Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_010960564.1 MCA_RS06330 dTDP-glucose 4,6-dehydratase
Query= BRENDA::P9WN67 (314 letters) >NCBI__GCF_000008325.1:WP_010960564.1 Length = 357 Score = 134 bits (337), Expect = 3e-36 Identities = 106/328 (32%), Positives = 150/328 (45%), Gaps = 27/328 (8%) Query: 4 LVTGAAGFIGSTLVDRLLADGH-SVVGLDNFA-TGRATNLEHLADNSAHVFVEADIVTAD 61 LVTG AGFIG V R L G VV LD +G L + DN H FV I + Sbjct: 5 LVTGGAGFIGGNFVLRQLRRGGVEVVNLDALTYSGNLRTLAEVEDNPNHDFVLGSIGDRE 64 Query: 62 L-HAILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAAR---------QT 111 L +LE+++P+ V + AA+ V RS+ P NVIGT L EA R + Sbjct: 65 LVEYLLERYQPDAVVNFAAETHVDRSIDGPDAFVHTNVIGTFELLEATRWYWRQLDGERR 124 Query: 112 GVRKIVHTSSGGSIYGT-PPEYPTPETAPTDPASPYAAGKVAGEIYLNTFRHLYGLDCSH 170 + +H S+ +YGT E P P SPY+A K + + + H YGL Sbjct: 125 KAFRFLHVST-DEVYGTLGATGKFTEETPYRPNSPYSASKAGSDHLVRAYFHTYGLPVLT 183 Query: 171 IAPANVYGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRVSA 230 +N YGP Q P ++ + L G P V+G GTN RD+++V+D A V A Sbjct: 184 TNCSNNYGPYQFPE---KLIPLMIDHALQGLPLPVYGAGTNVRDWLYVEDHCRAIETVLA 240 Query: 231 DVGGGLRFNIGTGKETSDRQLHSAVAAAVGG--PDDP--------EFHPPRLGDLKRSCL 280 G +N+G E ++ ++ + A + PD P F R G R + Sbjct: 241 RGRPGEVYNVGGNNEKTNIEVVETICALLDEFLPDSPHRPHRQLIRFVQDRPGHDLRYAI 300 Query: 281 DIGLAERVLGWRPQIELADGVRRTVEYF 308 D G R LGW+P+ G+R+TV ++ Sbjct: 301 DAGKIGRELGWQPEETFETGLRKTVRWY 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: 279 Number of extensions: 16 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: 314 Length of database: 357 Length adjustment: 28 Effective length of query: 286 Effective length of database: 329 Effective search space: 94094 Effective search space used: 94094 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