Align UDP-glucose 4-epimerase; UDP-galactose 4-epimerase; Uridine diphosphate galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate BWI76_RS18995 BWI76_RS18995 NAD-dependent epimerase
Query= SwissProt::A0R5C5 (313 letters) >FitnessBrowser__Koxy:BWI76_RS18995 Length = 334 Score = 146 bits (369), Expect = 6e-40 Identities = 105/333 (31%), Positives = 163/333 (48%), Gaps = 28/333 (8%) Query: 1 MRTLVTGAAGFIGSTLVDRLLADGHGVVGLDDLSSGRAENLHSAE----NSDKFEFVKAD 56 M+ LVTGAAGFIG RLL GH VVGLD+++ NL A S F F K D Sbjct: 1 MKFLVTGAAGFIGFHTCKRLLEAGHEVVGLDNMNDYYDVNLKQARLDLLQSPLFSFHKID 60 Query: 57 IVDAD-LTGLLAEFKPEVIFHLAAQISVKRSVDDPPFDATVNVVGTVRLAEAARLAGVRK 115 + D + + L A K + HLAAQ V+ S+++P A N++G + + E R V Sbjct: 61 LADREGIARLFANEKFNRVIHLAAQAGVRYSLENPFAYADANLIGYLNILEGCRHNNVEH 120 Query: 116 VVHTSSGGSVYGTPPAYPTSEDMPV-NPASPYAAGKVAGEVYLNMYRNLYDLDCSHIAPA 174 +++ SS SVYG P S D V +P S YAA K A E+ + Y +LY + + + Sbjct: 121 LLYASS-SSVYGLNRKMPFSTDDSVDHPVSLYAATKKANELMAHTYSHLYGIPTTGLRFF 179 Query: 175 NVYGPRQDPHGEAGVVAIFSEALLAGRTTKIFGDGSDTRDYVFVDDVVDAFVR------- 227 VYGP P + F++A+L G+ ++ G RD+ ++DD+V+A VR Sbjct: 180 TVYGPWGRPD---MALFKFTKAMLEGKPIDVYNYGKMKRDFTYIDDIVEAIVRMQDIIPQ 236 Query: 228 --------AGGPAGGG---QRFNVGTGVETSTRELHTAIAGAVGAPDEPEFHPPRLGDLR 276 G PA + +N+G + TA+ A+G E P + GD+ Sbjct: 237 PNPEWTVETGSPADSSAPYRVYNIGNSSPVELMDYITALEEAMGMVAEKNMMPIQPGDVL 296 Query: 277 RSRLDNTRAREVLGWQPQVALAEGIAKTVEFFR 309 + D + +G++PQ + +G+ V++++ Sbjct: 297 ETSADTKPLYDAVGFRPQTTVRQGVKNFVDWYK 329 Lambda K H 0.317 0.136 0.396 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: 236 Number of extensions: 12 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: 313 Length of database: 334 Length adjustment: 28 Effective length of query: 285 Effective length of database: 306 Effective search space: 87210 Effective search space used: 87210 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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