Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate RR42_RS15815 RR42_RS15815 NAD-dependent dehydratase
Query= BRENDA::P9WN67 (314 letters) >FitnessBrowser__Cup4G11:RR42_RS15815 Length = 316 Score = 150 bits (379), Expect = 4e-41 Identities = 101/316 (31%), Positives = 149/316 (47%), Gaps = 19/316 (6%) Query: 2 RALVTGAAGFIGSTLVDRLLADGHSVVGLDNFATGRATNLEHLADNSAHVFVEADIVTAD 61 R LVTG AGF+GS L DRL+ G+ V+ +DN TG N+EHL + F+ D VT Sbjct: 9 RILVTGGAGFLGSHLCDRLIEQGNEVLCVDNLFTGAKQNIEHLLSHPRFEFIRHD-VTFP 67 Query: 62 LHAILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVRKIVHTSS 121 L ++Q +++LA DP +V G + + A++ G + + +S Sbjct: 68 LFVEVDQ-----IYNLACPASPVHYQHDPVQTTKTSVHGAINMLGLAKRVGAK--IFQAS 120 Query: 122 GGSIYGTPPEYPTPE-----TAPTDPASPYAAGKVAGEIYLNTFRHLYGLDCSHIAPANV 176 +YG P +P PE P S Y GK E + +GL+ N Sbjct: 121 TSEVYGDPVVHPQPEAYWGNVNPIGIRSCYDEGKRCAETLFFDYHRQHGLEIKVARIFNT 180 Query: 177 YGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRVSA---DVG 233 YGPR + VV+ F L G+P VFG+G TR + FVDD++D V + + D Sbjct: 181 YGPRMH-QNDGRVVSNFIMQALRGEPITVFGEGKQTRSFCFVDDLIDGIVALMSTPKDFT 239 Query: 234 GGLRFNIGTGKETSDRQLHSAVAAAVGGPDDPEFHPPRLGDLKRSCLDIGLAERVLGWRP 293 G + N+G E + +L S + G EF P D + D LAE ++GW P Sbjct: 240 GPM--NLGNPHEMTMLELASHIVELTGSRSTIEFKPLPADDPTQRRPDTRLAEEMIGWNP 297 Query: 294 QIELADGVRRTVEYFR 309 + DG+ +TV+YF+ Sbjct: 298 SVHFRDGLSKTVDYFK 313 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: 269 Number of extensions: 16 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: 316 Length adjustment: 27 Effective length of query: 287 Effective length of database: 289 Effective search space: 82943 Effective search space used: 82943 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