Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate WP_012992498.1 THAL_RS07430 dTDP-glucose 4,6-dehydratase
Query= BRENDA::Q9WYX9 (309 letters) >NCBI__GCF_000025605.1:WP_012992498.1 Length = 318 Score = 180 bits (456), Expect = 4e-50 Identities = 111/310 (35%), Positives = 172/310 (55%), Gaps = 10/310 (3%) Query: 1 MNILVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSG----KVENLNRNALFYEQSIEDEE 56 M +L+TGGAGFIGS + ++ GY +VVD L+ ++E + FY I + E Sbjct: 1 MKLLITGGAGFIGSEFTRQAVKEGYQCVVVDKLTYAGDIRRLEEVLEKITFYRCDINNRE 60 Query: 57 MMERIFSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKKFIFSS 116 +E IFS +P+ V H AA++ V S+ +P+ TN++G+L LL+ + KYGVK FI S Sbjct: 61 FLEYIFSKEKPDVVVHWAAESHVDRSISDPSPFFTTNVLGTLNLLDTAKKYGVKSFINIS 120 Query: 117 TGGAIYGENVKVFPTPETEIPHPISPYGIAKYSTEMYLEFFAREYGLKYTVLRYANVYGP 176 T +YGE E P SPY ++K S +M + R YGL +R +N YGP Sbjct: 121 T-DEVYGELGDEGSFKEDSCLKPNSPYSVSKASADMLGRAYFRTYGLPVITVRPSNNYGP 179 Query: 177 RQDPYGEAGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAMEKGD-NEVFN 235 Q P VV + + ++ E + I+G G VR+++YV D A L ++KG+ E++N Sbjct: 180 WQYPEKLIPVVIV---KAIKNEPIPIYGRGLNVREWLYVSDCAEAVLEIIKKGEPGEIYN 236 Query: 236 IGTGRGTTVNQLFKLLKEITGYDKEPV-YKPPRKGDVRKSILDYTKAKEKLGWEPKVSLE 294 +G+G ++ KL+ I G ++ + + R G + LD + EKLGW+ K LE Sbjct: 237 VGSGEERRNIEVAKLILSILGKPEDLISFVQDRPGHDYRYSLDVSGTWEKLGWKAKTKLE 296 Query: 295 EGLKLTVEYF 304 EG++ TVE++ Sbjct: 297 EGIRRTVEWY 306 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: 298 Number of extensions: 20 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: 318 Length adjustment: 27 Effective length of query: 282 Effective length of database: 291 Effective search space: 82062 Effective search space used: 82062 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