Align D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) (characterized)
to candidate GFF443 PGA1_c04540 putative d-galactonate dehydratase
Query= metacyc::MONOMER-18070 (393 letters) >FitnessBrowser__Phaeo:GFF443 Length = 410 Score = 196 bits (497), Expect = 1e-54 Identities = 121/355 (34%), Positives = 189/355 (53%), Gaps = 20/355 (5%) Query: 26 VLVRVTTNDGRVGWGETVSA-LRAEAVANFVKKI-NTVLKGNDVFNVEKNRLEWYKHDFN 83 +LV+VTT+ G GWGE +A + +A+ + ++ + ++G + N+E Y F Sbjct: 24 ILVKVTTDTGITGWGECYAASVGPDAMTHVIRDVFERHMQGMNPENIEWMFRRAYSSGFT 83 Query: 84 MTISLESTTAYSAVDIASWDIIGKELGAPLYKLLGGKTRDKVLVYANGW---------YQ 134 L A+S ++IA WDI+GK+ P++ L+GG+ D++ Y + + Sbjct: 84 QRPDLSVMGAFSGLEIACWDILGKDRDRPVHALIGGRMNDRLRAYTYLYPLPHHDIDAFW 143 Query: 135 NCVKPEDFAEKAKEIVKMGYKALKFDPFGPYF----NDISKKGLDIAEERVKAVREAVGD 190 N PE AE A V+ GY A+KFDP GPY + ++ + + +A+REAVGD Sbjct: 144 NT--PELAAESAIAAVEKGYTAVKFDPAGPYTMRGGHMPAQSDITQSVAFCRAIREAVGD 201 Query: 191 NVDILIEHHGRFNANSAIMIAKRLEKYNPLFMEEPIHPEDVEGLRKYRNNTSLRIALGER 250 D+L HG+F AI + + LE Y PL+ EEP P+ V + + + + +A GER Sbjct: 202 RADLLFGTHGQFTPAGAIRLGQALESYEPLWFEEPTPPDLVADMARVADRVRIPVATGER 261 Query: 251 IINKQQALYFMKEGLVDFLQADLYRIGGVTETKKVVGIAETFDVQMAFHNAQGPILNAVT 310 + K + ++ G + LQ L R GG+ ETKK+ IAE F QMA H GP+ A Sbjct: 262 LTTKAEFAAILRAGAAEILQPALGRSGGIWETKKIAAIAEVFGAQMAPHLYAGPVEWAAN 321 Query: 311 LQFDAFIPNFLIQESFYDWFPSWKRELIYNGTPIDNGYAIIPERPGLGVEVNEKM 365 +Q A IPN L+ E+ F + LI G +++G+ I + PGLG+EV+E + Sbjct: 322 IQLAASIPNLLMIETIETPFHT---ALIKQGITVEDGFVIPSDTPGLGIEVDEDL 373 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: 359 Number of extensions: 19 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: 393 Length of database: 410 Length adjustment: 31 Effective length of query: 362 Effective length of database: 379 Effective search space: 137198 Effective search space used: 137198 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 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