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Category:Team TRUMP2016

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StatusPageUserDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
unacceptableTRYB2:Q38AY4Barlowrm, Team TRUMP20162016-05-16 09:04:52 CDTGO:0005634 nucleus (C)PMID:24558481ECO:0000250 sequence similarity evidence used in manual assertion

Figure two from the article shows sequence similarity between the two proteins. Along with a gel electrophoresis comparing the bands between of dna between the two proteins

challenge
unacceptableCALS4:Q8R7L0Barlowrm, Team TRUMP20162016-05-16 09:00:05 CDTGO:0000100 S-methylmethionine transmembrane transporter activity (F)PMID:17662107ECO:0000250 sequence similarity evidence used in manual assertion

The function and structure of this protein is to design compounds that would be effective inhibitors. "Almost all of the inhibitors available are analogues of the substrate or transition-state. The main drawback of these compounds is that there is poor differential inhibition among various HGPRTs. The reason maybe due to high structure similarity of HGPRTs from different species (especially the active site) even though there is only moderate sequence homology. The key residues in the active site are highly similar among HGPRTs (Table 1)."

challenge
unacceptableLUPLU:Q8VX11Barlowrm, Team TRUMP20162016-05-16 08:48:00 CDTGO:1904097 acid phosphatase complex (C)PMID:25075326ECO:0000314 direct assay evidence used in manual assertion

The homohexameric organization of PPD1, as revealed by a 1.65 Å resolution crystal structure and confirmed by solution X-ray scattering, is unique among plant PAPs, for which only homodimers have previously been reported. A phosphate anion is bound in a bidentate fashion at the active site, bridging the Fe and Mn atoms in a binding mode similar to that previously reported for sweet potato PAP, which suggests that common features occur in their catalytic mechanisms.

challenge
updatedbyinstructorHUMAN:AKAP8Iyerav, Team TRUMP20162016-05-04 22:13:04 CDTGO:0005730 nucleolus (C)PMID:26683827ECO:0000314 direct assay evidence used in manual assertion

Figure 1. shows the intra-nuclear localization of AKAP95 is dependent on both RNA polymerase I and RNA polymerase II.

challenge
unacceptableHUMAN:LKHA4Barlowrm, Team TRUMP20162016-05-04 15:45:10 CDTGO:0000175 3'-5'-exoribonuclease activity (F)PMID:24558481ECO:0000250 sequence similarity evidence used in manual assertion

HHPRED shows an e value of 1.4E-13. Figure two from the article shows sequence similarity between the two proteins. Along with a gel electrophoresis comparing the bands between of dna between the two proteins

challenge
unacceptableBPT4:UVSWPowellme, Team TRUMP20162016-05-02 10:29:07 CDTGO:0016787 hydrolase activity (F)PMID:17878153ECO:0000314 direct assay evidence used in manual assertion

figure 2 shows both primary and secondary structure assignment of entire molecule. A1, A2, B1,B2 reflects domain locations that are consistent with monomeric helicases

challenge
unacceptableBPT4:UVSWPowellme, Team TRUMP20162016-05-02 10:16:10 CDTGO:0016787 hydrolase activity (F)PMID:17878153ECO:0000314 direct assay evidence used in manual assertion

Domains 2a and B shown in figure 3 once combined create architecture this is typical of monomeric helicase .

challenge
updatedbyinstructorBPT4:TERLJermstadsb, Team TRUMP20162016-05-02 09:51:58 CDTGO:0004536 deoxyribonuclease activity (F)PMID:19109896ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3b compares the mutant gp17 proteins to the wild types. Arg406 in T4 participates in binding DNA and nuclease activity. Mutant "Arg406Ala" showed that any substitutions in amino acids at the 406 position produced a null phenotype. Meaning that when they tested the phages in a plating assay the mutants failed to produce plaques. See figure 3b shows that unlike the wild-type, the mutant R406A did not degrade the DNA after 2 hours of incubation.

