Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate PfGW456L13_2191 nucleotide sugar epimerase/dehydratase WbpM
Query= curated2:A8GWP0 (341 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2191 Length = 664 Score = 145 bits (365), Expect = 4e-39 Identities = 104/303 (34%), Positives = 157/303 (51%), Gaps = 31/303 (10%) Query: 5 KTLLITGGTGSFGNAVLSRFLKND----IIKDIKEIRIFS-RDEKKQEDMRIALNNPKIK 59 +++L+TG GS G+ + + L ++ + E ++S E +Q R +L+ ++ Sbjct: 298 QSVLVTGAGGSIGSELCRQILSLGPTTLLLFEHSEFNLYSILSELEQRVSRESLS-VRLL 356 Query: 60 FYIGDVRNYNSIDDAMK--DVDYVFHAAALKQVPTCEFYPMEAINTNILGAENVLRAATI 117 +G VRN + D M+ VD V+HAAA K VP E E + N++G N +AA + Sbjct: 357 PILGSVRNKEKLLDVMRVWRVDTVYHAAAYKHVPMVEHNIAEGVLNNVIGTLNTAQAALM 416 Query: 118 NKVAKVIVLSTDKAVYPINAMGLSKALMEKLAIAKAR----------MNVR--DKTVFCV 165 VA +++STDKAV P N MG +K L E A +R NV +KT F + Sbjct: 417 AGVANFVLISTDKAVRPTNVMGSTKRLAELTLQALSRELAPALFGDDTNVSRVNKTRFTM 476 Query: 166 TRYGNVMASRGSVIPLFINQIKQNKDLTITEPSMTRFLMSLVDSVDLVLYAFEYGHQGDI 225 R+GNV+ S GSVIPLF QIK LT+T P +TR+ M++ ++ LV+ A G GD+ Sbjct: 477 VRFGNVLGSSGSVIPLFHKQIKSGGPLTVTHPKITRYFMTIPEAAQLVIQAGSMGQGGDV 536 Query: 226 FV--QKSPASTIEVLAKALQ----GIFNSKN-----KIRFIGTRHGEKHYESLVSSEEMA 274 FV P +E+ K + + + KN I F G R GEK YE L+ + +A Sbjct: 537 FVLDMGEPVKIVELAEKMIHLSGLSVRSEKNPHGDISIEFTGLRPGEKLYEELLIGDNVA 596 Query: 275 KAE 277 + Sbjct: 597 ATQ 599 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: 377 Number of extensions: 21 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: 664 Length adjustment: 33 Effective length of query: 308 Effective length of database: 631 Effective search space: 194348 Effective search space used: 194348 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