Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate BWI76_RS19065 BWI76_RS19065 dTDP-glucose 4,6-dehydratase
Query= BRENDA::F6DEY6 (311 letters) >FitnessBrowser__Koxy:BWI76_RS19065 Length = 354 Score = 130 bits (327), Expect = 5e-35 Identities = 107/345 (31%), Positives = 166/345 (48%), Gaps = 53/345 (15%) Query: 1 MRVLVTGGAGFIGSHIVEDLLARGL-EVAVLD------NLATGKRENVPKGVPFFQVDLR 53 M++LVTGGAGFIGS +V ++ EV V+D NL + + +V F +V++ Sbjct: 1 MKILVTGGAGFIGSAVVRHIINDTTDEVVVVDCLTYAGNLESLTQVSVSDRFSFEKVNIC 60 Query: 54 DKEEVERAFREFRPTHVSHQAAQASVKVSVEDPVLDFEVNLLGGLNLLEACRQYGVE-KL 112 DK+E+ R F +P V H AA++ V S++ P E N++G LLE R Y + + Sbjct: 61 DKDELNRIFHYHKPDAVMHLAAESHVDRSIDGPAAFIETNIVGTYTLLEVARAYWNQLEE 120 Query: 113 VFAS-------TGGAIYGEV-PEGERAEETWPPRPKSPYAASKAAFEHYLSVYGQSYGLK 164 F S + +YG++ + E P SPY+ASKA+ +H + + ++YGL Sbjct: 121 QFKSNFRFHHISTDEVYGDLHGTDDLFTEKTSYSPSSPYSASKASSDHLVRAWLRTYGLP 180 Query: 165 WVSLRYGNVYGPRQDPHGEAGVVAIFAERVLNGLPVTLYARKTPGDEGCVRDYVYVGDVA 224 + N YGP P ++ + L G P+ +Y GD G +RD++YV D Sbjct: 181 TIVTNCSNNYGPFHFPE---KLIPLIILNALEGKPLPVY-----GDGGQIRDWLYVED-- 230 Query: 225 EAHALALFSL--EGI----YNVGTGEGHTTREVLEAVAEAAGKAPQVQPAPP-------- 270 HA AL+ + EGI YN+G GH R+ ++ V + P P Sbjct: 231 --HARALYKVVTEGIVGETYNIG---GHNERKNIDVVKTICLLLEEYVPTKPKGLNNYCD 285 Query: 271 -------RPGDLERSVLSPLKLMAH-GWRPKVGFQEGIRLTVDHF 307 RPG R + K++ GW+P+ F+ GIR TV+ + Sbjct: 286 LITYVKDRPGHDVRYAIDATKILNELGWKPQETFESGIRKTVEWY 330 Lambda K H 0.318 0.138 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: 261 Number of extensions: 15 Number of successful extensions: 5 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: 311 Length of database: 354 Length adjustment: 28 Effective length of query: 283 Effective length of database: 326 Effective search space: 92258 Effective search space used: 92258 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 (21.7 bits) S2: 49 (23.5 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