GONUTS has been updated to MW1.31 Most things seem to be working but be sure to report problems.
|Status||Page||User||Date/Time||GO Term (Aspect)||Reference||Evidence||Notes||Links|
|STREE:O85255||Mhassan, TeamGreen||2015-05-11 13:55:15 CDT||GO:0004146 dihydrofolate reductase activity (F)||PMID:19950924||ECO:0000315 mutant phenotype evidence used in manual assertion|
Figure 8 shows how the mutation of Val100 to Leu makes the leucine side chain clash with side chains of Ile8 and Phe34, shifting their positions and stacking interactions with the trimethoprim molecule. "Weaker binding of trimethoprim to Leu100 DHFR would lead to trimethoprim resistance". The KM values of NADPH and H2F for the wild type spDHFR and the mutant Sp9 were measured (Table 2B). The KM values for the wild type spDHFR were at least order of magnitude higher than those for the Sp9 mutant that showed full enzyme activity even at a limiting low concentration of 0.63 μM H2F consistent with a much lower KM value for this substrate.
|9CAUD:S5YPK3||Skatie, TeamGreen||2015-04-22 08:06:37 CDT||GO:0008409 5'-3' exonuclease activity (F)||PMID:17457612||ECO:0000315 mutant phenotype evidence used in manual assertion|
HHpred search on protein sequence of Gene 149 of Troll led to the first result being Klenow fragment of DNA polymerase I with an e-value of 1e-128 and 100% probability. The other 100% probability results show that this gene is most likely a part of DNA polymerase I. A search for the function of the Klenow fragment led to the PubMed article with ID number listed as a Reference. The function of Klenow in E.coli, according to the Reference article, is to decrease transition mutations.
|9CAUD:S5YPI0||Yravali, TeamGreen||2015-04-08 10:10:22 CDT||GO:0004386 helicase activity (F)||PMID:9233823||ECO:0000315 mutant phenotype evidence used in manual assertion|
UvsW acts as an Helicase in T4-bacteriophage, where it functions to unwind DNA/RNA double strands and suppress the R loops in order for the replication process to take place. Table 1. results show that when a UvsW protein was inserted into a E.coli double mutant, which lacked rnhA protein and caused formation of R loops and lead to cell death, it suppressed the R loop formation.
|9CAUD:S5YPI0||Pclarence, TeamGreen||2015-04-08 09:18:30 CDT||GO:0006268 DNA unwinding involved in DNA replication (P)||other:PMC3729639||ECO:0000314 direct assay evidence used in manual assertion|
Even though UvsW acts as a Helicase in T4-bacteriophage, it requires the help of another protein gp32. gp32 is a DNA-binding protein, when bounded to the unwinded DNA, enhances the conversion of D-loop structures into unwinded structures. Table1b, lanes 7-12 contains D-loop radioactively labeled dsDNA covered with 2uM of gp32 proteins and exposed to UvsW protein at different time points. Compared to the lanes 1-6, which do no contain gp32 proteins, D-loop structures were relieved at a faster rate in the presence of gp32 proteins.
|9CAUD:S5Y0G6||Mhassan, TeamGreen||2015-04-08 08:17:31 CDT||GO:0004146 dihydrofolate reductase activity (F)||GO_REF:0000100||ECO:0000247 sequence alignment evidence used in manual assertion|
HHPred showed promising alignment with e value=5E-45, p value=2.6E-50, and prob =100.0. This gene is a putative homologue of the prior one as evidenced by the alignment and shared function. Primary paper supports DHFR activity by mutant phenotpe. "e KM values of NADPH and H2F for the wild type spDHFR and the mutant Sp9 were measured (Table 2B). The KM values for the wild type spDHFR were at least order of magnitude higher than those for the Sp9 mutant that showed full enzyme activity even at a limiting low concentration of 0.63 μM H2F consistent with a much lower KM value for this substrate. "
|9CAUD:S5Y020||Gjulie, TeamGreen||2015-04-06 08:51:31 CDT||GO:0046080 regulation of dUTP diphosphatase activity (P)||PMID:381286||ECO:0000315 mutant phenotype evidence used in manual assertion|
The function of this gene in the T5 phage can be concluded from a mutant phenotype. Figure 4 in the referenced paper shows that the dut mutant T5 phage made was not able to induce dUTPase activity. This gives us evidence to conclude that the function of that gene is a dUTPase. IMP can also be assigned to this phage with evidence from an experimental paper that states the function of a dUTPase.
|9CAUD:S5Y020||Gjulie, TeamGreen||2015-04-06 08:51:31 CDT||GO:0004170 dUTP diphosphatase activity (F)||GO_REF:0000100||ECO:0000247 sequence alignment evidence used in manual assertion|
BlastP showed that the Troll gene is a homolog to a gene from another bacteriphage, Bacillus phage VB_BCEMBc431v3. The alignment gave an e-value of 1e-122, 93%query cover and 60% identity. Evidence for the function of the Bacillus phage gene is given through experimental evidence done on the phage, T5. The Troll gene also aligned with other dUTP diphosphatase proteins. This is evidence to conclude that the two genes are homologous. The function of this gene is in the reaction that converts dUTP to dUMP.