Align UDP-glucose 4-epimerase; UDP-galactose 4-epimerase; Uridine diphosphate galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate Pf6N2E2_3878 dTDP-glucose 4,6-dehydratase (EC 4.2.1.46)
Query= SwissProt::A0R5C5 (313 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3878 Length = 360 Score = 153 bits (387), Expect = 5e-42 Identities = 110/335 (32%), Positives = 168/335 (50%), Gaps = 32/335 (9%) Query: 1 MRTLVTGAAGFIGSTLVDRLLAD-GHGVVGLDDLS-SGRAENLHSAENSDKFEFVKADIV 58 MR LVTG AGFIGS L+ L+ D GH V+ LD L+ +G E+L S ++ ++EFV+ADIV Sbjct: 1 MRILVTGGAGFIGSALIRHLILDTGHQVLNLDKLTYAGNLESLSSIDHDSRYEFVQADIV 60 Query: 59 DAD-LTGLLAEFKPEVIFHLAAQISVKRSVDDPPFDATVNVVGTVRLAEAARL------- 110 D ++ +LA FKP+ I HLAA+ V RS+D P N+VGT L EA R Sbjct: 61 DQPTVSAVLARFKPDAIMHLAAESHVDRSIDGPADFIQTNIVGTYSLLEATRAYWQALPE 120 Query: 111 --AGVRKVVHTSSG---GSVYGTPPAYPTSEDMPVNPASPYAAGKVAGEVYLNMYRNLYD 165 + H S+ G ++G + +E P+SPY+A K A + + ++ Y Sbjct: 121 PQRRAFRFHHISTDEVYGDLHGVDDLF--TETTAYAPSSPYSASKAASDHLVRAWQRTYG 178 Query: 166 LDCSHIAPANVYGPRQDPHGEAGVVAIFSEALLAGRTTKIFGDGSDTRDYVFVDDVVDAF 225 L +N YGP P +V + + LAG+ ++GDG RD++FV+D A Sbjct: 179 LPVLLTNCSNNYGPFHFPEKLIPLVILNA---LAGKPLPVYGDGQQVRDWLFVEDHARAL 235 Query: 226 VRAGGPAGGGQRFNVGTGVETSTRELHTAIAGAVG--APDEPE----------FHPPRLG 273 ++ G+ +N+G E ++ +I + AP +PE F R G Sbjct: 236 LKVVTEGMVGETYNIGGHNEQKNIDVVRSICALLEELAPRKPEGIEHYADLISFVQDRPG 295 Query: 274 DLRRSRLDNTRAREVLGWQPQVALAEGIAKTVEFF 308 R +D ++ LGW P+ G+ KTV+++ Sbjct: 296 HDLRYAIDASKIERELGWTPRETFETGLRKTVQWY 330 Lambda K H 0.317 0.136 0.396 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: 280 Number of extensions: 20 Number of successful extensions: 6 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: 313 Length of database: 360 Length adjustment: 28 Effective length of query: 285 Effective length of database: 332 Effective search space: 94620 Effective search space used: 94620 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: 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