Align Putative UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_072905799.1 BUB13_RS03920 NAD-dependent dehydratase
Query= curated2:Q57664 (305 letters) >NCBI__GCF_900142125.1:WP_072905799.1 Length = 320 Score = 167 bits (422), Expect = 4e-46 Identities = 110/314 (35%), Positives = 175/314 (55%), Gaps = 21/314 (6%) Query: 2 ILVTGGAGFIGSHIVDKLIENNY-DVIILDNLTTGNKNNINPKAEFVNA-------DIRD 53 ILV GGAGFIGS +V +L++ + +V++ DN G +N+ + + DIRD Sbjct: 8 ILVIGGAGFIGSFVVSELLKTDVAEVVVYDNFARGEISNLEEQLKDSRCSIYEHGGDIRD 67 Query: 54 KDLDEKINFKDVEVVIHQAAQINVRNSVENPVYDGDINVLGTINILEMMRKYDIDKIVFA 113 DL K ++ V+H AA + + + P +N+ G N+LE +I ++V++ Sbjct: 68 VDLLNAA-MKGMDAVVHLAAMW-LLHCKDFPRTAFHVNIEGVFNVLEACVNNNIKRLVYS 125 Query: 114 SSGGAVYGEPNYLPVDENHPINPLSPYGLSKYVGEEYIKLYNRLYGIEYAILRYSNVYGE 173 SS +VYG+ +P+ E HP N + YG +K GE + + YG+ Y LRY NVYG Sbjct: 126 SSA-SVYGDAVEVPMTEEHPFNNRNFYGATKISGEAMCRAFYDRYGLSYVGLRYMNVYGP 184 Query: 174 RQDPKGE-AGVISIFIDKMLKNQSPIIFGDGNQTRDFVYVGDVAKANLMALNWK--NEIV 230 QD GVI I ++K+ N++P+I GDG+Q DF+YV DVA+ N+MAL + +E Sbjct: 185 HQDQTAAYTGVIPIMLNKIAANEAPVINGDGSQAYDFIYVEDVARCNVMALEAEVADEFY 244 Query: 231 NIGTGKETSVNELFDIIKH------EIGFRGEAIYDKPREGEVYRIYLDIKKAESLGWKP 284 N+GTG +TS+ EL D I ++ +R + D R+ RI K + LG+K Sbjct: 245 NVGTGVQTSIKELCDTILDLKQSDLKVEYRPYS-EDDARQLVQNRIGGPEKAQKDLGFKS 303 Query: 285 EIDLKEGIKRVVNW 298 + L +G++++++W Sbjct: 304 KYGLIDGLQQLIDW 317 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: 305 Number of extensions: 19 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: 320 Length adjustment: 27 Effective length of query: 278 Effective length of database: 293 Effective search space: 81454 Effective search space used: 81454 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