challenge
unacceptableBPT4:TERLPowellme, Team TRUMP20162016-05-02 09:19:00 CDTGO:0043493 viral terminase complex (C)ECO:0000255 match to sequence model evidence used in manual assertion

Terminate acts as a an ATP driven molecular motor for viral DNA translocation

challenge
unacceptableBPT4:TERLJermstadsb, Team TRUMP20162016-05-01 16:59:20 CDTGO:0004518 nuclease activity (F)PMID:19109896ECO:0000314 direct assay evidence used in manual assertion

The assay experiment of the gp17 terminase can be viewed in figure 3b. Lane's 0, 1, and 2 are how many hours after the addition of isopropyl β-D-1-thiogalactopyranoside (IPTG). This induces the expression of the DNA samples. The mutant sample are then compared to the known DNA. It is then compared to the mutant types, the mutant types did not have cleaved DNA. Proving its identity as a nuclease.

challenge
acceptableBPT4:PORTLJermstadsb, Team TRUMP20162016-05-01 15:25:34 CDTGO:0046798 viral portal complex (C)PMID:26144253ECO:0000314 direct assay evidence used in manual assertion

This is a ring of proteins where DNA enters and exits the phages capsid. The structure was determined by cryo-electron microscopy (cryo-EM) Figure 1.

challenge
unacceptableCLOTH:A3DJ38Powellme, Team TRUMP20162016-04-27 09:42:27 CDTGO:0004721 phosphoprotein phosphatase activity (F)PMID:23595150ECO:0000247 sequence alignment evidence used in manual assertion

figure 2D shows aligned structures of the Cth and lambda phosphatase

challenge
unacceptableCLOTH:A3DJ38Powellme, Team TRUMP20162016-04-27 09:13:57 CDTPMID:23595150ECO:0000255 match to sequence model evidence used in manual assertion

Figure 2A tertiary structures as well as overlay shows conservation of structure to lambda phosphatase (with a citrase that mimics phosphate).

challenge
unacceptableLAMBD:PPPowellme, Team TRUMP20162016-04-27 09:07:35 CDTGO:0004721 phosphoprotein phosphatase activity (F)PMID:11112522ECO:0000314 direct assay evidence used in manual assertion

Figure 3 lambda active site with bound sulfate(its a phosphate mimic is consistent with the active site components of phosphatase) and solvent molecules

challenge
unacceptableLEGPH:COAEJermstadsb, Team TRUMP20162016-04-25 10:08:03 CDTGO:0004140 dephospho-CoA kinase activity (F)PMID:25449315ECO:0000255 match to sequence model evidence used in manual assertion

Structure of Lp-DPCK-Bu2 was determined by molecular replacement with Phaser

challenge
unacceptableECOLI:RBNJermstadsb, Team TRUMP20162016-04-25 09:37:36 CDTGO:0000100 S-methylmethionine transmembrane transporter activity (F)other:GO REF: 10097147ECO:0000250 sequence similarity evidence used in manual assertion

Blastp results showed 100.0% sequence similarity with Bacillus phage Vinny and HHpred showed a 100% probability and a e-value of 3.2E-28

challenge
unacceptableECOLI:RBNJermstadsb, Team TRUMP20162016-04-24 22:45:46 CDTGO:0004519 endonuclease activity (F)PMID:16452444ECO:0000314 direct assay evidence used in manual assertion

E. Coli's ZiPD gene has been identified as an endonuclease which cleaves the 3′ extension from various tRNA precursors, which makes it a tRNase Z enzyme. This was proven by comparing the structure of E Coli's tRNase Z to the structure of various known tRNase Z structures. This comparison can be seen in figure 4.

challenge
unacceptableARATH:PPA26Barlowrm, Team TRUMP20162016-04-23 17:58:34 CDTGO:1904097 acid phosphatase complex (C)PMID:25075326ECO:0000314 direct assay evidence used in manual assertion

