Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_077280367.1 B1C78_RS17145 hypothetical protein
Query= curated2:Q56623 (328 letters) >NCBI__GCF_002000365.1:WP_077280367.1 Length = 263 Score = 154 bits (389), Expect = 2e-42 Identities = 82/240 (34%), Positives = 129/240 (53%), Gaps = 1/240 (0%) Query: 81 AHVMDDKEAEPLTLYREVNTAGTVNLAKQAIDSGVKRFIFISSIKVNGEGTLVGCPFKTE 140 AH+ + A L R N G V + A SG +R +F+S+I V+G P E Sbjct: 15 AHIHQNASASLLADLRRSNVDGAVRAVQAATMSGARRVVFVSTIGVHGSALSGPAPVTEE 74 Query: 141 DNHAPEDDYGLSKSEAEKQLVALAKDSSMEVVIIRPTIVYGPGVKANFASLMRLVSKGIP 200 P + Y LSK EAE+QL+ ++ + E+V++RP +V G G N A L RLVS G+P Sbjct: 75 SAVDPLEAYALSKWEAEEQLLRMSAEDGFELVVLRPALVAGGGAPGNLARLARLVSAGVP 134 Query: 201 LPFGSITQNKRSLVSINNLVDLIVTCIDHPKAANQVFLVSDGHDVSTAEMVRELAIALDK 260 LP N RS + + NL +IV C+DHP+AA + F+V++ ST E++ + + + Sbjct: 135 LPVPR-EDNARSFIGLKNLAKIIVACLDHPRAAGETFVVAEPEWPSTREVLEHIGEGMGQ 193 Query: 261 PTWQLPVPIWCYKLFGKLFGKSDIVDRLTGTLQVDISHTKETLGWKPPQTLQEGFKQTAQ 320 + +P + +L GK+ + +++ G L+VD S E+LGW+P Q L E + + Sbjct: 194 SVRMMRIPANAMRTAARLLGKAALYEKVFGDLRVDASKLHESLGWRPTQPLTEALRDVGR 253 Lambda K H 0.318 0.134 0.388 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: 157 Number of extensions: 3 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: 328 Length of database: 263 Length adjustment: 26 Effective length of query: 302 Effective length of database: 237 Effective search space: 71574 Effective search space used: 71574 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