Align D-xylulose reductase; Xylitol dehydrogenase; XDH; EC 1.1.1.9 (characterized)
to candidate WP_043527898.1 JH15_RS05915 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
Query= SwissProt::Q07993 (356 letters) >NCBI__GCF_000759345.1:WP_043527898.1 Length = 369 Score = 99.8 bits (247), Expect = 1e-25 Identities = 103/370 (27%), Positives = 157/370 (42%), Gaps = 50/370 (13%) Query: 4 LTTQEAIVLERPGKITLTNVSI--PKISDPNEVIIQIKATGICGSDIHYYTHGRIANYVV 61 + ++ A+ LE + LT + + PK EV++QIKAT +C +D + Sbjct: 1 MKSRAAVALEAGKPLELTEIEVDGPKAG---EVLVQIKATSVCHTDAFTLSGADPEGLF- 56 Query: 62 ESPMVLGHESSGIVALIGENVKTLKVGDRVALEPGIPDRFSPEMKEGRYNLDPNLKFAAT 121 P VLGHE +GIV +GE V +LK GD V IP ++ E + ++ L + Sbjct: 57 --PSVLGHEGAGIVQEVGEGVTSLKPGDHV-----IP-LYTAECGKCKFCLSGKTNLCSA 108 Query: 122 P----------------PFDGTLTKYYKTMKDFV-YKLPDDVSFEEGALIEPL------- 157 +G +Y F Y + +VS + + PL Sbjct: 109 VRATQGRGVMPDGTSRFSLNGQTLHHYMGCSTFSEYTVLPEVSLAKVSPEAPLDKICLLG 168 Query: 158 ---SVAIHA-NKLAKIKFGARCVVFGAGPIGLLAGKVASVFGAADVVFVDLLENKLETAR 213 + I A AK++ G+ VFG G IGL + A + GA+ ++ +D+ +K E AR Sbjct: 169 CGVTTGIGAVMNTAKVEPGSTVAVFGLGAIGLAVIQGAQMVGASRIIAIDINADKFELAR 228 Query: 214 QFGATHIVNSGDLPHGVTVDSVIKKAIGKKGADVVFECSGAEPCVRAGIEVCKAG---GT 270 QFGAT VN D H + VI + G D FEC G +R +E C G Sbjct: 229 QFGATDFVNPKD--HADPIQQVIVD-MTDGGVDYSFECIGNVNVMRQALECCHKGWGESV 285 Query: 271 IVQVGMGQEEIQFPISIIPTKELTFQGCFRYCQG--DYSDSIELVSSRKLSLKPFITHRY 328 I+ V EEI + T + F +G + +E ++ + F+TH Sbjct: 286 IIGVAGAGEEISTRPFQLVTGRVWRGSAFGGVKGRTELPGYVERYMKGEIKIDEFVTHDM 345 Query: 329 SFKDAVEAFE 338 F+ EAFE Sbjct: 346 PFEQINEAFE 355 Lambda K H 0.319 0.138 0.402 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: 353 Number of extensions: 25 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 356 Length of database: 369 Length adjustment: 29 Effective length of query: 327 Effective length of database: 340 Effective search space: 111180 Effective search space used: 111180 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: 49 (23.5 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