Align xylonate dehydratase monomer (EC 4.2.1.82) (characterized)
to candidate Ga0059261_4216 Ga0059261_4216 Dihydroxyacid dehydratase/phosphogluconate dehydratase
Query= metacyc::MONOMER-20629 (591 letters) >FitnessBrowser__Korea:Ga0059261_4216 Length = 573 Score = 240 bits (613), Expect = 1e-67 Identities = 169/518 (32%), Positives = 263/518 (50%), Gaps = 31/518 (5%) Query: 35 GITPEELRSGKPIIGIAQTGSDISPCNRIHLDLVQRVRDGIRDAGGIPMEFPVHPIFENC 94 GI+ EE+ +P + +A G+D +PCN R G+ D GG+P F + + Sbjct: 32 GISEEEI--ARPFVALASAGNDSAPCNTTLDAQADAARKGVADNGGLPRRFNTITVTDGI 89 Query: 95 RRPTAALDRNLSYLGLVE-----TLHGYPIDAVVLTTGCDKTTPAGIMAATTVNIPAIVL 149 + +L ++ ++ G+ DA+V GCDK+ P +MA +NIP+I + Sbjct: 90 AMGHQGMKSSLVSREVIADSVELSVRGHCYDALVGFAGCDKSLPGMMMAMLRLNIPSIFV 149 Query: 150 SGGPMLDGWHENELVGSGTVIWRSRRKLAAGE--ITEEEFIDRAASSAPSAGHCNTMGTA 207 GG +L G +++ V + ++ K AAG I+E +++ A P G C TA Sbjct: 150 YGGSILPGRYQDRDV-TVVDVFEVVGKFAAGTCPISEVHALEKVA--CPGHGACGGQYTA 206 Query: 208 STMNAVAEALGLSLTGCAAIPAPYRERGQMAYKTGQRIVDLAYDDVKPLDILTKQAFENA 267 +TM V EA+GLSL +PAPY R Q+A G ++++L +++P DI T++AF NA Sbjct: 207 NTMACVGEAIGLSLPNSNMVPAPYTSREQIAVAAGYQVMELLERNIRPRDICTREAFINA 266 Query: 268 IALVAAAGGSTNAQPHIVAMARHAGVEITADDWRAAY-DIPLIVNMQPAGKYLGERFHRA 326 +VAA GGSTN H+ AMA AG++ D + P +++P GKY+ + + A Sbjct: 267 ARIVAATGGSTNGALHLPAMASEAGIDFDLFDVAEVFKSTPYAADLKPGGKYVAKDMYEA 326 Query: 327 GGAPAVLWELLQQGRLHGDVLTVTGKTMSENL-QGRETSDREVIFPYHEPLAEKAGFLVL 385 GG ++ +L+ G L+GD +TVTGKT+ EN+ Q D++VI+ P+ G + L Sbjct: 327 GGVYMLMKSMLENGLLYGDCMTVTGKTLGENIDQVTWNPDQKVIYDVRTPITPTGGVVGL 386 Query: 386 KGNLF-DFAIMKSSVIGEEFRKRYLSQPGQEGVFEARAIVFDGSDDYHKRINDPALEIDE 444 +G L + AI+K + + VFE A FD +D + EI E Sbjct: 387 RGTLAPNGAIVKVAGMSRL-------------VFEGPARCFDCEEDAFAAVE--KREIRE 431 Query: 445 RCILVIRGAGPIGWPGSAEVVNMQPPDHLLKKGIMSLPTLGDGRQSGTADSPSILNASPE 504 ++VIR GP G PG E+++ + L G + + DGR SG I + PE Sbjct: 432 GEVVVIRYEGPKGGPGMREMLSTTAALYGLGMG-EKVALITDGRFSGATRGFCIGHVGPE 490 Query: 505 SAIGGGLSWLRTGDTIRIDLNTGRCDALVDEATIAARK 542 +A G ++ + GDTIRID G D V E +A R+ Sbjct: 491 AAECGPIALVEDGDTIRIDAEAGTIDLHVAEDVLAERR 528 Lambda K H 0.319 0.136 0.411 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: 803 Number of extensions: 35 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 591 Length of database: 573 Length adjustment: 36 Effective length of query: 555 Effective length of database: 537 Effective search space: 298035 Effective search space used: 298035 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: 53 (25.0 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