Align UDP-glucose 4-epimerase; UDP-galactose 4-epimerase; Uridine diphosphate galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate Echvi_4409 Echvi_4409 Nucleoside-diphosphate-sugar epimerases
Query= SwissProt::A0R5C5 (313 letters) >FitnessBrowser__Cola:Echvi_4409 Length = 362 Score = 168 bits (425), Expect = 2e-46 Identities = 115/339 (33%), Positives = 173/339 (51%), Gaps = 32/339 (9%) Query: 2 RTLVTGAAGFIGSTLVDRLLADGHGVVGLDDLSSGRAENLHSAENSDKFEFVKADIVDAD 61 + LVTG AGFIGS L+D LL G VV LD+ S+G+ NL A S +F ++ DI D Sbjct: 14 KVLVTGGAGFIGSNLIDALLEAGSRVVCLDNFSTGKRTNLEKALTSSRFSLIEGDIRDYT 73 Query: 62 LTGLLAEFKPEVIFHLAAQISVKRSVDDPPFDATVNVVGTVRLAEAARLAGVRKVVHTSS 121 E + +FH AA SV RS+ DP VN+ G V++ AA+ AGV++VV+ +S Sbjct: 74 TCAEAVE-GCKWVFHQAALGSVPRSIADPMTSTDVNIGGFVKVLFAAKEAGVQRVVYAAS 132 Query: 122 GGSVYGTPPAYPTSEDMPVNPASPYAAGKVAGEVYLNMYRNLYDLDCSHIAPANVYGPRQ 181 S YG P P E + N SPYA K E++ + + Y L+ + NV+G RQ Sbjct: 133 -SSTYGDHPDLPKVEHVIGNALSPYAITKYVDELFAKNFADTYGLETIGLRYFNVFGRRQ 191 Query: 182 DPHGE-AGVVAIFSEALLAGRTTKIFGDGSDTRDYVFVDDVVDAFVRA------------ 228 DP G A V+ F L+ G + +I GDGS +RD+ ++D+V+ A V+A Sbjct: 192 DPDGAYAAVIPKFVRCLVEGESPRINGDGSFSRDFTYIDNVIQANVKAAVTGTALMKANL 251 Query: 229 -------GGP----AGGGQRFNVGTGVETSTRELHTAIAGAVGAPDEP------EFHPPR 271 G P A + FNV G + EL + + + D+ E+ P R Sbjct: 252 AEYHAHIGRPFNTDAVISEVFNVAFGERVNLNELGSYLKEELSKFDKEISGIPMEYGPQR 311 Query: 272 LGDLRRSRLDNTRAREVLGWQPQVALAEGIAKTVEFFRN 310 GD+ S + R+V+G++P+ ++ +G+ E++ N Sbjct: 312 AGDVPHSLASIEKGRKVIGYEPEYSVRQGLGLACEWYWN 350 Lambda K H 0.317 0.136 0.396 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: 269 Number of extensions: 12 Number of successful extensions: 4 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: 313 Length of database: 362 Length adjustment: 28 Effective length of query: 285 Effective length of database: 334 Effective search space: 95190 Effective search space used: 95190 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 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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