Align 5-keto-L-gluconate epimerase; Bifunctional nonphosphorylated sugar isomerase; D-erythrose/D-threose isomerase; L-ribulose 3-epimerase; R3E; Nonphosphorylated sugar 3-epimerase; Nonphosphorylated sugar aldose-ketose isomerase; EC 5.1.3.-; EC 5.3.1.- (characterized)
to candidate SMa1353 SMa1353 epimerase
Query= SwissProt::Q9WYP7 (270 letters) >FitnessBrowser__Smeli:SMa1353 Length = 295 Score = 93.6 bits (231), Expect = 4e-24 Identities = 69/219 (31%), Positives = 115/219 (52%), Gaps = 24/219 (10%) Query: 31 KRVGYQAVEIAVRDPSIVDWNEVKILSEELNLPICAIGTGQAYLADG-LSLTHPNDEIRK 89 K+ GY+++EI+ +P+ D + + L +E + G L G +L ++ R Sbjct: 22 KKYGYESIEIS-GEPAQYDIKDTRALLKEHGIRCW----GAVTLTLGERNLAAKDESQRA 76 Query: 90 KAIERV----VKHTEVAGMFGALVIIGLVRGRREGRSYEE-------TEELFIESMKRLL 138 K+++ V +E+ G LV + + +G EE T+E F + ++ + Sbjct: 77 KSVDYVKSVITMVSELEGEIVTLVPATVGKVVPDGTEEEEWQWVVDATKECFAHAREKGV 136 Query: 139 ELTEHAKFVIEPLNRYETDFINTIDDALRILRKINSNRVGILADTFHMNIEEVNIPESLK 198 L IEPLNR+ET N AL + ++ + G+ D FH+NIEE +I ++++ Sbjct: 137 RLA------IEPLNRFETYLFNRAAQALALADAVDPD-CGVCLDAFHLNIEEEDIYDAIR 189 Query: 199 RAGEKLYHFHVADSNRWAPGCGHFDFRSVFNTLKEIGYN 237 AG +L+ FHVAD+NR+A G GH D+ + TLKEIGY+ Sbjct: 190 LAGNRLFDFHVADNNRFAAGLGHLDWPKIVATLKEIGYD 228 Lambda K H 0.320 0.138 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: 187 Number of extensions: 11 Number of successful extensions: 2 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: 270 Length of database: 295 Length adjustment: 26 Effective length of query: 244 Effective length of database: 269 Effective search space: 65636 Effective search space used: 65636 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: 47 (22.7 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