Align L-rhamnonate dehydratase (EC 4.2.1.90) (characterized)
to candidate Pf1N1B4_3383 Mandelate racemase (EC 5.1.2.2)
Query= BRENDA::A3LZU6 (429 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3383 Length = 391 Score = 210 bits (534), Expect = 7e-59 Identities = 117/338 (34%), Positives = 185/338 (54%), Gaps = 15/338 (4%) Query: 63 GSFCVEIEATNGVKGFATGFGGPP-ACWLVANHFRRFLIGADPRDTTLLWDKMFRASMFY 121 G VE+E G+ G P A ++ + IG DP D +W KM+R S + Sbjct: 46 GWLVVEVETDTGLVGIGNCALAPRVAKEIIDTYLAPIAIGEDPFDNEYIWQKMYRQSHAW 105 Query: 122 GRKGLTVAVISVIDLAIWDLLGKLRNEPVYKMIGGATRERLDFYCTGCRPDIAKEV---- 177 GRKG+ +A IS ID+AIWD++GK N+PV+K++GG T+E++ Y + + ++ Sbjct: 106 GRKGIGMAAISAIDIAIWDIMGKAVNKPVFKLLGGRTKEKIWTYASKLYANDNLDLFLEE 165 Query: 178 -------GFWGGKVALPYGPAEGHDGLRRNVEFLRKHRKSVGPDFPIMVDCYMSLNVSYV 230 GF K+ YGP +G G+R+N+E +R R+ GPD IM++CYM + Y Sbjct: 166 AQGYLNQGFTALKMRFGYGPKDGPAGMRKNIEQVRALRELAGPDIDIMLECYMGWTLEYA 225 Query: 231 IDLVNACKDLNINWFEEVLHPDDFDGFQKLKSACPWMKFTTGEHEYSKYGFRKLIEGRNV 290 ++ + W EE + DD +G+ +LK M + GEHE++ YGF+ L+E R + Sbjct: 226 RRMLPKLAEFEPRWLEEPVIADDIEGYIELKK-MGIMPISGGEHEFTSYGFKDLLERRAI 284 Query: 291 DILQPDIMWVGGLTEILKISHQAAAYDIPVVPHASGPYSYHFVISQENTPFHEYLSNSPD 350 D++Q D VGG+T KI+ A A+ +PV+PHA ++YH +S +P E+ D Sbjct: 285 DVIQYDTNRVGGITAARKINALAEAWSVPVIPHAGQMHNYHLTMSTTASPMAEFFPVF-D 343 Query: 351 SMSVLPVFGELFTDEPVPTEGYLSITEFDKPGFGLTLN 388 +F +F EP P +GY+ + + +KPG GL ++ Sbjct: 344 VEVGNELFYYVFKGEPQPVKGYIQLDD-NKPGLGLEIS 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: 477 Number of extensions: 25 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: 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