Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_084058582.1 B9A12_RS13210 hypothetical protein
Query= curated2:Q56623 (328 letters) >NCBI__GCF_900176285.1:WP_084058582.1 Length = 325 Score = 270 bits (691), Expect = 3e-77 Identities = 143/320 (44%), Positives = 208/320 (65%), Gaps = 5/320 (1%) Query: 10 KSILLTGSTGFVGTNLVKSLTLKSDYIVKSAVRHAVNKDDGLLFEVGDINASTDFELP-- 67 +++L+TG+TGFVG LV L+ + ++V+SAVR + + VGD+ A L Sbjct: 4 RTVLVTGATGFVGRALVSVLSSRG-HVVRSAVRRCGSGAPNEV-AVGDLQAPNRDSLKDA 61 Query: 68 LKNTTVVVHCAARAHVMDDKEAEPLTLYREVNTAGTVNLAKQAIDSGVKRFIFISSIKVN 127 L + VVH AAR HVM D E +PL +YR VN T ++A+ A + GV+RF+F+SSIKVN Sbjct: 62 LAGSDAVVHLAARVHVMSDSEDDPLAVYRAVNVVATESVARMAAEVGVERFVFLSSIKVN 121 Query: 128 GEGTLVGCPFKTEDNHAPEDDYGLSKSEAEKQLVALAKDSSMEVVIIRPTIVYGPGVKAN 187 GEGT G F D AP+D Y +SK EAE+ L +A+++ ++VVI+RP +VYGPGV+AN Sbjct: 122 GEGTPGGTAFTERDKPAPQDAYAVSKHEAERALHQVAQETGLQVVIVRPPLVYGPGVRAN 181 Query: 188 FASLMRLVSKGIPLPFGSITQNKRSLVSINNLVDLIVTCIDHPKAANQVFLVSDGHDVST 247 F LM +V++ +PLP G++ N+RSLV + NLVD +VTC+DHP A + FLVSDG D+ST Sbjct: 182 FLRLMNMVARCLPLPLGAV-DNRRSLVGLTNLVDFLVTCLDHPMAVGETFLVSDGEDLST 240 Query: 248 AEMVRELAIALDKPTWQLPVPIWCYKLFGKLFGKSDIVDRLTGTLQVDISHTKETLGWKP 307 E++ +A A+ +P P P + G+L G V+RL G+LQVDI + LGW+P Sbjct: 241 PELIGRIAGAMGRPARLFPFPPGWLQAGGRLLGLEATVERLCGSLQVDIGKARGVLGWQP 300 Query: 308 PQTLQEGFKQTAQAFLQANN 327 ++ E +TA ++Q+ + Sbjct: 301 VSSVDEELARTADWYIQSRS 320 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: 261 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: 325 Length adjustment: 28 Effective length of query: 300 Effective length of database: 297 Effective search space: 89100 Effective search space used: 89100 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