Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_013707581.1 DESAC_RS13215 polysaccharide biosynthesis protein CapD
Query= curated2:A8GWP0 (341 letters) >NCBI__GCF_000195295.1:WP_013707581.1 Length = 354 Score = 187 bits (476), Expect = 3e-52 Identities = 111/335 (33%), Positives = 179/335 (53%), Gaps = 11/335 (3%) Query: 2 FVDKTLLITGGTGSFGNAVLSRFLKNDIIKDIKEIRIFSRDEKKQEDMRIALNNPKIKFY 61 + +K +LITG G+ G ++ + + E+R+ +E + + I + Sbjct: 7 YKNKNILITGAAGTVGRELIRQLINYQP----GELRLMDNNESEMFFLMEEYRTSNIFCF 62 Query: 62 IGDVRNYNSIDDAMKDVDYVFHAAALKQVPTCEFYPMEAINTNILGAENVLRAATINKVA 121 +GD+R+ + I+ KDVD + H AA K V E P +A+ TNI+G +N+++AA+ KV Sbjct: 63 LGDIRDRDKIEKLAKDVDIIIHTAAFKHVILSEINPFDAVQTNIMGVQNIIKAASARKVK 122 Query: 122 KVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMNVRDKTVFCVTRYGNVMASRGSVIPL 181 V+ S+DKAV P N MG SK + E+L A + VF TR+GNV+ SRGSV+PL Sbjct: 123 YVLFTSSDKAVNPTNVMGTSKLMGERLITAANAFDSPRTAVFSSTRFGNVLGSRGSVVPL 182 Query: 182 FINQIKQNKDLTITEPSMTRFLMSLVDSVDLVLYAFEYGHQGDIFVQKSPASTIEVLAKA 241 F+ QI+Q +T+T+ MTRF+M++ +S +LVL + G++FV K P + I LA+ Sbjct: 183 FMKQIRQGGPVTLTDKRMTRFIMTVAESANLVLQSLTLARGGEVFVTKMPVARIPDLAEV 242 Query: 242 LQGIFNSKN-------KIRFIGTRHGEKHYESLVSSEEMAKAEDLGNYYRIPMDGRDLNY 294 L + K KI IG + GEK YE L+S EEM ++ +L + + + + + Sbjct: 243 LIELLAPKYGYAPEDIKIIEIGIKPGEKLYEELMSEEEMHRSLELKDMFVVTPAFKSVYQ 302 Query: 295 AKYFVEGEKKIALLEDYTSHNTKRLNLEEVKELLL 329 + + + Y S L E +K+ L+ Sbjct: 303 ITFEYPDTISPQVRKPYASSGESALIKEAIKDYLV 337 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: 14 Number of successful extensions: 2 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: 354 Length adjustment: 29 Effective length of query: 312 Effective length of database: 325 Effective search space: 101400 Effective search space used: 101400 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