Align UDP-glucose 4-epimerase; UDP-galactose 4-epimerase; Uridine diphosphate galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate Ac3H11_1880 dTDP-glucose 4,6-dehydratase (EC 4.2.1.46)
Query= SwissProt::A0R5C5 (313 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1880 Length = 363 Score = 129 bits (325), Expect = 8e-35 Identities = 103/330 (31%), Positives = 148/330 (44%), Gaps = 30/330 (9%) Query: 4 LVTGAAGFIGSTLV-DRLLADGHGVVGLDDLS-SGRAENLHSAENSDKFEFVKADIVDAD 61 LVTG AGFIG+ V D L A VV LD L+ +G NL S + + FV+ DI D Sbjct: 3 LVTGGAGFIGANFVLDWLAASSEPVVNLDKLTYAGNLHNLDSVQGDARHIFVQGDIGDTA 62 Query: 62 LTG-LLAEFKPEVIFHLAAQISVKRSVDDPPFDATVNVVGTVRLAEAARL---------A 111 L LLAE KP + + AA+ V RS+ P N+VG+ RL EA R Sbjct: 63 LVARLLAECKPRAVVNFAAESHVDRSIHGPEDFIQTNIVGSFRLLEAVRAYWGALPEGDR 122 Query: 112 GVRKVVHTSSG---GSVYGTPPAYPTSEDMPVNPASPYAAGKVAGEVYLNMYRNLYDLDC 168 + +H S+ GS+ T PA+ +E P SPY+A K A + + + + Y L Sbjct: 123 AAFRFLHVSTDEVYGSLAPTDPAF--AETRGFEPNSPYSASKAASDHLVRAWHHTYGLPV 180 Query: 169 SHIAPANVYGPRQDPHGEAGVVAIFSEALLAGRTTKIFGDGSDTRDYVFVDDVVDAFVRA 228 +N YGP P ++ + LAG+ ++GDG RD+++V D A R Sbjct: 181 LTTNCSNNYGPYHFPE---KLIPLMIVNALAGKNLPVYGDGMQVRDWLYVKDHCSAIRRV 237 Query: 229 GGPAGGGQRFNVGTGVETSTRELHTAI----------AGAVGAPDEPEFHPPRLGDLRRS 278 G+ +NVG E E+ + A + + R G RR Sbjct: 238 LEAGAPGETYNVGGWNEKPNIEIVNMVCSLLDELRPRADGQSYRTQITYVKDRPGHDRRY 297 Query: 279 RLDNTRAREVLGWQPQVALAEGIAKTVEFF 308 +D + LGW+P GI KTV+++ Sbjct: 298 AIDARKIERELGWKPAETFDTGIRKTVQWY 327 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: 265 Number of extensions: 17 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: 313 Length of database: 363 Length adjustment: 28 Effective length of query: 285 Effective length of database: 335 Effective search space: 95475 Effective search space used: 95475 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