Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate RR42_RS15840 RR42_RS15840 spore coat protein
Query= BRENDA::F6DEY6 (311 letters) >FitnessBrowser__Cup4G11:RR42_RS15840 Length = 354 Score = 129 bits (323), Expect = 1e-34 Identities = 113/337 (33%), Positives = 156/337 (46%), Gaps = 49/337 (14%) Query: 3 VLVTGGAGFIGSHIVEDLLAR-GLEVAV----------LDNLATGKRENVPKGVPFFQVD 51 +LVTGGAGFIG++ V D L G + V L++LA+ K N F Q D Sbjct: 4 ILVTGGAGFIGANFVLDWLREDGADAVVNVDKLTYAGNLESLASLKCSNRHI---FSQTD 60 Query: 52 LRDKEEVERAFREFRPTHVSHQAAQASVKVSVEDPVLDFEVNLLGGLNLLEACRQY---- 107 + D+ ++R F E+RP V H AA++ V S+E P + N++G LLEA R Y Sbjct: 61 ICDRAALDRLFAEYRPRAVVHFAAESHVDRSIEGPGGFIQTNVVGTFTLLEAARAYWSGL 120 Query: 108 -GVEKLVF----ASTGGAIYGEVPEGERAEETWPPRPKSPYAASKAAFEHYLSVYGQSYG 162 G E+ VF ST P ET P SPY+ASKAA +H + Y +YG Sbjct: 121 HGSERDVFRFLHVSTDEVFGSLQPSDPAFTETTAFAPNSPYSASKAAADHLVRAYYHTYG 180 Query: 163 LKWVSLRYGNVYGPRQDPHGEAGVVAIFAERVLNGLPVTLYARKTPGDEGCVRDYVYVGD 222 L ++ N YGP P ++ + + L G P+ +Y GD VRD++YVGD Sbjct: 181 LPVLTTNCSNNYGPYHFPE---KLIPLVLMKALAGEPLPVY-----GDGLNVRDWLYVGD 232 Query: 223 --VAEAHALALFSLEGIYNVGTGEGHTTREVLEAVAEAAGKAPQVQP------------A 268 A LA + YNVG G+ T+ L+ V G +++P Sbjct: 233 HCAAVRAVLAKGRVGETYNVG---GNNTKTNLDVVHTLCGLLDELRPKVTGSYRQQITFV 289 Query: 269 PPRPGDLERSVLSPLKLMAH-GWRPKVGFQEGIRLTV 304 RPG R + KL GW K F+ G+R TV Sbjct: 290 ADRPGHDRRYAVDSRKLQVELGWTCKETFETGLRKTV 326 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: 296 Number of extensions: 16 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: 354 Length adjustment: 28 Effective length of query: 283 Effective length of database: 326 Effective search space: 92258 Effective search space used: 92258 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: 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