Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_051116147.1 A3OQ_RS0120650 NAD-dependent epimerase/dehydratase family protein
Query= BRENDA::P9WN67 (314 letters) >NCBI__GCF_000385335.1:WP_051116147.1 Length = 329 Score = 144 bits (364), Expect = 2e-39 Identities = 99/316 (31%), Positives = 150/316 (47%), Gaps = 19/316 (6%) Query: 2 RALVTGAAGFIGSTLVDRLLADGHSVVGLDNFATGRATNLEHLADNSAHVFVEADIVTAD 61 R LVTG AGFIGS L ++LLA G+ V+ +DNF TG N++HL N + D V Sbjct: 5 RTLVTGGAGFIGSHLCEQLLARGNEVLCVDNFYTGTRKNVQHLLANPRFELMRHD-VCFP 63 Query: 62 LHAILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVRKIVHTSS 121 L+ ++Q +++LA DP +V G + + A++ V+ + +S Sbjct: 64 LYVEVDQ-----IYNLACPASPVHYQFDPVQTTKTSVHGAINMLGLAKR--VKAKILQAS 116 Query: 122 GGSIYGTPPEYPTPET-----APTDPASPYAAGKVAGEIYLNTFRHLYGLDCSHIAPANV 176 +YG P +P PE+ P P S Y GK E +R + L+ N Sbjct: 117 TSEVYGDPTVHPQPESYWGNINPIGPRSCYDEGKRCAETLFFDYRRQHNLNIKVARIFNT 176 Query: 177 YGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRVSA---DVG 233 YGPR P+ + VV+ F L ++GDG TR + +VDD+VD +R+ D+ Sbjct: 177 YGPRMHPN-DGRVVSNFVMQALGNDDITIYGDGNQTRSFCYVDDLVDGLIRLMETPDDIT 235 Query: 234 GGLRFNIGTGKETSDRQLHSAVAAAVGGPDDPEFHPPRLGDLKRSCLDIGLAERVLGWRP 293 G + N+G E + RQL + G P D ++ D+G A +LGW+P Sbjct: 236 GPI--NLGNPGEFTIRQLAETIIELTGSSSRLVSRPLPQDDPRQRQPDLGRANSILGWQP 293 Query: 294 QIELADGVRRTVEYFR 309 L DG+ ++YFR Sbjct: 294 TTRLRDGLALVIDYFR 309 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: 243 Number of extensions: 10 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: 314 Length of database: 329 Length adjustment: 28 Effective length of query: 286 Effective length of database: 301 Effective search space: 86086 Effective search space used: 86086 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 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