Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate N515DRAFT_3549 N515DRAFT_3549 UDP-glucuronate 4-epimerase
Query= BRENDA::F6DEY6 (311 letters) >FitnessBrowser__Dyella79:N515DRAFT_3549 Length = 336 Score = 147 bits (372), Expect = 3e-40 Identities = 110/341 (32%), Positives = 162/341 (47%), Gaps = 43/341 (12%) Query: 1 MRVLVTGGAGFIGSHIVEDLLARGLEVAVLDNL----------ATGKRENVPKGVPFFQV 50 M+VLVTG AGFIGSH+ LLARG EV LDNL A R G Sbjct: 1 MKVLVTGTAGFIGSHVARKLLARGDEVIGLDNLNDYYDVGLKQARLARVQAYPGYTHVHA 60 Query: 51 DLRDKEEVERAFREFRPTHVSHQAAQASVKVSVEDPVLDFEVNLLGGLNLLEACRQYGVE 110 DL D+ VE+ F +P V + AAQA V+ + +P + N+ G L++LE CRQ+GV+ Sbjct: 61 DLADRAAVEKLFATHKPERVVNLAAQAGVRYAATNPHVYVSSNVTGFLHILEGCRQHGVQ 120 Query: 111 KLVFASTGGAIYGEVPEGERAEETWPPRPKSPYAASKAAFEHYLSVYGQSYGLKWVSLRY 170 LVFAST ++YG + +E P + YAA+K A E Y YG+ LR+ Sbjct: 121 HLVFAST-SSVYGANRDLPFSEHRPAEHPLTLYAATKKANEQMAHSYAHLYGVPATGLRF 179 Query: 171 GNVYGPRQDPHGEAGVVAIFAERVLNGLPVTLYARKTPGDEG-CVRDYVYVGDVAEAHAL 229 VYGP P + +F + +L G P+ ++ +EG R + Y+ D+ E Sbjct: 180 FTVYGPWGRPD---MALFLFTKAILAGEPIRVF------NEGRHKRSFTYIDDIVEGVVR 230 Query: 230 ALFSLEG---------------------IYNVGTGEGHTTREVLEAVAEAAGKAPQVQPA 268 AL ++ G +YN+G + +E + + G+ ++ Sbjct: 231 ALDTVPGKDPAWDATQPDPSTSGVAPYRLYNIGNEQPVELLRYIEVLEQCLGRKATMELL 290 Query: 269 PPRPGDLERSVLSPLKLMAH-GWRPKVGFQEGIRLTVDHFR 308 P + GD+ + L+A G+RPKV +EGI V +R Sbjct: 291 PLQAGDVPETEADVSSLVAAVGYRPKVSVEEGIAAFVKWYR 331 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: 318 Number of extensions: 22 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: 336 Length adjustment: 28 Effective length of query: 283 Effective length of database: 308 Effective search space: 87164 Effective search space used: 87164 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