Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate 7024172 Shewana3_1379 dTDP-glucose 4,6 dehydratase (RefSeq)
Query= BRENDA::Q9WYX9 (309 letters) >FitnessBrowser__ANA3:7024172 Length = 359 Score = 140 bits (354), Expect = 3e-38 Identities = 107/341 (31%), Positives = 169/341 (49%), Gaps = 41/341 (12%) Query: 1 MNILVTGGAGFIGSHVVDKLIEN-GYGVIVVD------NLSSGKVENLNRNALFYEQSIE 53 M ILVTGGAGFIGS V+ +I N VI VD NL S K+ + N F + I Sbjct: 1 MKILVTGGAGFIGSAVIRHIIMNTNDSVINVDKLTYAGNLESLKLVSTNPRYNFEQVDIC 60 Query: 54 DEEMMERIFSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVK--- 110 D +ER+FS ++P+ V HLAA++ V S+ P+ +TNI+G+ +LLE + +Y + Sbjct: 61 DRATLERVFSQYQPDAVMHLAAESHVDRSITGPSDFIQTNIVGTYILLEAARQYWTQLDA 120 Query: 111 ------KFIFSSTGGAIYGE------------NVKVFPTPETEIPHPISPYGIAKYSTEM 152 +F ST +YG+ N + ET P SPY +K S++ Sbjct: 121 ERKAAFRFHHIST-DEVYGDLPHPDEQEGQAVNQYLPLFTETTPYAPSSPYSASKASSDH 179 Query: 153 YLEFFAREYGLKYTVLRYANVYGPRQDPYGEAGVVAIFTERMLRGEEVHIFGDGEYVRDY 212 + + R YG V +N YGP P ++ + L G+ + I+G G+ +RD+ Sbjct: 180 LVRAWLRTYGFPTIVTNCSNNYGPYHFP---EKLIPLVILNALEGKSLPIYGKGDQIRDW 236 Query: 213 VYVDDVVRANLLAMEKGD-NEVFNIGTGR--------GTTVNQLFKLLKEITGYDKEPVY 263 +YV+D RA + +G E +NIG T + L L+ + T Y ++ + Sbjct: 237 LYVEDHARALYKVVTEGKVGETYNIGGHNEKQNIEVVKTICSILDSLVPKATPYAEQITF 296 Query: 264 KPPRKGDVRKSILDYTKAKEKLGWEPKVSLEEGLKLTVEYF 304 R G R+ +D +K +L W+P+ + E GL+ T+E++ Sbjct: 297 VTDRPGHDRRYAIDASKMSAELNWQPQETFETGLRKTIEWY 337 Lambda K H 0.318 0.139 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: 267 Number of extensions: 14 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: 309 Length of database: 359 Length adjustment: 28 Effective length of query: 281 Effective length of database: 331 Effective search space: 93011 Effective search space used: 93011 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