Align Putative UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_005453649.1 SACCYDRAFT_RS03525 dTDP-glucose 4,6-dehydratase
Query= curated2:Q57664 (305 letters) >NCBI__GCF_000244975.1:WP_005453649.1 Length = 330 Score = 140 bits (353), Expect = 4e-38 Identities = 103/319 (32%), Positives = 165/319 (51%), Gaps = 21/319 (6%) Query: 2 ILVTGGAGFIGSHIVDKLIENNY------DVIILDNLT-TGNKNNINPKAE-----FVNA 49 +LVTGGAGFIGSH V + + Y ++++LD LT G+++N++P A+ FV Sbjct: 3 VLVTGGAGFIGSHYVRQALSGEYAALRDAEIVVLDKLTYAGSRSNLDPVADSPRLRFVRG 62 Query: 50 DIRDKDLDEKINFKDVEVVIHQAAQINVRNSVENPVYDGDINVLGTINILEMMRKYDIDK 109 DI D + + V++V+H AA+ +V S+ NVLGT +L+ + + Sbjct: 63 DICDPAVVVEA-MAGVDLVVHFAAESHVDRSILGAADFVLTNVLGTQTLLQAALDAGVGR 121 Query: 110 IVFASSGGAVYGEPNYLPVDENHPINPLSPYGLSKYVGEEYIKLYNRLYGIEYAILRYSN 169 V S+ VYG E+H + P SPY SK + + ++R YG+ I R SN Sbjct: 122 FVHVSTD-EVYGSIERGSWSEDHVLEPNSPYSASKASSDLVARSFHRTYGLPVCITRCSN 180 Query: 170 VYGERQDPKGEAGVISIFIDKMLKNQSPIIFGDGNQTRDFVYVGDVAKA-NLMALNWK-N 227 YG Q P+ VI +F+ +L +S ++GDG RD+++V D + L+A + Sbjct: 181 NYGPYQFPE---KVIPLFVTNLLDGKSVPLYGDGLNVRDWLHVDDHCRGIQLVAEGGRPG 237 Query: 228 EIVNIGTGKETSVNELFDIIKHEIGFRGEAIYD-KPREGEVYRIYLDIKK-AESLGWKPE 285 EI NIG G E + EL + + +G E + + R+G R +DI K + LG+ P+ Sbjct: 238 EIYNIGGGTELTNRELTERLLAAVGVGWEMVERVEDRKGHDRRYSVDITKISRELGYSPK 297 Query: 286 IDLKEGIKRVVNWMKNNNR 304 +D + G+ V W +N + Sbjct: 298 VDFETGLADTVRWYADNRQ 316 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: 256 Number of extensions: 18 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: 330 Length adjustment: 27 Effective length of query: 278 Effective length of database: 303 Effective search space: 84234 Effective search space used: 84234 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