Align D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) (characterized)
to candidate BWI76_RS27935 BWI76_RS27935 galactonate dehydratase
Query= metacyc::MONOMER-18070 (393 letters) >FitnessBrowser__Koxy:BWI76_RS27935 Length = 382 Score = 164 bits (416), Expect = 3e-45 Identities = 109/359 (30%), Positives = 179/359 (49%), Gaps = 9/359 (2%) Query: 26 VLVRVTTNDGRVGWGETVSALRAEAVANFVKKINTVLKGNDVFNVEKNRLEWYKHDFNMT 85 + +++ T++G VGWGE V RA V V ++ L G D + Y+ F Sbjct: 16 MFLKIDTDEGVVGWGEPVIEGRARTVEAAVHELGDYLIGQDPARINDLWQVMYRAGFYRG 75 Query: 86 ISLESTTAYSAVDIASWDIIGKELGAPLYKLLGGKTRDKVLVYANGWYQNCVKPEDFAEK 145 + +A + +D A WDI GK L AP+++L+GG RDK+ Y+ + +P + + Sbjct: 76 GPI-LMSAIAGIDQALWDIKGKVLNAPVWQLMGGLVRDKIKAYS---WVGGDRPAEVIDG 131 Query: 146 AKEIVKMGYKALKFDPFGPYFNDISKKGLDIAEERVKAVREAVGDNVDILIEHHGRFNAN 205 K++ +G+ K + + + +D A V +REA G+ ++ ++ HGR +A Sbjct: 132 IKKLRGIGFDTFKLNGCEELGLIDNSRAVDAAVNTVAQIREAFGNEIEFGLDFHGRVSAP 191 Query: 206 SAIMIAKRLEKYNPLFMEEPIHPEDVEGLRKYRNNTSLRIALGERIINKQQALYFMKEGL 265 A ++ K LE+Y PLF+EEP+ E E + TS+ IA GER+ ++ + ++ G Sbjct: 192 MAKVLIKELEQYRPLFIEEPVLAEQAEYYPRLAAQTSIPIAAGERMFSRFEFKRVLEAGG 251 Query: 266 VDFLQADLYRIGGVTETKKVVGIAETFDVQMAFHNAQGPILNAVTLQFDAFIPNFLIQES 325 + LQ DL GG+TE K+ G+AE +DV +A H GPI A L D N + QE Sbjct: 252 LAILQPDLSHAGGITECYKIAGMAEAYDVALAPHCPLGPIALAACLHVDFVSYNAVFQEQ 311 Query: 326 FYDWFPSWKRELI-----YNGTPIDNGYAIIPERPGLGVEVNEKMLDSLKVKGEEYFNP 379 + EL+ ++ G+ +PGLGVE++E + L ++ NP Sbjct: 312 SMGIHYNKGAELLDFVKNKEDFNMEGGFFKPLMKPGLGVEIDEARVMELSQNAPDWRNP 370 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: 402 Number of extensions: 18 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: 382 Length adjustment: 30 Effective length of query: 363 Effective length of database: 352 Effective search space: 127776 Effective search space used: 127776 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