Align Putative UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_044409892.1 NA59_RS06655 NAD-dependent dehydratase
Query= curated2:Q57664 (305 letters) >NCBI__GCF_000934765.1:WP_044409892.1 Length = 332 Score = 147 bits (372), Expect = 3e-40 Identities = 98/311 (31%), Positives = 158/311 (50%), Gaps = 19/311 (6%) Query: 2 ILVTGGAGFIGSHIVDKLIENNYDVIILDNLTTGN------KNNINPKAEFVNADIRDKD 55 +LVTG GFIGSH+ + L++ V L + N ++ + + + V+ DIRD Sbjct: 10 VLVTGADGFIGSHLAEALVQAGAQVRALVQYNSFNSWGWLDQSTLAGQMDIVSGDIRDPF 69 Query: 56 LDEKINFKDVEVVIHQAAQINVRNSVENPVYDGDINVLGTINILEMMRKYDIDKIVFASS 115 L + + KDV+ V H AA I + S P D NV GT+N+++ R ++ + + S+ Sbjct: 70 LCQTL-CKDVDTVFHLAALIAIPYSYIAPGSYVDTNVTGTLNMVQAARDQNVRRFMHTST 128 Query: 116 GGAVYGEPNYLPVDENHPINPLSPYGLSKYVGEEYIKLYNRLYGIEYAILRYSNVYGERQ 175 YG Y+P+DE HP+ P SPY SK + Y + I R N YG RQ Sbjct: 129 S-ETYGTAQYVPIDEQHPMQPQSPYSASKIGADAMAMSYFLAFQTPVTIARPFNTYGPRQ 187 Query: 176 DPKGEAGVISIFIDKMLKNQSPIIFGDGNQTRDFVYVGDVAKANLMALNWKNEI---VNI 232 + VI I ++ S I GD + TRDF YV D + + + + I VNI Sbjct: 188 SAR---AVIPTIIGQIASGVSQIKLGDTSPTRDFNYVADTCQGMMALMESERTIGQTVNI 244 Query: 233 GTGKETSVNELFDIIKH----EIGFRGEAIYDKPREGEVYRIYLDIKK-AESLGWKPEID 287 + E SV + D+IK ++ F +A +P++ EV+R++ D +K E G++P Sbjct: 245 SSNYEVSVQDTLDLIKRLMKSDVEFVQDAQRLRPKDSEVFRLWGDNRKLIELTGYQPTTS 304 Query: 288 LKEGIKRVVNW 298 L++G+++ ++W Sbjct: 305 LEQGLQQTIDW 315 Lambda K H 0.317 0.140 0.405 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: 203 Number of extensions: 8 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: 305 Length of database: 332 Length adjustment: 27 Effective length of query: 278 Effective length of database: 305 Effective search space: 84790 Effective search space used: 84790 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 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