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 CA265_RS12255 CA265_RS12255 epimerase
Query= SwissProt::Q9WYP7 (270 letters) >FitnessBrowser__Pedo557:CA265_RS12255 Length = 294 Score = 105 bits (262), Expect = 1e-27 Identities = 61/144 (42%), Positives = 87/144 (60%), Gaps = 12/144 (8%) Query: 124 EETEELFIESMKRLLELTEHA--KFVIEPLNRYETDFINTIDDALRILRKINSNRVGILA 181 EE + SMK + E +E A IEP+NR+ET FIN + AL + ++ N G+ Sbjct: 114 EEEWAWAVNSMKEIYEYSESAGISLGIEPINRFETYFINRAEQALALAAEVGPN-CGVCL 172 Query: 182 DTFHMNIEEVNIPESLKRAGEKLYHFHVADSNRWAPGCGHFDFRSVFNTLKEIGYNRYVS 241 DTFHMNIEE ++ E++K A ++L FHVAD+NR APG G+ D++ + +TL E+ Y +S Sbjct: 173 DTFHMNIEERDMFEAIKMAKDRLVGFHVADNNRMAPGMGNLDWQKIVDTLHEVNYKGALS 232 Query: 242 VE-CLPL--------PGGMEEAAE 256 VE C PL PG ++E E Sbjct: 233 VEFCSPLDRTPANPYPGSIDEKPE 256 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: 194 Number of extensions: 9 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: 294 Length adjustment: 26 Effective length of query: 244 Effective length of database: 268 Effective search space: 65392 Effective search space used: 65392 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