Align D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) (characterized)
to candidate WP_085125981.1 B9O00_RS27750 mandelate racemase/muconate lactonizing enzyme family protein
Query= metacyc::MONOMER-18070 (393 letters) >NCBI__GCF_900177295.1:WP_085125981.1 Length = 400 Score = 198 bits (504), Expect = 2e-55 Identities = 125/386 (32%), Positives = 195/386 (50%), Gaps = 16/386 (4%) Query: 3 KISEIEAYILGKEVTSAQWASLMVLVRVTTNDGRVGWGETVSA-LRAEAVANFVKKI-NT 60 KI+++ +++G S V V++ T+ G G GE V ++ + Sbjct: 2 KITDVRTFVVGNPPPSFG-GRYFVFVKLVTDGGVEGLGEVYCLPFHPRVVVAMIEDLAGR 60 Query: 61 VLKGNDVFNVEKNRLEWYKHDFNMTISLESTTAYSAVDIASWDIIGKELGAPLYKLLGGK 120 L G D +E Y + L S +++A WDI+GKE G P++ LLGG+ Sbjct: 61 YLVGQDPTRIESLWRRVYSAGYGQRPDLSVAGILSGLEMACWDILGKETGKPVHALLGGR 120 Query: 121 TRDKVLVYANGWYQNCVKPEDF-------AEKAKEIVKMGYKALKFDPFGPYF----NDI 169 +++ Y Y + DF AE+A E V+ G+ A+KFDP GPY Sbjct: 121 VHERLRSYTY-LYPGEGETADFYHDAERSAERAAEYVRQGFTAIKFDPAGPYSAFDPRMP 179 Query: 170 SKKGLDIAEERVKAVREAVGDNVDILIEHHGRFNANSAIMIAKRLEKYNPLFMEEPIHPE 229 ++ L +E+ + +R AVG D+L HG+F A+ +A+RLE Y+PL++EEP PE Sbjct: 180 DQESLARSEQFCRLIRAAVGGGADLLFGTHGQFTPAGALRLARRLEPYDPLWLEEPTPPE 239 Query: 230 DVEGLRKYRNNTSLRIALGERIINKQQALYFMKEGLVDFLQADLYRIGGVTETKKVVGIA 289 E + T++ +A GER+ K + + G LQ +L R+GG+ E KK+ G+A Sbjct: 240 MPEQMALVARGTTIPVAAGERLATKYEFARLLDAGAAAILQPNLGRVGGLLEAKKIAGLA 299 Query: 290 ETFDVQMAFHNAQGPILNAVTLQFDAFIPNFLIQESFYDWFPSWKRELIYNGTPIDNGYA 349 E Q+A H GP++ A +Q A +PNFLI ES W + EL+ GY Sbjct: 300 EARYAQVAPHLYCGPVVGAANIQLAATLPNFLILESIQTW-GGFHAELLKTPIRWQEGYV 358 Query: 350 IIPERPGLGVEVNEKMLDSLKVKGEE 375 ++P+ PGLGVE++E + + +GEE Sbjct: 359 LVPDAPGLGVELDEAVALAHPYEGEE 384 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: 397 Number of extensions: 16 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: 400 Length adjustment: 31 Effective length of query: 362 Effective length of database: 369 Effective search space: 133578 Effective search space used: 133578 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 Apr 09 2024. 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