Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate 6938114 Sama_2235 NAD dependent epimerase/dehydratase family protein (RefSeq)
Query= BRENDA::P9WN67 (314 letters) >FitnessBrowser__SB2B:6938114 Length = 334 Score = 154 bits (389), Expect = 3e-42 Identities = 105/333 (31%), Positives = 164/333 (49%), Gaps = 29/333 (8%) Query: 1 MRALVTGAAGFIGSTLVDRLLADGHSVVGLDNF-----ATGRATNLEHLADNSAHVFVEA 55 M+ LVTGAAGFIG+ RLL+ GH V G+DN + + L LA + F Sbjct: 1 MKILVTGAAGFIGAAACKRLLSQGHQVHGIDNLNDYYDVSLKQARLAALASHPHFQFQRM 60 Query: 56 DIVTADLHAIL-EQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVR 114 ++ A L +P+ V HL AQ VR S+ +P A N++G + + E RQTGV+ Sbjct: 61 ELADRGAIATLFSTIKPDWVLHLGAQAGVRYSIDNPHAYADANLVGHLNILEGCRQTGVK 120 Query: 115 KIVHTSSGGSIYGTPPEYPTPETAPTD-PASPYAAGKVAGEIYLNTFRHLYGLDCSHIAP 173 +V+ SS S+YG + P + D P S YAA K A E+ +++ HLYG+ C+ + Sbjct: 121 HLVYASS-SSVYGLNKKLPFATSDSVDHPVSLYAATKKANELMSHSYAHLYGVPCTGLRF 179 Query: 174 ANVYGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRV----- 228 VYGP P +FA+A+++G+P +VF G +RD+ F+DD+++ + V Sbjct: 180 FTVYGPWGRPD---MAPMLFARAIMAGEPIKVFNQGDMSRDFTFIDDIIEGVIGVLPLPP 236 Query: 229 ------SADVGGGLR-------FNIGTGKETSDRQLHSAVAAAVGGPDDPEFHPPRLGDL 275 S + G NIG G S + A+G +F P + GD+ Sbjct: 237 STSSQWSVESGSSSESSAPYRVLNIGHGSPVSLMHFIETLENALGRKAIKQFLPMQDGDV 296 Query: 276 KRSCLDIGLAERVLGWRPQIELADGVRRTVEYF 308 K + D + G RP++ + GV+ +++ Sbjct: 297 KATWADTEDLFAITGVRPKVGIEQGVKAFADWY 329 Lambda K H 0.320 0.137 0.410 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: 232 Number of extensions: 14 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: 314 Length of database: 334 Length adjustment: 28 Effective length of query: 286 Effective length of database: 306 Effective search space: 87516 Effective search space used: 87516 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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