Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate WP_013460983.1 SULKU_RS10705 SDR family oxidoreductase
Query= BRENDA::Q9WYX9 (309 letters) >NCBI__GCF_000183725.1:WP_013460983.1 Length = 312 Score = 141 bits (356), Expect = 2e-38 Identities = 99/311 (31%), Positives = 162/311 (52%), Gaps = 15/311 (4%) Query: 3 ILVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENLNRNALFYEQSIEDEEMMERIF 62 ILVTGGAGF+GSH+ +L+ G VI +DN +G EN+ + ++ E I Sbjct: 5 ILVTGGAGFVGSHLCRRLLNEGNDVICLDNFFTGSKENIIDLLPHPYFELIRHDVQEPI- 63 Query: 63 SLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKKFIFSSTGGAIY 122 L + +++LA AS +P +T+++G++ +L+ + K K I ++ +Y Sbjct: 64 -LLEVDEIYNLACPASPPHYQFDPVATTRTSVLGAINMLDIARKCKAK--ILQASTSEVY 120 Query: 123 GENVKVFPTPETEIPHPISPYGI------AKYSTEMYLEFFAREYGLKYTVLRYANVYGP 176 G+ +V P PE+ +S GI K E + R++G+K V+R N YGP Sbjct: 121 GDP-EVHPQPES-YRGSVSTTGIRACYDEGKRCAETLFFDYYRQHGVKIKVIRIFNTYGP 178 Query: 177 RQDPYGEAGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAMEKGDNEV--F 234 +P + VV+ F + LR +++ I+G G R + YVDD+V + M D+ Sbjct: 179 YMNP-DDGRVVSNFIMQALRNQDITIYGAGTQTRSFQYVDDLVEGMIRLMNSDDSFTGPV 237 Query: 235 NIGTGRGTTVNQLFKLLKEITGYDKEPVYKPPRKGDVRKSILDYTKAKEKLGWEPKVSLE 294 NIG T+ +L + + +TG + YKP + D + D + AK++L WEP ++LE Sbjct: 238 NIGNPGEFTMLELAQKIITLTGSSSKLTYKPLPQDDPLQRQPDISLAKKELDWEPTIALE 297 Query: 295 EGLKLTVEYFR 305 EGLK T+ YF+ Sbjct: 298 EGLKKTIAYFK 308 Lambda K H 0.318 0.139 0.396 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: 255 Number of extensions: 15 Number of successful extensions: 3 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: 309 Length of database: 312 Length adjustment: 27 Effective length of query: 282 Effective length of database: 285 Effective search space: 80370 Effective search space used: 80370 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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