Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_086508739.1 BZY95_RS04325 polysaccharide biosynthesis protein
Query= SwissProt::Q9ZDJ5 (341 letters) >NCBI__GCF_002151265.1:WP_086508739.1 Length = 670 Score = 146 bits (369), Expect = 1e-39 Identities = 97/293 (33%), Positives = 159/293 (54%), Gaps = 25/293 (8%) Query: 5 KTLMITGGTGSFGNAVLSRFLKSN----IINDIKEIRIFSRDEKKQ---EDMRIALNNSK 57 K +M+TG GS G+ + + L+ ++ +I E +++ + + Q E+ R+A++ Sbjct: 282 KVVMVTGAGGSIGSELCRQVLQQGPTRLLLYEINEYSLYTIEHELQQRIEEQRLAVS--- 338 Query: 58 LKFYIGDVRNYQSIDDAMH--GVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAA 115 +K +G V++ + +D M GVD ++HAAA K VP E+ + I NV G AA Sbjct: 339 VKALLGSVQDRERLDSVMRVFGVDTIYHAAAYKHVPLVEYNSIPGILNNVFGTLATAQAA 398 Query: 116 INNKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASR 175 I+ V +++STDKAV P N MG +K L E A A +S T + R+GNV+ S Sbjct: 399 IDGGVETFVLVSTDKAVRPTNVMGTTKRLAELCCQALAEQQS--TTRFTMVRFGNVLGSS 456 Query: 176 GSVIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFV--QKSPAS 233 GSV+PLF QI +G +T+T +TR+ M++ ++ LV+ A G GD+FV +P Sbjct: 457 GSVVPLFHAQIARGGPVTVTHSEVTRYFMTIPEAAQLVIQAGAMGTGGDVFVLDMGAPVK 516 Query: 234 TIEVLAKALQ----EIFGSKN-----AIRFIGTRHGEKHYESLVSSEDMAKAD 277 ++ A+ ++ E+ +N IRF G R GEK YE L+ +++ + Sbjct: 517 IADLAAEMIRLSGLEVRQKENPQGDIEIRFTGLRPGEKLYEELLIGKNVVDTE 569 Lambda K H 0.319 0.135 0.373 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: 406 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: 341 Length of database: 670 Length adjustment: 33 Effective length of query: 308 Effective length of database: 637 Effective search space: 196196 Effective search space used: 196196 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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