Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_013819281.1 METME_RS13395 dTDP-glucose 4,6-dehydratase
Query= BRENDA::P9WN67 (314 letters) >NCBI__GCF_000214665.1:WP_013819281.1 Length = 356 Score = 134 bits (337), Expect = 3e-36 Identities = 105/333 (31%), Positives = 156/333 (46%), Gaps = 30/333 (9%) Query: 1 MRALVTGAAGFIGSTLV-DRLLADGHSVVGLDNFA-TGRATNLEHLADNSAHVFVEADIV 58 M LVTG AGFIGS V D L VV +D G NL L ++ HVFV+ADI Sbjct: 1 MTILVTGGAGFIGSNFVLDWLAGCDEPVVNIDKLTYAGNLENLASLQGDARHVFVKADIG 60 Query: 59 TADLHA-ILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAAR-------- 109 D+ +L+ V + AA+ V RS+ P+ N++G+ RL EA R Sbjct: 61 DYDVVLDLLKNRHVRAVVNFAAESHVDRSIHGPEDFIQTNILGSFRLLEAVRCYWNGLAD 120 Query: 110 -QTGVRKIVHTSSG---GSIYGTPPEYPTPETAPTDPASPYAAGKVAGEIYLNTFRHLYG 165 + +++H S+ GS+ T P P E+ P SPY+A K A + + ++ H YG Sbjct: 121 AEKQAFRLLHVSTDEVYGSLEKTDP--PFSESNQYQPNSPYSASKAASDHLVRSYHHTYG 178 Query: 166 LDCSHIAPANVYGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAF 225 L +N YGP P ++ + Q L+GK ++GDG RD+++V D A Sbjct: 179 LPVLTTNCSNNYGPYHFPEK---LIPLCIQNALTGKALPIYGDGQQIRDWLYVKDHCSAI 235 Query: 226 VRVSADVGGGLRFNIGTGKETSD--------RQLHSAVAAAVGGP--DDPEFHPPRLGDL 275 RV A+ G +N+G E ++ L A G P + + R G Sbjct: 236 RRVLAEGQVGQVYNVGGWNEKANLDVVHTLCGMLDELQPRADGKPYAEQITYVTDRPGHD 295 Query: 276 KRSCLDIGLAERVLGWRPQIELADGVRRTVEYF 308 +R +D ER LGW+P G+R+TV+++ Sbjct: 296 RRYAIDATKLERELGWKPAETFETGIRKTVQWY 328 Lambda K H 0.320 0.137 0.410 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: 265 Number of extensions: 11 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: 314 Length of database: 356 Length adjustment: 28 Effective length of query: 286 Effective length of database: 328 Effective search space: 93808 Effective search space used: 93808 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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