Align UDP-glucose 4-epimerase; UDP-galactose 4-epimerase; Uridine diphosphate galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate GFF3921 PGA1_65p00240 dTDP-glucose 4,6-dehydratase RffG
Query= SwissProt::A0R5C5 (313 letters) >FitnessBrowser__Phaeo:GFF3921 Length = 350 Score = 160 bits (404), Expect = 5e-44 Identities = 112/329 (34%), Positives = 169/329 (51%), Gaps = 24/329 (7%) Query: 1 MRTLVTGAAGFIGSTLVDRLLADGHGVVGLDDLSSGRA-ENLHSAENSDKFEFVKADIVD 59 M+ LVTG AGFIGS +V +A GH VV LD L+ +N+ + +S + F + DI D Sbjct: 1 MKILVTGGAGFIGSAVVRLAVARGHQVVNLDALTYAACLDNVAAVADSPNYAFEQVDIRD 60 Query: 60 -ADLTGLLAEFKPEVIFHLAAQISVKRSVDDPPFDATVNVVGTVRLAEAARL----AGVR 114 A L + A +P+V+ HLAA+ V RS+D P N+ GT ++ EAAR AG Sbjct: 61 RAALDTVFARHRPDVVMHLAAESHVDRSIDGPGDFIETNITGTYQMLEAARKYWAEAGRP 120 Query: 115 KV--VHTSSGGSVYGTPPAYPT---SEDMPVNPASPYAAGKVAGEVYLNMYRNLYDLDCS 169 + H S VYG+ PA P+ +E+ +P SPY+A K A + + + Y L Sbjct: 121 EAFRFHHISTDEVYGSLPADPSVMFTEETGYDPRSPYSASKAASDHLVRAWGETYGLPVV 180 Query: 170 HIAPANVYGPRQDPHGEAGVVAIFSEALLAGRTTKIFGDGSDTRDYVFVDDVVDAFVRAG 229 +N YGP P VV + + LAG+ I+GDGS+ RD+++V+D DA + Sbjct: 181 LTNCSNNYGPYHFPEKLIPVVILNA---LAGKPLPIYGDGSNVRDWLYVEDHADALLLVV 237 Query: 230 GPAGGGQRFNVGTGVETSTRELHTAIAGAV----------GAPDEPEFHPPRLGDLRRSR 279 G+ +N+G E + EL + + D+ F R G R Sbjct: 238 SKGRVGRSYNIGGENERTNLELVETLCAILDEKRPREDGGSYKDQITFVTDRPGHDARYA 297 Query: 280 LDNTRAREVLGWQPQVALAEGIAKTVEFF 308 +D +R R+ LGW+P V + EG+A+TV+++ Sbjct: 298 IDPSRIRDELGWRPSVTVEEGLARTVQWY 326 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: 262 Number of extensions: 12 Number of successful extensions: 5 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: 350 Length adjustment: 28 Effective length of query: 285 Effective length of database: 322 Effective search space: 91770 Effective search space used: 91770 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