Align Putative UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate 202299 SO3189 polysaccharide biosynthesis protein (NCBI ptt file)
Query= curated2:Q57664 (305 letters) >FitnessBrowser__MR1:202299 Length = 340 Score = 190 bits (483), Expect = 3e-53 Identities = 114/320 (35%), Positives = 177/320 (55%), Gaps = 24/320 (7%) Query: 3 LVTGGAGFIGSHIVDKLIENNYDVIILDNLTTGNKNNINP-----------KAEFVNADI 51 L+TG AGFIGS+++++L++ N VI LDN TG ++N++ + F+N DI Sbjct: 19 LITGVAGFIGSNLLEQLLKLNQTVIGLDNFATGRQHNLDEVQSLVTSEQWMRFSFINGDI 78 Query: 52 RDKDLDEKINFKDVEVVIHQAAQINVRNSVENPVYDGDINVLGTINILEMMRKYDIDKIV 111 RD + E + V+ V+HQAA +V S+ +P+ N+ G +N+L+ ++ ++ Sbjct: 79 RDYAICEAV-VNGVDYVLHQAALGSVPRSIADPITTNAANITGFLNMLQAAKEAEVKSFT 137 Query: 112 FASSGGAVYGEPNYLPVDENHPINPLSPYGLSKYVGEEYIKLYNRLYGIEYAILRYSNVY 171 +A+S + YG+ LP E + NPLSPY ++KYV E Y +Y R YG E LRY NV+ Sbjct: 138 YAASS-STYGDHPALPKVEQNIGNPLSPYAVTKYVNELYASVYARTYGFETIGLRYFNVF 196 Query: 172 GERQDPKGE-AGVISIFIDKMLKNQSPIIFGDGNQTRDFVYVGDVAKANLMAL----NWK 226 G RQDP G A VI + M+K + I GDG +RDF Y+ +V + N++A K Sbjct: 197 GRRQDPNGAYAAVIPKWTSSMIKGEDVFINGDGETSRDFCYIDNVVQMNILAATAASEAK 256 Query: 227 NEIVNIGTGKETSVNELFDIIKHEIGFRGEAIYDKP-----REGEVYRIYLDIKKAES-L 280 NE+ N+ G T++N+L+ IK + G + P R G+V D+ KA + L Sbjct: 257 NEVYNVAVGDRTTLNDLYFAIKDSLNANGINVNQNPNYRDFRAGDVRHSQADVSKAVTRL 316 Query: 281 GWKPEIDLKEGIKRVVNWMK 300 G++ + EGI + W K Sbjct: 317 GYQYTHKILEGISEAMPWYK 336 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: 306 Number of extensions: 19 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: 305 Length of database: 340 Length adjustment: 28 Effective length of query: 277 Effective length of database: 312 Effective search space: 86424 Effective search space used: 86424 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 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