Align gluconate/galactonate dehydratase (EC 4.2.1.140); gluconate dehydratase (EC 4.2.1.39) (characterized)
to candidate WP_085636267.1 MGEO_RS08380 mandelate racemase/muconate lactonizing enzyme family protein
Query= BRENDA::Q6L1T2 (391 letters) >NCBI__GCF_002115805.1:WP_085636267.1 Length = 411 Score = 195 bits (496), Expect = 2e-54 Identities = 130/386 (33%), Positives = 198/386 (51%), Gaps = 27/386 (6%) Query: 15 PGEKSSPWSSTILIVKLTSSNGNIGYGEAPTTFMTLPVKESMRE--VERVFKDQNYFNIE 72 PG W+ VK+T+ G G+GE + + +++ E +R K +N NIE Sbjct: 16 PGWGGRYWT----FVKVTTDTGITGWGECYASSVGPTAMKAVIEDVFDRHMKGENPENIE 71 Query: 73 KNMREFYKHSFYLSRSMEATSALSAFEIASWDLIGKDLGTPVYNLLGGEYNSELRAYA-- 130 R Y F + A S EIA WD++GK PV+ LLGG N +RAY Sbjct: 72 LMFRRAYSSGFTQRPDLTVMGAFSGLEIACWDILGKARNRPVWALLGGRMNERVRAYTYL 131 Query: 131 --------NGWYSDCLEPDDFVSRAKEYIKKGYTAFKFDPFRNNFDRIGND----GIKKA 178 N +++D PD AKEY+++G+TA KFDP G+ + + Sbjct: 132 YPLPHHDLNSFWTD---PDAQAEAAKEYVRQGFTALKFDPAGPYTIHGGHQPALTDVSLS 188 Query: 179 VDIVSAMRSELGENIDLLIECHGRFSTKYAIKVGQALDEFNPLFIEEPIHPEMELGLFDF 238 V++ A+R+ +G+ DLL HG+F+T AI++GQA++ + PL+ EEPI P+ L + Sbjct: 189 VEMCKAIRAAVGDRADLLFGTHGQFTTSGAIRLGQAIEPYLPLWYEEPIPPDNLLEFAEV 248 Query: 239 KRYVNTPVALGERLLNKEDFARYISQGMVDIVQADLTNSKGILEAKKISAIVESFGGLMA 298 R V P+A GER+ K +FA + G I+Q L + GI E KK++A+ E+F MA Sbjct: 249 ARAVRIPIATGERMTTKAEFATLLRTGGAKILQPALGRAGGIWEMKKLAAMAEAFNAEMA 308 Query: 299 FHNAFGPVQTAATLNVDYTLTNFLIQESFEDSWPDWKRNLFSGYRIENGHFKLSGKPGLG 358 H GPV+ AA +++ ++ N LI E+ E P + + R+E+G+ PGLG Sbjct: 309 PHLYAGPVEWAANIHLCASIPNVLIAETIET--PFHAALIRNSIRVEDGYITPPETPGLG 366 Query: 359 ITADEKLMEKLIY--DGMEEFNKNEP 382 I DE+ + DG+ +NEP Sbjct: 367 IEFDEEFARAHPFTGDGLHLQMQNEP 392 Lambda K H 0.317 0.136 0.401 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: 366 Number of extensions: 27 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: 391 Length of database: 411 Length adjustment: 31 Effective length of query: 360 Effective length of database: 380 Effective search space: 136800 Effective search space used: 136800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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