Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_013136335.1 ARNIT_RS12690 epimerase
Query= curated2:Q56623 (328 letters) >NCBI__GCF_000092245.1:WP_013136335.1 Length = 286 Score = 162 bits (409), Expect = 1e-44 Identities = 114/307 (37%), Positives = 166/307 (54%), Gaps = 30/307 (9%) Query: 10 KSILLTGSTGFVGTNLVKSLTLKSDYIVKSAVRHAVNKDDGLLFEVGDINASTDFELPLK 69 K +L+TGS+GF+G + K+ Y +K+ F DIN+ L Sbjct: 2 KELLITGSSGFIGNYFINKY--KNKYNIKT-----------FSFLKDDINS-----LDCN 43 Query: 70 NTTVVVHCAARAHVMDDKEAEPLTLYREVNTAGTVNLAKQAIDSGVKRFIFISSIKVNGE 129 +V H +A H M A Y+ VN T+N+A++A +SG+K+F+F+S++KV GE Sbjct: 44 GIDIVFHLSALVHQMGGASASE---YKRVNVTQTLNIAQKAKESGIKQFVFMSTVKVYGE 100 Query: 130 GTLVGCPFKTEDNHAPEDDYGLSKSEAEKQLVALAKDSSMEVVIIRPTIVYGPGVKANFA 189 T C + +PED+YG SK AE +L L +D + +V IIR IVYG GVKAN Sbjct: 101 ETT--CKYTENSICSPEDEYGKSKFTAELELRKL-EDENFKVSIIRTPIVYGYGVKANIK 157 Query: 190 SLMRLVSKGIPLPFGSITQNKRSLVSINNLVDLIVTCIDHPKAANQVFLVSDGHDVSTAE 249 SL+ L +K LPFG I +NKRS+V I NL L+ I K+ +FL SD +ST Sbjct: 158 SLVNLTNKVPVLPFGKI-ENKRSMVYIGNLCHLVDEVIKQQKSG--IFLASDDEPLSTTR 214 Query: 250 MVRELAIALDKPTWQLPVPIWCYKLFGKLFGKSDIVDRLTGTLQVDISHTKETLGWKPPQ 309 ++ +A LDK + +P ++ KL K RL G+L++D + TKE L K P Sbjct: 215 LIELIAKNLDKKICLIKIPF--FESLLKLL-KPSFYKRLYGSLEIDNTITKEKLNLKNPY 271 Query: 310 TLQEGFK 316 +++EG K Sbjct: 272 SVEEGIK 278 Lambda K H 0.318 0.134 0.388 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: 211 Number of extensions: 13 Number of successful extensions: 7 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: 328 Length of database: 286 Length adjustment: 27 Effective length of query: 301 Effective length of database: 259 Effective search space: 77959 Effective search space used: 77959 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 (21.7 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