Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate 8502212 DvMF_2922 NAD-dependent epimerase/dehydratase (RefSeq)
Query= BRENDA::P9WN67 (314 letters) >FitnessBrowser__Miya:8502212 Length = 339 Score = 188 bits (477), Expect = 2e-52 Identities = 118/311 (37%), Positives = 166/311 (53%), Gaps = 6/311 (1%) Query: 1 MRALVTGAAGFIGSTLVDRLLADGHSVVGLDNFATGRATNLEHLADNSAHVFVEADIVTA 60 + LVTGAAGFIG LV L ++ A + L L H DI Sbjct: 26 LSVLVTGAAGFIGINLVKALAPRCRRLICYGRRAQEILSPLG-LPGTECHTGETGDIDR- 83 Query: 61 DLHAILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVRKIVHTS 120 L +L H + V HLA+ + D DA NV+ T++L A GV ++V S Sbjct: 84 -LGPLL--HGVDRVIHLASSSTPVNADWDLVTDAEQNVLTTLKLFRACLAAGVGRVVFVS 140 Query: 121 SGGSIYGTPPEYPTPETAPTDPASPYAAGKVAGEIYLNTFRHLYGLDCSHIAPANVYGPR 180 SGG++YG PTPE+APTDP + Y KVA E YL+ FRHL+ LD + AN YGP Sbjct: 141 SGGTVYGPGAVVPTPESAPTDPITAYGVAKVAIEKYLHVFRHLHHLDYRVLRVANPYGPY 200 Query: 181 QDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRVSADVGGGLRFNI 240 Q G++ F + L+G+P ++GDG+ RDYV++DD+ DA +R + G G FN+ Sbjct: 201 QLATKGQGIIGAFIRKALAGQPLEIWGDGSTVRDYVYIDDLTDALLRAAVHDGPGRVFNV 260 Query: 241 GTGKETSDRQLHSAVAAAVGGPDDPEFHPPRLGDLKRSCLDIGLAERVLGWRPQIELADG 300 G+G+ T+ ++ + A +G + +HPPR D+ S LD A R +GWR LADG Sbjct: 261 GSGRGTTINEVADTLEAVLGRRLERLYHPPRPVDVPVSVLDCAAAWREMGWRATTPLADG 320 Query: 301 VRRTVEYF-RH 310 + T+ +F RH Sbjct: 321 MTDTLRWFTRH 331 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: 287 Number of extensions: 13 Number of successful extensions: 2 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: 339 Length adjustment: 28 Effective length of query: 286 Effective length of database: 311 Effective search space: 88946 Effective search space used: 88946 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: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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