Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate RR42_RS15810 RR42_RS15810 UDP-N-acetylglucosamine 4,6-dehydratase
Query= curated2:A8GWP0 (341 letters) >FitnessBrowser__Cup4G11:RR42_RS15810 Length = 333 Score = 226 bits (576), Expect = 6e-64 Identities = 143/338 (42%), Positives = 200/338 (59%), Gaps = 24/338 (7%) Query: 1 MFVDKTLLITGGTGSFGN----AVLSRFLKNDIIKDIKEIRIFSRDEKKQEDMRIALNNP 56 MF +K++LITGGTGSFG +L+R+ K + I+SRDE KQ +M+ ++ P Sbjct: 1 MFNNKSILITGGTGSFGRKYARTILARYKP-------KRLVIYSRDELKQFEMQQDIDAP 53 Query: 57 KIKFYIGDVRNYNSIDDAMKDVDYVFHAAALKQVPTCEFYPMEAINTNILGAENVLRAAT 116 ++++IGDVR+ + + AM+ +DYV HAAALKQVP E+ P+E I TNI GAENV+ AA Sbjct: 54 PMRYFIGDVRDGDRLSQAMRGIDYVIHAAALKQVPAAEYNPLECIKTNIHGAENVINAAI 113 Query: 117 INKVAKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMNVRDKTVFCVTRYGNVMASRG 176 N V KVI LSTDKA PIN G +K +KL +A M ++T F V RYGNV+ SRG Sbjct: 114 ANNVHKVIALSTDKAANPINLYGATKLASDKLFVAANNMVGANQTSFAVVRYGNVVGSRG 173 Query: 177 SVIPLFINQI-KQNKDLTITEPSMTRFLMSLVDSVDLVLYAFEYGHQGDIFVQKSPASTI 235 SV+P F + + K+L IT MTRF +SL D VD VL FE H G+IFV K P+ I Sbjct: 174 SVVPFFEQLLARGEKELPITHAEMTRFWISLQDGVDFVLKNFERMHGGEIFVPKIPSIRI 233 Query: 236 EVLAKAL-QGIFNSKNKIRFIGTRHGEKHYESLVSSEEMAKAEDLGNYY----RIPMDGR 290 LA+A+ G+ R IG R GEK +E + S++ + ++Y I Sbjct: 234 TDLAEAVAPGV-----ATRVIGIRPGEKLHEIMCPSDDSHLTLEFSDHYVLRPTIKFHHS 288 Query: 291 DLNYAKYFV--EGEKKIALLEDYTSHNTKRLNLEEVKE 326 D++Y + +GE+ E + +N L+ EE++E Sbjct: 289 DIDYTVNALGEQGEQVSQGFEYNSGNNPHFLSPEEIRE 326 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: 278 Number of extensions: 10 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: 333 Length adjustment: 28 Effective length of query: 313 Effective length of database: 305 Effective search space: 95465 Effective search space used: 95465 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