Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate GFF453 PS417_02315 NAD-dependent dehydratase
Query= BRENDA::F6DEY6 (311 letters) >FitnessBrowser__WCS417:GFF453 Length = 308 Score = 209 bits (532), Expect = 7e-59 Identities = 125/293 (42%), Positives = 177/293 (60%), Gaps = 15/293 (5%) Query: 2 RVLVTGGAGFIGSHIVEDLLARGLEVAVLDNLATGKRENVPKGVP---FFQVDLRDKEEV 58 RVL+TGGAGFIGSH+V+ LLA+G V VLDNL+TGKR N+P P + D+ D E V Sbjct: 4 RVLITGGAGFIGSHLVDALLAKGYGVRVLDNLSTGKRSNLPLDNPRVELLEGDVADAELV 63 Query: 59 ERAFREFRPTHVSHQAAQASVKVSVEDPVLDFEVNLLGGLNLLEACRQYGVEKLVFASTG 118 RA + T V H AA ASV+ SV+DPV + N +G LN+ EA R+ GV+++V+AS+ Sbjct: 64 ARAAVD--TTAVVHLAAVASVQASVDDPVSTHQSNFVGTLNVCEAMRKAGVKRVVYASS- 120 Query: 119 GAIYGEVPEGERAEETWPPRPKSPYAASKAAFEHYLSVYGQSYGLKWVSLRYGNVYGPRQ 178 A+YG EG +E P +PYA+ K A EHY Y + +GL+ V R+ N++GPRQ Sbjct: 121 AAVYGNNGEGASIDEETTKAPLTPYASDKLAGEHYFDFYRRQHGLEPVIFRFFNIFGPRQ 180 Query: 179 DPHGE-AGVVAIFAERVLNGLPVTLYARKTPGDEGCVRDYVYVGDVAEAHALALFSLE-- 235 DP +GV++IF+ER G+P+ ++ GD RD++YV D+ + A+ + Sbjct: 181 DPSSPYSGVISIFSERAQQGVPIAVF-----GDGEQTRDFMYVEDLVDVLVQAIEAPSAP 235 Query: 236 -GIYNVGTGEGHTTREVLEAVAEAAGKAPQVQPAPPRPGDLERSVLSPLKLMA 287 G NVG T ++VL+A+ E GK P V P R GD+ S + +L+A Sbjct: 236 LGAINVGWNRTTTLKQVLQALEEIVGKLPTVTYGPARSGDIRHSRANNQRLLA 288 Lambda K H 0.318 0.138 0.411 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: 287 Number of extensions: 18 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: 311 Length of database: 308 Length adjustment: 27 Effective length of query: 284 Effective length of database: 281 Effective search space: 79804 Effective search space used: 79804 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 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