Align NAD(P)H-dependent D-xylose reductase XYR1; XR; EC 1.1.1.307 (characterized)
to candidate Pf1N1B4_128 Methylglyoxal reductase, acetol producing (EC 1.1.1.-) / 2,5-diketo-D-gluconic acid reductase B (EC 1.1.1.274)
Query= SwissProt::G4N708 (324 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_128 Length = 267 Score = 141 bits (355), Expect = 2e-38 Identities = 93/301 (30%), Positives = 147/301 (48%), Gaps = 43/301 (14%) Query: 12 LDMPQVGFGLWKVENSVCADVVYNAIKAGYRLFDGACDYGNEVECGQGVKRAIDEGLVKR 71 + +P G G ++++ V D V ++ GYR+ D A Y NE E GQ AI + R Sbjct: 1 MSIPAFGLGTFRLQGQVVIDSVSTGLELGYRVIDTAQIYKNEAEVGQ----AIAASGIAR 56 Query: 72 EELFIVSKLWNTFHDGERVEPIVKKQLADWGIEYFDLYLIHFPVALEYVDPSVRYPPGWH 131 +ELFI SK+W +R+ +K+ L +Y DL LIH+P P + P Sbjct: 57 DELFITSKIWVANFAKDRLIDSLKESLNKLQTDYLDLTLIHWP------SPEDQVP---- 106 Query: 132 YDDAGTEIRPSKASIQETWTAMEKLVDAGLSKAIGVSNFQAQLLYDMLRYARIRP-ATLQ 190 ++E A+ + GL++ IGVSNF L+ + AT Q Sbjct: 107 --------------VEEFMGALLQAKQLGLTRKIGVSNFTVDLMQQAITAIGAENIATNQ 152 Query: 191 IEHHPYLVQQRLIEACKTEGIVVTAYSSFGPASFKEFNMEHAEALTPLLEEPTIVKLAEK 250 IE HPYL ++++E +++GI +T+Y + A +L++P I ++A++ Sbjct: 153 IELHPYLQNRKVVEFAQSQGIRITSYMTL--------------AYGEVLKDPLIQQIADR 198 Query: 251 YGKDPGQVLLRWATQRGLAVIPKSSREKTMKSNFEAVGWDMEDSDIKTISALDKGIRFNQ 310 P QV L WA Q G AVIP S++ ++ N +A + D+D+ I+ALD+G R Sbjct: 199 LQATPAQVTLAWAMQLGYAVIPSSTKRANLQGNLQACALTLSDADMALIAALDRGQRLTS 258 Query: 311 P 311 P Sbjct: 259 P 259 Lambda K H 0.319 0.136 0.418 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: 172 Number of extensions: 6 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: 324 Length of database: 267 Length adjustment: 26 Effective length of query: 298 Effective length of database: 241 Effective search space: 71818 Effective search space used: 71818 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 (21.7 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