSITAWSP--------LAQGKVAQDPVLIE------IGRAHGKT 211 Query: 253 PAQVLLRWATQRGIAVIPKSNNPQRLKQNLDVTGWNLEEEEIKAISGLDR 302 P QV LRW Q+GI IP+++NP+R+++N D+ + L E+E+ I GL R Sbjct: 212 PGQVTLRWIIQQGIIAIPRTSNPKRIEENFDILDFELSEKEMAQIHGLAR 261 Lambda K H 0.319 0.138 0.421 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: 256 Number of extensions: 17 Number of successful extensions: 4 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: 319 Length of database: 279 Length adjustment: 27 Effective length of query: 292 Effective length of database: 252 Effective search space: 73584 Effective search space used: 73584 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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