Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_092482018.1 BM299_RS03115 NAD-dependent epimerase/dehydratase family protein
Query= curated2:A8GWP0 (341 letters) >NCBI__GCF_900115975.1:WP_092482018.1 Length = 359 Score = 229 bits (585), Expect = 6e-65 Identities = 143/344 (41%), Positives = 210/344 (61%), Gaps = 26/344 (7%) Query: 1 MFVDKTLLITGGTGSFGNAVLSRFLKNDIIKDIKEIRIFSRDEKKQEDMRIALNNPK--- 57 +F +K ++ITGGTGS G ++ R L + K++ +FSRDE KQ MR++ Sbjct: 2 IFDNKVVVITGGTGSLGKTLVRRILTGKMGIP-KKVIVFSRDEAKQHAMRVSYLQSSATT 60 Query: 58 -----------IKFYIGDVRNYNSIDDAMKDVDYVFHAAALKQVPTCEFYPMEAINTNIL 106 ++F IGDVRNY + +D D + +AAALKQVP+CE++P +A+ TN + Sbjct: 61 DEVIYRNFMNVLEFRIGDVRNYADVCSITRDADILINAAALKQVPSCEYFPAQALMTNCI 120 Query: 107 GAENVLRAATINK--VAKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMNVRDKTVFC 164 GA N++RA N V V+ +STDKA P+N MG++KAL E++ I+ +N KT F Sbjct: 121 GAVNIVRAIEENNYPVDTVVAVSTDKACKPVNVMGMTKALQERIFISANILN--PKTRFI 178 Query: 165 VTRYGNVMASRGSVIPLFINQIKQNKDLTITEPSMTRFLMSLVDSVDLVLYAFEYGHQGD 224 RYGNV+ASRGSVIPLF++QIK +T+TEP M+RFL+SL D+VD V+ A Y +G+ Sbjct: 179 CVRYGNVLASRGSVIPLFLDQIKHGGPVTVTEPGMSRFLLSLNDAVDTVIEALRYAERGE 238 Query: 225 IFVQKSPASTIEVLAKALQGIFNSKNKIRFIGTRHGEKHYESLVSSEEMAKAEDLGNYYR 284 ++ +PA+T+ +A AL G N I+ +G R GEK +E LVS EEM + G++Y Sbjct: 239 TYIPIAPAATVINIAGALIG--NRGIDIKVVGIRPGEKMHEVLVSEEEMHRCVKRGDFYV 296 Query: 285 IPMDGRDLNYAKYFVEGEKKIALLEDYTSHNTKRLNLEEVKELL 328 I +L AK E+K L ++Y+S + ++L+ ELL Sbjct: 297 IQPLLPELCNAK---SNEQKY-LTKEYSSAD-HVMDLKSTVELL 335 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: 284 Number of extensions: 15 Number of successful extensions: 6 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: 359 Length adjustment: 29 Effective length of query: 312 Effective length of database: 330 Effective search space: 102960 Effective search space used: 102960 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