Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate 202379 SO3271 polysaccharide biosynthesis protein (NCBI ptt file)
Query= curated2:A8GWP0 (341 letters) >FitnessBrowser__MR1:202379 Length = 331 Score = 217 bits (553), Expect = 3e-61 Identities = 130/286 (45%), Positives = 167/286 (58%), Gaps = 8/286 (2%) Query: 1 MFVDKTLLITGGTGSFGNAVLSRFLKNDIIKDIKEIRIFSRDEKKQEDMRIALNNPKIKF 60 MF +KT+LITGGTGSFG L+ K + IFSRDE KQ +M+ N P +++ Sbjct: 1 MFDNKTILITGGTGSFGQKYTKTILER---YKPKRLIIFSRDELKQYEMQQVFNAPCMRY 57 Query: 61 YIGDVRNYNSIDDAMKDVDYVFHAAALKQVPTCEFYPMEAINTNILGAENVLRAATINKV 120 +IGDVR+ + A KDVD+V HAAALKQVP E+ PME I TNI GAENV+RAA N V Sbjct: 58 FIGDVRDGERLKQAFKDVDFVIHAAALKQVPAAEYNPMECIKTNIHGAENVIRAAISNNV 117 Query: 121 AKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMNVRDKTVFCVTRYGNVMASRGSVIP 180 KVI LSTDKA PIN G +K +KL +A + KT F RYGNV+ SRGSV+P Sbjct: 118 KKVIALSTDKAASPINLYGATKLASDKLFVAANNVVGDGKTRFAAVRYGNVVGSRGSVVP 177 Query: 181 LFINQIKQN-KDLTITEPSMTRFLMSLVDSVDLVLYAFEYGHQGDIFVQKSPASTIEVLA 239 F I L IT P MTRF ++L D VD VL F G+IFV K P+ I LA Sbjct: 178 FFKQLIANGATSLPITHPDMTRFWITLQDGVDFVLKNFSRMQGGEIFVPKIPSIRITDLA 237 Query: 240 KALQGIFNSKNKIRFIGTRHGEKHYESLVSSEEMAKAEDLGNYYRI 285 A + + + +G R GEK +E + ++ + +++ I Sbjct: 238 AA----YGPSLEQQIVGIRPGEKMHEVMCPGDDSHHTIEFDDHFVI 279 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: 293 Number of extensions: 12 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: 331 Length adjustment: 28 Effective length of query: 313 Effective length of database: 303 Effective search space: 94839 Effective search space used: 94839 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: 49 (23.5 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