Align D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) (characterized)
to candidate WP_086509088.1 BZY95_RS06130 galactonate dehydratase
Query= metacyc::MONOMER-18070 (393 letters) >NCBI__GCF_002151265.1:WP_086509088.1 Length = 384 Score = 179 bits (453), Expect = 2e-49 Identities = 112/364 (30%), Positives = 184/364 (50%), Gaps = 10/364 (2%) Query: 26 VLVRVTTNDGRVGWGETVSALRAEAVANFVKKINTVLKGNDVFNVEKNRLEWYKHDFNMT 85 + +++ T++G GWGE V RA V V ++ L G D +E Y+ F Sbjct: 16 LFLKIETDEGCYGWGEPVIEGRAATVEAAVHELADYLIGQDPHRIEHLWNTLYRAGFYRG 75 Query: 86 ISLESTTAYSAVDIASWDIIGKELGAPLYKLLGGKTRDKVLVYANGWYQNCVKPEDFAEK 145 + +A + +D A WD+ G++LG P+++LLGG R+++ + W +P + Sbjct: 76 GPI-LMSAIAGIDQALWDLKGRDLGVPVHQLLGGAVRERMRMRMYAWTGGD-RPSEVGAG 133 Query: 146 AKEIVKMGYKALKFDPFGPYFNDISKKGLDIAEERVKAVREAVGDNVDILIEHHGRFNAN 205 A+E+V G+ A K + S + +D A RV REAVG V I I+ HGR + Sbjct: 134 ARELVARGFTAFKMNGTAEMQIVDSHRKIDEAVARVAEAREAVGPEVGISIDFHGRVHRP 193 Query: 206 SAIMIAKRLEKYNPLFMEEPIHPEDVEGLRKYRNNTSLRIALGERIINKQQALYFMKEGL 265 A + + LE Y+P+F+EEP+ PE + L+ + + +A GER+ + + + EG+ Sbjct: 194 MAKALLRELEPYHPMFVEEPLAPEHLPALKHIADGLAYPLATGERLHTRFEFRDLLAEGM 253 Query: 266 VDFLQADLYRIGGVTETKKVVGIAETFDVQMAFHNAQGPILNAVTLQFDAFIPNFLIQES 325 +D +Q DL G++E K+ +A DV +A H GP+ A +LQ DA N IQE Sbjct: 254 IDIVQPDLSHCDGISEGLKIAALASAHDVALAPHCPLGPLTLAASLQLDAVSHNAFIQEQ 313 Query: 326 FYDWFPSWKRELI-----YNGTPIDNGYAIIPERPGLGVEVNEKMLDSLKVKGEEYFNPE 380 + +++ + I+ G+ IP+ PGLGVE++E ++ G + N Sbjct: 314 SMGIHYNQGNDVLDYLVDKSALAIEEGFCAIPQGPGLGVEIDEAFVEERAKLGHRWRN-- 371 Query: 381 EPVW 384 PVW Sbjct: 372 -PVW 374 Lambda K H 0.319 0.137 0.409 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: 368 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: 393 Length of database: 384 Length adjustment: 30 Effective length of query: 363 Effective length of database: 354 Effective search space: 128502 Effective search space used: 128502 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: 50 (23.9 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