Align Putative UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_011187291.1 DP_RS00210 Vi polysaccharide biosynthesis UDP-N-acetylglucosaminuronic acid C-4 epimerase TviC
Query= curated2:Q57664 (305 letters) >NCBI__GCF_000025945.1:WP_011187291.1 Length = 345 Score = 166 bits (419), Expect = 9e-46 Identities = 102/318 (32%), Positives = 170/318 (53%), Gaps = 24/318 (7%) Query: 3 LVTGGAGFIGSHIVDKLIENNYDVIILDNLTTGNKNNINP-----------KAEFVNADI 51 L+TG AGFIGS++++ L+ V+ LDN TG ++N++ F+ DI Sbjct: 19 LITGVAGFIGSNLLETLLGLGQKVVGLDNFVTGYQHNLDEVEGAVTDAQWQNFRFIEGDI 78 Query: 52 RDKDLDEKINFKDVEVVIHQAAQINVRNSVENPVYDGDINVLGTINILEMMRKYDIDKIV 111 D ++ + V+ V+ QAA +V S+ +P+ + N+ G +N+L R ++ Sbjct: 79 CSLDACQEA-CQGVDYVLQQAALGSVPRSIVDPITTNNTNISGFLNMLVAARDAEVKSFT 137 Query: 112 FASSGGAVYGEPNYLPVDENHPINPLSPYGLSKYVGEEYIKLYNRLYGIEYAILRYSNVY 171 +A+S + YG+ LP E + NPLSPY ++KYV E Y ++ R Y + LRY N+ Sbjct: 138 YAASS-STYGDHPALPKVEENIGNPLSPYAVTKYVNELYASVFARTYSFKTIGLRYFNIL 196 Query: 172 GERQDPKGE-AGVISIFIDKMLKNQSPIIFGDGNQTRDFVYVGDVAKANLMALNWKNE-- 228 G+RQDP G A VI ++ M+ +++ I GDG +RDF ++ + +AN++A E Sbjct: 197 GKRQDPNGAYAAVIPLWTAAMINDETVFINGDGETSRDFCFIENAVQANILAATATEEAR 256 Query: 229 --IVNIGTGKETSVNELFDIIKHEIGFRG-----EAIYDKPREGEVYRIYLDIKKAES-L 280 + N+ G T++NELF++IKH + G + Y R G+V D K + L Sbjct: 257 DNVYNVAVGDRTTLNELFNLIKHNLADHGIVYNLDPSYRDFRAGDVRHSQADTTKIKRLL 316 Query: 281 GWKPEIDLKEGIKRVVNW 298 G+ P+ + GI++ + W Sbjct: 317 GYSPQYKIGAGIEKAMGW 334 Lambda K H 0.317 0.140 0.405 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: 294 Number of extensions: 23 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: 305 Length of database: 345 Length adjustment: 28 Effective length of query: 277 Effective length of database: 317 Effective search space: 87809 Effective search space used: 87809 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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