Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate 16149 b2041 dTDP-glucose 4,6 dehydratase, NAD(P)-binding (NCBI)
Query= BRENDA::Q9WYX9 (309 letters) >FitnessBrowser__Keio:16149 Length = 361 Score = 144 bits (364), Expect = 2e-39 Identities = 115/338 (34%), Positives = 168/338 (49%), Gaps = 38/338 (11%) Query: 1 MNILVTGGAGFIGSHVVDKLIENGYGVIV-VDNLS-SGKVENL-----NRNALFYEQSIE 53 M ILVTGGAGFIGS VV +I N +V VD L+ +G E+L + +F I Sbjct: 1 MKILVTGGAGFIGSAVVRHIINNTQDSVVNVDKLTYAGNRESLADVSDSERYVFEHADIC 60 Query: 54 DEEMMERIFSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKY-----G 108 D M RIF+ H+P+ V HLAA++ V S+ PA +TNI+G+ VLLE + Y Sbjct: 61 DAPAMARIFAQHQPDAVMHLAAESHVDRSITGPAAFIETNIVGTYVLLEAARNYWSALDS 120 Query: 109 VKKFIF---SSTGGAIYGE--------NVKVFPT-PETEIPHPISPYGIAKYSTEMYLEF 156 KK F + +YG+ N + P ET P SPY +K S++ + Sbjct: 121 DKKNSFRFHHISTDEVYGDLPHPDEVNNTEELPLFTETTAYAPSSPYSASKASSDHLVRA 180 Query: 157 FAREYGLKYTVLRYANVYGPRQDPYGEAGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVD 216 + R YGL V +N YGP P ++ + L G+ + I+G G+ +RD++YV+ Sbjct: 181 WKRTYGLPTIVTNCSNNYGPYHFP---EKLIPLVILNALEGKALPIYGKGDQIRDWLYVE 237 Query: 217 DVVRANLLAMEKGD-NEVFNIGTGRGTTVN-----QLFKLLKEIT----GYDKEPVYKPP 266 D RA + +G E +NIG G N + LL EI Y ++ Y Sbjct: 238 DHARALYTVVTEGKAGETYNIG-GHNEKKNIDVVLTICDLLDEIVPKEKSYREQITYVAD 296 Query: 267 RKGDVRKSILDYTKAKEKLGWEPKVSLEEGLKLTVEYF 304 R G R+ +D K LGW+P+ + E G++ TVE++ Sbjct: 297 RPGHDRRYAIDAEKIGRALGWKPQETFESGIRKTVEWY 334 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: 248 Number of extensions: 11 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: 361 Length adjustment: 28 Effective length of query: 281 Effective length of database: 333 Effective search space: 93573 Effective search space used: 93573 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