Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate 6938123 Sama_2244 polysaccharide biosynthesis protein (RefSeq)
Query= SwissProt::Q9ZDJ5 (341 letters) >FitnessBrowser__SB2B:6938123 Length = 644 Score = 135 bits (341), Expect = 2e-36 Identities = 108/345 (31%), Positives = 173/345 (50%), Gaps = 36/345 (10%) Query: 5 KTLMITGGTGSFGNAVLSRFLK----SNIINDIKEIRIFSRDEKKQEDMRIALN-NSKLK 59 K +M+TG GS G+ + + L+ ++ ++ E ++S E++ + +R L + +L Sbjct: 281 KVVMVTGAGGSIGSELCRQILRLAPRKLVLFELSEFGLYSI-ERELQAIRAELGLDVELF 339 Query: 60 FYIGDVRNYQSIDDAMHG--VDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAIN 117 +G V+ + M V V+HAAA K VP E +E + NV G AAI Sbjct: 340 PMMGSVQRQNRVQAVMEAFKVQTVYHAAAYKHVPLVEHNVVEGVRNNVFGTLYTAQAAIA 399 Query: 118 NKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRGS 177 V +++STDKAV P N MG +K + E + A +++ S T C+ R+GNV+ S GS Sbjct: 400 TGVETFVLISTDKAVRPTNVMGTTKRMAELVLQALSKLNSG--TRFCMVRFGNVLGSSGS 457 Query: 178 VIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPAST-IE 236 V+PLF QI G +T+T P +TRF M++ ++ LV+ A G GD+FV S I Sbjct: 458 VVPLFRKQIANGGPVTVTHPEITRFFMTIPEASQLVIQAGAMGIGGDVFVLDMGQSVKIV 517 Query: 237 VLAKALQEIFG----------SKNAIRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRIP 286 LA+ + + G I+F G R GEK YE L+ +++ G+ RI Sbjct: 518 DLARKMIRLSGFEVKDEHNPDGDIEIQFSGLRPGEKLYEELLIGDNVEGT----GHERI- 572 Query: 287 MDGRDLNYAKYFVTGEKKVALLD--DYTSHNTKRLNLKEVKELLL 329 + + F+T E+ +LD D H + + ++EL+L Sbjct: 573 -----MTAHEVFLTWEELKPVLDKLDMACH---AFDHESIRELML 609 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: 417 Number of extensions: 23 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: 644 Length adjustment: 33 Effective length of query: 308 Effective length of database: 611 Effective search space: 188188 Effective search space used: 188188 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 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