Align gluconate/galactonate dehydratase (EC 4.2.1.140) (characterized)
to candidate 3609058 Dshi_2447 Mandelate racemase/muconate lactonizing protein (RefSeq)
Query= BRENDA::Q97U27 (395 letters) >FitnessBrowser__Dino:3609058 Length = 391 Score = 139 bits (351), Expect = 1e-37 Identities = 106/344 (30%), Positives = 177/344 (51%), Gaps = 17/344 (4%) Query: 26 IVTRVITENGEVGYGEAVPTLRVISVYNAIKQ-VSKAYIGKEVEEVEKNYHEWYKQDFYL 84 + V TE+G +G G A V+ AI + + IG++ + + + Y++ Sbjct: 49 LTCEVETEDGTIGIGNAALAPNVVK--QAIDEWYAPLVIGEDPFDYAYLWEKMYRRTHAW 106 Query: 85 ARSFESATAVSAIDIASWDIIGKELGAPIHKLLGGKTRDRVPVYANGWYQDCVTPEEFAE 144 R TA+SAIDIA WD++GK +G P+ KLLGG+T++++PVY + Y D + P AE Sbjct: 107 GRKGIGMTAISAIDIAIWDLMGKLVGKPVFKLLGGRTKEKIPVYYSKLYADSI-PAMQAE 165 Query: 145 KAKDVVKMGYKALKFDPFGPYYDWIDERGLREAEERVKAVREAVGDNVDILIEHHGRFNA 204 A++ K GY+ K FG Y G+RE +RV+A+RE +G +VD+++E + +N Sbjct: 166 -AEEAQKHGYQGYK-TRFG-YGPKDGPAGMRENLKRVEALREVLGYDVDLMLECYMGWNL 222 Query: 205 NSAIMIAKRLEKYNPGFMEEPVHHEDVIGLRKYKASTHLRVALGERLISEKETAFYVEEG 264 + + +LE++ P ++EEPV +DV G + A + ++ GE S A + Sbjct: 223 DYTKRMLPKLERFEPRWLEEPVIADDVAGYAELNAMGIVPISGGEHEFSVMGCAELINRK 282 Query: 265 LVNILQPDLTNIGGVTVGRSVIKIAEANDVEVAFHNAFGSIQNAVEIQLSAVTQNLYLLE 324 V++LQ D +GG+T + + IAEA + V H G + N L+ N + E Sbjct: 283 AVSVLQYDTNRVGGITAAQKINAIAEAAQIIVIPH--AGQMHN---YHLTMANMNCPISE 337 Query: 325 NFYDWFPQWKRDLVY-----NETPVEGGHVKVPYKPGLGVSINE 363 F + + +L Y + V+G PGLG++I++ Sbjct: 338 YFPVFDVEVGNELFYYIFDGDPEAVDGYLQLDDDTPGLGITISD 381 Lambda K H 0.317 0.136 0.405 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: 394 Number of extensions: 15 Number of successful extensions: 2 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: 395 Length of database: 391 Length adjustment: 31 Effective length of query: 364 Effective length of database: 360 Effective search space: 131040 Effective search space used: 131040 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 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