Align L-rhamnonate dehydratase (EC 4.2.1.90) (characterized)
to candidate 3609058 Dshi_2447 Mandelate racemase/muconate lactonizing protein (RefSeq)
Query= BRENDA::A3LZU6 (429 letters) >FitnessBrowser__Dino:3609058 Length = 391 Score = 188 bits (477), Expect = 3e-52 Identities = 111/332 (33%), Positives = 175/332 (52%), Gaps = 14/332 (4%) Query: 68 EIEATNGVKGFATGFGGPPAC-WLVANHFRRFLIGADPRDTTLLWDKMFRASMFYGRKGL 126 E+E +G G P + + +IG DP D LW+KM+R + +GRKG+ Sbjct: 52 EVETEDGTIGIGNAALAPNVVKQAIDEWYAPLVIGEDPFDYAYLWEKMYRRTHAWGRKGI 111 Query: 127 TVAVISVIDLAIWDLLGKLRNEPVYKMIGGATRERLDFYCTGCRPDI----------AKE 176 + IS ID+AIWDL+GKL +PV+K++GG T+E++ Y + D A++ Sbjct: 112 GMTAISAIDIAIWDLMGKLVGKPVFKLLGGRTKEKIPVYYSKLYADSIPAMQAEAEEAQK 171 Query: 177 VGFWGGKVALPYGPAEGHDGLRRNVEFLRKHRKSVGPDFPIMVDCYMSLNVSYVIDLVNA 236 G+ G K YGP +G G+R N++ + R+ +G D +M++CYM N+ Y ++ Sbjct: 172 HGYQGYKTRFGYGPKDGPAGMRENLKRVEALREVLGYDVDLMLECYMGWNLDYTKRMLPK 231 Query: 237 CKDLNINWFEEVLHPDDFDGFQKLKSACPWMKFTTGEHEYSKYGFRKLIEGRNVDILQPD 296 + W EE + DD G+ +L +A + + GEHE+S G +LI + V +LQ D Sbjct: 232 LERFEPRWLEEPVIADDVAGYAEL-NAMGIVPISGGEHEFSVMGCAELINRKAVSVLQYD 290 Query: 297 IMWVGGLTEILKISHQAAAYDIPVVPHASGPYSYHFVISQENTPFHEYLSNSPDSMSVLP 356 VGG+T KI+ A A I V+PHA ++YH ++ N P EY D Sbjct: 291 TNRVGGITAAQKINAIAEAAQIIVIPHAGQMHNYHLTMANMNCPISEYFPVF-DVEVGNE 349 Query: 357 VFGELFTDEPVPTEGYLSITEFDKPGFGLTLN 388 +F +F +P +GYL + + D PG G+T++ Sbjct: 350 LFYYIFDGDPEAVDGYLQLDD-DTPGLGITIS 380 Lambda K H 0.321 0.141 0.454 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: 467 Number of extensions: 24 Number of successful extensions: 3 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: 429 Length of database: 391 Length adjustment: 31 Effective length of query: 398 Effective length of database: 360 Effective search space: 143280 Effective search space used: 143280 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 (21.8 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