The homohexameric organization of PPD1, as revealed by a 1.65 Å resolution crystal structure and confirmed by solution X-ray scattering, is unique among plant PAPs, for which only homodimers have previously been reported. A phosphate anion is bound in a bidentate fashion at the active site, bridging the Fe and Mn atoms in a binding mode similar to that previously reported for sweet potato PAP, which suggests that common features occur in their catalytic mechanisms.

challenge
unacceptable9CAUD:A0A024B0Y1Barlowrm, Team TRUMP20162016-04-23 16:14:39 CDTGO:0000100 S-methylmethionine transmembrane transporter activity (F)PMID:24004689ECO:0000250 sequence similarity evidence used in manual assertion

Figure 3 shows a multiple sequence alignments of representative sequences in the DUF4424 and YARHG families.

challenge
unacceptableHUMAN:HPRTBarlowrm, Team TRUMP20162016-04-11 11:22:55 CDTGO:0000100 S-methylmethionine transmembrane transporter activity (F)PMID:17662107ECO:0000250 sequence similarity evidence used in manual assertion

The main protein ribose-phosphate pyrophosphokinase from the Hakuna Genome, shares a homology with guanine phosphoribosyltransferase with an e score of 4e-10 according to HHPRED. The function and structure of this protein is to design compounds that would be effective inhibitors. "Almost all of the inhibitors available are analogues of the substrate or transition-state. The main drawback of these compounds is that there is poor differential inhibition among various HGPRTs. The reason maybe due to high structure similarity of HGPRTs from different species (especially the active site) even though there is only moderate sequence homology. The key residues in the active site are highly similar among HGPRTs (Table 1)."

challenge
unacceptableHUMAN:PNCBBarlowrm, Team TRUMP20162016-04-11 03:20:12 CDTGO:0004516 nicotinate phosphoribosyltransferase activity (F)PMID:18321072ECO:0000314 direct assay evidence used in manual assertion

According to HHPRED the protein nicotinate phosphoribosyltransferase shares a homology with the protein Quinolinate Phosphoribosyl Transferase, with an e value of 1.2E-12. Figure 3 shows the structural homology between Dimer of scQAPRTase complexed with phthalate and PRPP. (B) Hexamer of aposcQAPRTase. The function of nicotinate phosphoribosyltransferase is to catalyze the conversion of nicotinic acid (NA) to NA mononucleotide (NaMN).

challenge
unacceptableRAT:GLRA1Iyerav, Team TRUMP20162016-04-10 11:44:14 CDTGO:0060080 response to alcohol (P)PMID:27058626ECO:0000250 sequence similarity evidence used in manual assertion

The graphical display figure in the paper describes and explains the effect of glycine in rat's brains. The figure is also indirectly an info-graphic that helps in understanding the protein's function.

Glycine receptors are ligand gated chloride channels that are found in a rat's brain. In this investigation, the researchers investigated the inhibitory potential of glycine against alcohol-induced oxidative stress, neuroinflammation and neurodegeneration in the rat brain. The researchers performed Gly co-treatment on the rat pups to investigate it's effects by injecting ethanol into the rat brains. They found that glycine reduced the alcohol induced stress and neuronal loss in the rat brain. Therefore with this finding, they concluded that glycine could be a potential treatment against alcohol-intoxication for newborns and infants.

challenge
unacceptableHUMAN:CXCR4Iyerav, Team TRUMP20162016-04-10 11:14:35 CDTGO:0016494 C-X-C chemokine receptor activity (F)PMID:27058821ECO:0000316 genetic interaction evidence used in manual assertion

CXCR4 is a chemokine receptor that is recognized by C-X-C motif chemokine 12 (CXCL12) a.k.a stromal cell-divided factor 1 (SDF1). CXCL12 plays a big role in immune responses and metastatic cancer. Calculations and Virtual Screening with the help of the NMR complex structure was performed. This investigation proved that interfaces between proteins may often possess lead compounds for fragment-based optimization.

