Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_104914032.1 C3B54_RS08030 dTDP-glucose 4,6-dehydratase
Query= BRENDA::F2NQX6 (314 letters) >NCBI__GCF_002950575.1:WP_104914032.1 Length = 327 Score = 139 bits (349), Expect = 1e-37 Identities = 110/328 (33%), Positives = 157/328 (47%), Gaps = 33/328 (10%) Query: 1 MRVLVTGGAGFIGSHLVHALHQKGIP------VAVLDDLS-TGKRAHIP-----PDVPLY 48 M++ VTGGAGFIGS+ V +P + V D L+ +G ++ P Sbjct: 1 MKLFVTGGAGFIGSNFVRMALGGRLPGLEEAEITVFDALTYSGTLTNLESVANHPRFRFI 60 Query: 49 QTDIRDLNAVLHAFQDFQPTHVAHQAAQASVKHSVQNPCKDAEINLLGGLNILEAMRATG 108 Q DIRD+ A+L + H AA++ V SV + + N+ G +LEA R G Sbjct: 61 QGDIRDMPALLEHVAGHDA--IVHFAAESHVDRSVSDAGIFVDTNVAGTQKLLEAARQLG 118 Query: 109 TQKIVFASTGGAIYGEVPEGRRAPETWPPKPKSPYAASKAAFEHYLEVYRQTHGLTYTTL 168 T + + ST +YG + EG E P P SPYAASKAA + + Y QTHGL Sbjct: 119 TDRFLQVSTD-EVYGSIDEGEWDEEE-PLLPNSPYAASKAASDLMVRAYHQTHGLDTVMT 176 Query: 169 RYANVYGPRQDPHGEAGVVAIFTNRLLHAQPVTLYARKEPGDPGCIRDYIHVEDVTRANL 228 R +N YGP P V+ +F LL PV LY GD G RD++HV+D R Sbjct: 177 RCSNNYGPHHFPE---KVIPLFVTNLLDGHPVPLY-----GDGGNQRDWLHVDDHCRGIA 228 Query: 229 LALETNLEG-TYNVSTGQGRTTEDVLYTIARALGTTPR----VTYAPPRDG-DLEVSVLD 282 L L+ G YN+ G T +++ + + LG T R +++ R G D V Sbjct: 229 LVLQKGTSGEVYNIGGGTELTNKELTHML---LGLTGRDDSFISHVEDRLGHDRRYCVSI 285 Query: 283 PTQLQAHGWRPQVPFEEGIRRTVAWFRE 310 + G+ P+V F+EG+ V W+R+ Sbjct: 286 DKISRELGYAPEVDFQEGLADVVQWYRD 313 Lambda K H 0.318 0.135 0.411 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: 256 Number of extensions: 19 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: 314 Length of database: 327 Length adjustment: 28 Effective length of query: 286 Effective length of database: 299 Effective search space: 85514 Effective search space used: 85514 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