Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate WP_043743043.1 AMB_RS00750 NAD-dependent epimerase/dehydratase family protein
Query= BRENDA::Q9WYX9 (309 letters) >NCBI__GCF_000009985.1:WP_043743043.1 Length = 317 Score = 157 bits (398), Expect = 2e-43 Identities = 106/312 (33%), Positives = 166/312 (53%), Gaps = 16/312 (5%) Query: 3 ILVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENLNRNALFYEQSIEDEEMMERIF 62 +LVTGGAGF+GSH+ ++L+ G V+ VDN +G N+ A + + + F Sbjct: 8 VLVTGGAGFLGSHLCERLLAEGCDVLCVDNFFTGTKANI---AHLLDNPYFEMMRHDVTF 64 Query: 63 SLH-RPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKKFIFSSTGGAI 121 L+ + +F+LA AS R+P + KT++ G++ +L + + G K IF S+ + Sbjct: 65 PLYVEVDEIFNLACPASPIHYQRDPVQTTKTSVHGAINMLGLAKRVGAK--IFQSSTSEV 122 Query: 122 YGENVKVFPTPET--EIPHPISP---YGIAKYSTEMYLEFFAREYGLKYTVLRYANVYGP 176 YG+ V P PE+ +PI P Y K E + R++ L+ V R N YGP Sbjct: 123 YGD-PDVHPQPESYRGNVNPIGPRACYDEGKRCAETLFFDYWRQHSLRIKVARIFNTYGP 181 Query: 177 RQDPYGEAGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAMEKGDNEV--F 234 R P + VV+ F + L+G+ + ++GDG R + YVDD++ + M D+ Sbjct: 182 RMHP-DDGRVVSNFIMQALQGQPITLYGDGSQTRSFCYVDDLIEGFIRLMNSPDDITGPI 240 Query: 235 NIGTGRGTTVNQLFKLLKEITGYDKEPVYKPPRKGDVRKSILDYTKAKEKLG-WEPKVSL 293 N+G R T+ QL +L+ +TG E +YKP D + D T+AK L WEPKV+L Sbjct: 241 NLGNPREMTIRQLAELVVRMTGAKSEIIYKPLPADDPMQRKPDITQAKAVLNDWEPKVAL 300 Query: 294 EEGLKLTVEYFR 305 E+GL+ T+ YF+ Sbjct: 301 EQGLEKTIAYFK 312 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: 254 Number of extensions: 17 Number of successful extensions: 6 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: 317 Length adjustment: 27 Effective length of query: 282 Effective length of database: 290 Effective search space: 81780 Effective search space used: 81780 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 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