Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_012102435.1 CKL_RS10275 KR domain-containing protein
Query= curated2:A8GWP0 (341 letters) >NCBI__GCF_000016505.1:WP_012102435.1 Length = 338 Score = 235 bits (599), Expect = 1e-66 Identities = 138/337 (40%), Positives = 204/337 (60%), Gaps = 14/337 (4%) Query: 2 FVDKTLLITGGTGSFGNAVLSRFLKNDIIKDIKEIRIFSRDEKKQEDMRIALNN-PKIKF 60 + DK +LI GGTG+ G + + L + + IRIFSRDE KQ M+ L++ K ++ Sbjct: 4 YTDKNILIIGGTGTIGRGLAKKLL----YQKPRVIRIFSRDEYKQFIMQKELDHISKFRY 59 Query: 61 YIGDVRNYNSIDDAMKDVDYVFHAAALKQVPTCEFYPMEAINTNILGAENVLRAATINKV 120 IGDVR+Y ++ AM ++D VF+ AA+K VP+CE+ P EAI TN+ G ENV++A+ N V Sbjct: 60 LIGDVRDYERVERAMNNIDVVFNLAAMKHVPSCEYNPTEAIKTNVQGMENVIKASIYNNV 119 Query: 121 AKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMNVRDKTVFCVTRYGNVMASRGSVIP 180 V+ S+DKA+ P N G +K L EKL A + KT F R+GNVM SRGSVIP Sbjct: 120 DSVLFTSSDKAINPTNTYGATKLLAEKLVQAANFSKGKVKTRFSAVRFGNVMGSRGSVIP 179 Query: 181 LFINQIKQNKDLTITEPSMTRFLMSLVDSVDLVLYAFEYGHQGDIFVQKSPA-STIEVLA 239 LF QI + + +T+T+ +MTRF+M+L SV L++ E H G+ FV K P ++++ Sbjct: 180 LFKKQILEKRYITVTDSNMTRFMMTLSQSVSLIMETAEKSHGGEAFVLKMPVIKLLDLVE 239 Query: 240 KALQGIFNS-----KN-KIRFIGTRHGEKHYESLVSSEEMAKAEDLGNYYRIPMDGRDLN 293 ++ + N KN +I IG R GE+ +E L++ EE A DLG+ Y + D Sbjct: 240 IVIEEVCNKYDIDPKNIQIENIGLRAGERKFEELMTHEESENAYDLGSMYAVISDTYADK 299 Query: 294 YAKYFVEGEKKIALLEDYTSHNTKRLNLEEVKELLLN 330 +KY+ GEK A + Y S+++ + EEV+ELL++ Sbjct: 300 LSKYYSTGEK--AGIGSYNSYDSVPITKEEVRELLVS 334 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: 272 Number of extensions: 15 Number of successful extensions: 4 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: 338 Length adjustment: 28 Effective length of query: 313 Effective length of database: 310 Effective search space: 97030 Effective search space used: 97030 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 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