Align D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) (characterized)
to candidate BPHYT_RS16405 BPHYT_RS16405 galactonate dehydratase
Query= metacyc::MONOMER-18070 (393 letters) >FitnessBrowser__BFirm:BPHYT_RS16405 Length = 382 Score = 210 bits (534), Expect = 6e-59 Identities = 137/387 (35%), Positives = 207/387 (53%), Gaps = 21/387 (5%) Query: 3 KISEIEAYILGKEVTSAQWASLMVLVRVTTNDGRVGWGETVSALRAEAVANFVKKINTVL 62 KI+++E +I+ +W L ++ T++G VGWGE V RA VA V++++ L Sbjct: 2 KITKLETFIV-----PPRWCFL----KIETDEGIVGWGEPVVEGRAHTVAAAVEELSDYL 52 Query: 63 KGNDVFNVEKNRLEWYKHDFNMTISLESTTAYSAVDIASWDIIGKELGAPLYKLLGGKTR 122 G D +E + Y+ F + + +A + VD A WDI GK G P++ LLGG+ R Sbjct: 53 IGKDPLLIEDHWQVMYRSGFYRGGPI-TMSAIAGVDQALWDIKGKHHGVPIHALLGGQVR 111 Query: 123 DKVLVYANGWYQNCVKPEDFAEKAKEIVKMGYKALKFDPFGPYFNDISKKGLDIAEERVK 182 DK+ VY+ W +P D A A+ +V+ G+KA+K + + + V Sbjct: 112 DKIKVYS--WIGGD-RPSDVANNARAVVERGFKAVKMNGSEELQIIDTFDKVQGVINNVA 168 Query: 183 AVREAVGDNVDILIEHHGRFNANSAIMIAKRLEKYNPLFMEEPIHPEDVEGLRKYRNNTS 242 AVREAVG N+ I ++ HGR + A ++AK L+ Y LF+EEP+ E+ E LR N T+ Sbjct: 169 AVREAVGPNIGIGVDFHGRVHKPMAKVLAKELDPYKLLFIEEPVLSENAEALRDIVNQTN 228 Query: 243 LRIALGERIINKQQALYFMKEGLVDFLQADLYRIGGVTETKKVVGIAETFDVQMAFHNAQ 302 IALGER+ ++ + + G VD +Q D GG+TE +K+ +AE +DV +A H Sbjct: 229 TPIALGERLYSRWDFKHILSGGYVDIIQPDASHAGGITECRKIASMAEAYDVALALHCPL 288 Query: 303 GPILNAVTLQFDAFIPNFLIQESFYDWFPSWKRELI-YNGTP----IDNGYAIIPERPGL 357 GPI A LQ DA N IQE + +L+ Y P ++G+ IP+ PGL Sbjct: 289 GPIALATCLQIDAVSYNAFIQEQSLGIHYNQGNDLLDYIKNPEVFKYEDGFVSIPQGPGL 348 Query: 358 GVEVNEKMLDSLKVKGEEYFNPEEPVW 384 G+EVNE+ + + G + N PVW Sbjct: 349 GIEVNEEKVREMAKVGHRWRN---PVW 372 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: 412 Number of extensions: 25 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: 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