Align Putative UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_007690593.1 C447_RS02500 GDP-mannose 4,6-dehydratase
Query= curated2:Q57664 (305 letters) >NCBI__GCF_000336675.1:WP_007690593.1 Length = 326 Score = 221 bits (563), Expect = 2e-62 Identities = 124/320 (38%), Positives = 181/320 (56%), Gaps = 23/320 (7%) Query: 1 MILVTGGAGFIGSHIVDKLIENNYDVIILDNLT----TGNKNNINPKA----------EF 46 MILVTGGAGFIG H+ + + +DV+ LDNL G K A EF Sbjct: 1 MILVTGGAGFIGGHLAETFVREGHDVVALDNLEPFYDVGIKRRTIEAARTAAEDGGSYEF 60 Query: 47 VNADIRDKDLDEKINFKDVEVVIHQAAQINVRNSVENPVYDGDINVLGTINILEMMRKYD 106 V D+RD + + D E V HQAAQ VR SVENP DINV GT+N+L+ R+ Sbjct: 61 VEGDVRDAETVHDL-VADAEYVFHQAAQAGVRTSVENPRKVDDINVEGTLNVLDAARESG 119 Query: 107 IDKIVFASSGGAVYGEPNYLPVDENHPINPLSPYGLSKYVGEEYIKLYNRLYGIEYAILR 166 ++++VFASS +VYG+P LP E+ P P+SPYG+SK E Y+++Y LY I LR Sbjct: 120 VERVVFASSS-SVYGKPVSLPYQEDQPTTPVSPYGVSKLAAENYVRVYGDLYDIPTVALR 178 Query: 167 YSNVYGERQDPKGEAGVISIFIDKMLKNQSPIIFGDGNQTRDFVYVGDVAKANLMALNW- 225 Y VYG R P IS F+ + ++ P+++GDG+QTRDF YV D+ +AN L+ Sbjct: 179 YFTVYGPRMRPN---MAISNFVSRCTNDEPPVVYGDGSQTRDFTYVADIVRANAKLLDTD 235 Query: 226 --KNEIVNIGTGKETSVNELFDIIKHEIGFRGEAIYDKPREGEVYRIYLDIKKA-ESLGW 282 E +NIG+ S+ L ++ I + Y + + G+ + D+ KA E +G+ Sbjct: 236 AADGETMNIGSTDTVSIETLATTVRDAIAPELDIEYGERQAGDAEHTHADVSKAGELIGY 295 Query: 283 KPEIDLKEGIKRVVNWMKNN 302 +P D++ G++R ++W ++N Sbjct: 296 EPTEDIRSGVERFIDWYQDN 315 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: 320 Number of extensions: 16 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: 305 Length of database: 326 Length adjustment: 27 Effective length of query: 278 Effective length of database: 299 Effective search space: 83122 Effective search space used: 83122 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