Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_092998985.1 BLP65_RS15335 hypothetical protein
Query= curated2:Q56623 (328 letters) >NCBI__GCF_900102855.1:WP_092998985.1 Length = 320 Score = 309 bits (792), Expect = 5e-89 Identities = 160/314 (50%), Positives = 218/314 (69%), Gaps = 4/314 (1%) Query: 11 SILLTGSTGFVGTNLVKSLTLKSDYIVKSAVRH--AVNKDDGLLFEVGDINASTDFELPL 68 ++L+TG+TGF+G ++++ LT + V AVR AV + + +VGD+ ++ L Sbjct: 3 TVLVTGATGFLGGSVLRKLTAEGKPAVV-AVRSSTAVLSAEVPMVQVGDLTPEANWREAL 61 Query: 69 KNTTVVVHCAARAHVMDDKEAEPLTLYREVNTAGTVNLAKQAIDSGVKRFIFISSIKVNG 128 VVVH AAR HVM + + L ++REVN GT+NLA+QA D+GV+R +FISSIKVNG Sbjct: 62 NEVDVVVHAAARVHVMHETATDALAVFREVNVEGTLNLARQAADAGVRRLVFISSIKVNG 121 Query: 129 EGTLVGCPFKTEDNHAPEDDYGLSKSEAEKQLVALAKDSSMEVVIIRPTIVYGPGVKANF 188 E T G F +D P+D YG+SK EAE++L+ LA +S MEVV IRP++VYGPGVKANF Sbjct: 122 EQTAPGQVFGADDKPLPQDPYGVSKWEAEERLMELADESGMEVVCIRPSLVYGPGVKANF 181 Query: 189 ASLMRLVSKGIPLPFGSITQNKRSLVSINNLVDLIVTCIDHPKAANQVFLVSDGHDVSTA 248 S+MR V+KG+PLP G+I N+RSLV+++NLVDLI+TCIDHP AANQ FL DG D+ST Sbjct: 182 LSMMRWVAKGVPLPLGAI-HNQRSLVALDNLVDLIITCIDHPAAANQTFLAGDGEDLSTT 240 Query: 249 EMVRELAIALDKPTWQLPVPIWCYKLFGKLFGKSDIVDRLTGTLQVDISHTKETLGWKPP 308 E++R L AL KP LPVP+W + + GK + RL G+LQVDIS ++ LGW PP Sbjct: 241 ELLRRLGDALGKPARLLPVPVWVLEAGAAMVGKQAVARRLCGSLQVDISKARDVLGWTPP 300 Query: 309 QTLQEGFKQTAQAF 322 ++ E ++TA+ F Sbjct: 301 VSVDEALRETAREF 314 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: 290 Number of extensions: 9 Number of successful extensions: 3 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: 320 Length adjustment: 28 Effective length of query: 300 Effective length of database: 292 Effective search space: 87600 Effective search space used: 87600 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