challenge
unacceptableHUMAN:SAA1Iyerav, Team TRUMP20162016-04-10 10:11:20 CDTGO:0045087 innate immune response (P)PMID:27058895ECO:0000317 genomic context evidence used in manual assertion

The acute-phase protein, Serum amyloid A (SAA1) is usually found in the liver and has been recently been proven to be found in cancer tissues. SAA1's content in breast cancer hadn't been described hence the researchers of this protein decided to study the protein's abundance. Immunohistochemistry was applied in this investigation to determine the quantity of SAA1 in tumor-associated macrophage (TAM). Fluorescent in situ hybridization (FISH) was performed to examine the expression and location of the mRNA of SAA1. The results of this investigation showed that TAM's may be the main source of SAA1's in breast cancer. Therefore presence of SAA1 in TAM's could correlate with the occurrence of breast cancer.

challenge
unacceptableHUMAN:HMOX1Iyerav, Team TRUMP20162016-04-10 09:08:31 CDTGO:0004392 heme oxygenase (decyclizing) activity (F)PMID:27058954ECO:0000316 genetic interaction evidence used in manual assertion

A group of experimental scientists analyzed the global mRNa expression and the methylation profiles in APP to identify the genes involved to be able to treat Alzheimer's. They particularly focused on the functions of protein heme oxygenase 1 found in gene HMOX1. The group of researchers basically evaluated the how important the protein HMOX1 is in Alzheimer's. For this experiment, the scientists used human blood and lab mice. This was an extremely extensive project as plenty of processes were involved. The processes were: - RNA extraction (qRT), quantitative reverse-transcription polymerase chain reaction (PCR), Transcriptome sequential analysis, Western blot analysis, genomic DNA extraction, genomic DNA modification, Methylation microarray, Quantitative methylation-specific PCR (qMSP), bisulfite sequential analysis, deoxycytidine treatment, amyloid preparation and treatment and in the end Statistical Analysis.

Figure 1 shows the HMOX1 expression up-regulated in an APP-mutant cell line and transgenic mice.The effect of the protein is heavily evaluated by the virtue of its effects on the minds of mice. Alzheimer's is a disease that is becoming increasingly common in humans and therefore, this experiment is significant in understanding the pros and cons of this enzyme so that we can come up with better treatments for this amnesic disease.

The results of this experiment showed that heme oxygenase 1 is in fact directly correlated with Alzheimer's as shown from the results in Figures 1,2,3,4,5 and 6. The statistical analysis also convinced the researchers that HMOX1 is a key factor in cognitive impairment of Alzheimer's.


challenge
updatedbyinstructorBACSU:TYSY1Barlowrm, Team TRUMP20162016-04-05 07:33:24 CDTGO:0004799 thymidylate synthase activity (F)PMID:9778348ECO:0000314 direct assay evidence used in manual assertion

"Activity assays indicate that bsTS-A has a significantly higher specific activity (SA ≈ 22 units/mg) than either E. coli TS (SA ∼13.5 units/mg) or L. casei TS (SA ≈ 6 units/mg) when measured using the identical materials and instruments." Data not shown.

challenge
acceptableBPT4:TERLJermstadsb, Team TRUMP20162016-04-05 07:32:33 CDTGO:0016887 ATPase activity (F)PMID:19109896ECO:0000315 mutant phenotype evidence used in manual assertion

The ATPase protein was compared to two mutants (W533A and ΔS527G538) which had weakened interactions between their domains. The mutants were then compared to the wild-type with a Packaging ATPase assay. Both of the mutants had a loss of their ATPase activity. This is proven in figure 3e, where the concentration of cold ATP was increased every hour, for the wild-type and mutants. The third phosphate group was only cleaved in only the wild-type samples, which is seen in the appearance of the upper bands in the thin layer chromotherapy.

challenge

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Pages in category "Team TRUMP2016"

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