Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_007692672.1 C447_RS07955 NAD-dependent epimerase/dehydratase family protein
Query= BRENDA::O73960 (318 letters) >NCBI__GCF_000336675.1:WP_007692672.1 Length = 309 Score = 266 bits (679), Expect = 6e-76 Identities = 144/316 (45%), Positives = 205/316 (64%), Gaps = 16/316 (5%) Query: 2 RVLVTGGAGFIGSHLVDRLMEEGYKVRVLDDLSAGSLKNIEGWLGNENFEFIKGDMRDVE 61 RVL+TGGAG +GSHL RL+++ +V V DD S G + + E EF++ DM + Sbjct: 7 RVLITGGAGLVGSHLAGRLLDDN-EVVVADDCSKGDRERVP-----EGAEFVEADMTSED 60 Query: 62 IVSKAV-KDVDAVFHLAANPEVRIGSQSPELLYETNVLITYNLLNAVRNSGVKYLVFTSS 120 V++A+ D+D VFH AA + P L+E N +TYN+L + GV + FTSS Sbjct: 61 DVAEAITSDLDCVFHFAAYTDTNYAD--PRRLFEENGAMTYNVLERMDEVGVSNVAFTSS 118 Query: 121 STVYGDAKVIPTPEDYAPLEPISVYGAAKLAAEALISGYAHTFDFRALIIRLANIIGKRS 180 STVYG+A + PTPED+APLEPIS+YGA+KLA E L+S YAH+ F + R ANI+G Sbjct: 119 STVYGEAPM-PTPEDHAPLEPISIYGASKLADEGLLSTYAHSHGFTVWLYRFANIVGPNQ 177 Query: 181 NHGVIYDFINKLKANPNELEILGDGTQRKSYLHISDTIDGIMKLFEHFLNGEERVDFYNL 240 V+ DFI KL NP+ELEILGDG Q KSYLH+SD ++ + + E + ++ ++ YNL Sbjct: 178 RGNVVPDFIEKLDENPDELEILGDGRQEKSYLHVSDCVEAVRHVVE---STDKPMNTYNL 234 Query: 241 GNEDWITVKEIAEIVSEEMNLNPRFKFTGGVDGGRGWKGDVKLMLLSIEKAKRTGWKPRM 300 G +V +IA+IV++EM ++P + +TG G RGW GDV M L++EK G++P + Sbjct: 235 GTRTTTSVTDIADIVADEMGVDPEYSYTG---GDRGWTGDVPKMRLAVEKLTDLGYEPEL 291 Query: 301 NSYEAVRKTVREMLEE 316 +S EAVR+ RE+++E Sbjct: 292 SSDEAVRRGARELIDE 307 Lambda K H 0.318 0.138 0.397 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: 261 Number of extensions: 13 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: 318 Length of database: 309 Length adjustment: 27 Effective length of query: 291 Effective length of database: 282 Effective search space: 82062 Effective search space used: 82062 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 (21.7 bits) S2: 48 (23.1 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