Align xylonate dehydratase monomer (EC 4.2.1.82) (characterized)
to candidate WP_078427497.1 BK574_RS03330 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-20629 (591 letters) >NCBI__GCF_002019605.1:WP_078427497.1 Length = 556 Score = 236 bits (601), Expect = 2e-66 Identities = 170/523 (32%), Positives = 270/523 (51%), Gaps = 31/523 (5%) Query: 35 GITPEELRSGKPIIGIAQTGSDISPCNRIHLD-LVQRVRDGIRDAGGIPMEFPVHPIFEN 93 GI E+ KP +GIA T S+++PCN +H+D L ++ + G DAGG P F + + Sbjct: 29 GIKDEDFN--KPFVGIASTWSEVTPCN-MHIDELARKAKKGALDAGGTPFIFNTITVSDG 85 Query: 94 CRRPTAALDRNLSYLGLV----ETLHGYP-IDAVVLTTGCDKTTPAGIMAATTVNIPAIV 148 T + +L ++ ET+ G D VV GCDK P ++A +N+PA+ Sbjct: 86 ISMGTEGMRFSLPSREVIADSIETVVGAQNYDGVVAIGGCDKNMPGCMIAIGRLNLPAVF 145 Query: 149 LSGGPMLDGWHENELVGSGTVIWRSRRKLAAGEITEEEFIDRAASSAPSAGHCNTMGTAS 208 + GG + G + + + + + + K G+I +E + P AG C M TA+ Sbjct: 146 VYGGTIRPGNVDGKDIDIVSA-FEAVGKYNNGDIDRDELHKIECHACPGAGSCGGMYTAN 204 Query: 209 TMNAVAEALGLSLTGCAAIPAPYRERGQMAYKTGQRIVDLAYDDVKPLDILTKQAFENAI 268 TM + EA+G+SL G ++ PA E+ + K G+ +++L + P DI+TK+AFENAI Sbjct: 205 TMASAIEAMGMSLPGSSSNPAETEEKLEDCIKAGKAVMNLLNKGITPKDIMTKKAFENAI 264 Query: 269 ALVAAAGGSTNAQPHIVAMARHAGVEITADDW-RAAYDIPLIVNMQPAGKYLGERFHRAG 327 +V A GGSTNA H++A+A V++ DD+ R +P I +++P+G+Y+ E G Sbjct: 265 TVVMALGGSTNAVLHLLALAHTVDVDLNLDDFERIRKKVPHIADLKPSGRYVMENLSEIG 324 Query: 328 GAPAVLWELLQQGRLHGDVLTVTGKTMSENL-QGRETSDREVIFPYHEPLAEKAGFLVLK 386 G PAV+ LL +G LHGD LTVT T+ +NL + + + + I + P E ++LK Sbjct: 325 GVPAVMKLLLDKGLLHGDCLTVTSNTIEQNLSEIQPLKEGQEIISFENPKRETGPLVILK 384 Query: 387 GNLF-DFAIMKSSVIGEEFRKRYLSQPGQEGVFEARAIVFDGSDDYHKRINDPALEIDER 445 GNL D A+ K S G + +K A VFD D + + E++ Sbjct: 385 GNLAPDGALAKMS--GLKIKK-----------ITGPARVFDSETDATNAVLNN--EVNPG 429 Query: 446 CILVIRGAGPIGWPGSAEVVNMQPPDHLLKKGI-MSLPTLGDGRQSGTADSPSILNASPE 504 ++VIR GP G PG AE++++ ++ KG + + DGR SG + + SPE Sbjct: 430 DVIVIRYVGPKGGPGMAEMLSITA--IVVGKGFGEKVGLITDGRFSGGTHGLVVGHISPE 487 Query: 505 SAIGGGLSWLRTGDTIRIDLNTGRCDALVDEATIAARKQDGIP 547 + +GG ++ ++ GD I ID V + R +D P Sbjct: 488 AQVGGPIALIKEGDMITIDSELQELAVDVSPEDLNERLKDWSP 530 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: 792 Number of extensions: 43 Number of successful extensions: 7 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: 591 Length of database: 556 Length adjustment: 36 Effective length of query: 555 Effective length of database: 520 Effective search space: 288600 Effective search space used: 288600 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 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