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Category:Catalyzers

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StatusPageUserDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
acceptableECOLI:CHEAZoe13, Catalyzers2019-04-14 17:37:46 CDTGO:0000155 phosphorelay sensor kinase activity (F)PMID:16176121ECO:0001202 in vitro protein kinase assay evidence used in manual assertion

Figure 4 (E&F)

Phosphorelay histidine sensor kinase Escherichia coli CheA. Sensory histidine kinase member of two-component regulatory system with CheB and CheY

challenge
acceptableECOLI:CHEYZoe13, Catalyzers2019-04-14 13:41:04 CDTGO:0000156 phosphorelay response regulator activity (F)PMID:16176121ECO:0001202 in vitro protein kinase assay evidence used in manual assertion

Figure 4 (F)

Involved in the transmission of sensory signals. Phosphorylated by CheA, acts as an in vivo cognate regulator for CheA in Figure 4 (F) Escherichia coli (strain K12)

challenge
acceptableECOLI:CPXRZoe13, Catalyzers2019-04-14 13:23:38 CDTGO:0000156 phosphorelay response regulator activity (F)PMID:16176121ECO:0001202 in vitro protein kinase assay evidence used in manual assertion

Figure 4 (G&H)

Transcriptional regulatory protein Escherichia coli (strain K12) CpxR; phosphorelay response regulator. Response regulator member of the two-component regulatory system CpxA/CpxR

challenge
acceptableECOLI:CPXAZoe13, Catalyzers2019-04-14 13:08:05 CDTGO:0000155 phosphorelay sensor kinase activity (F)PMID:16176121ECO:0001202 in vitro protein kinase assay evidence used in manual assertion

Figure 4 (G&H)

Phosphorelay sensor kinase Escherichia coli (strain K12) CpxA; phosophorelay sensor histidine kinase. Histidine kinase member of the two-component regulatory system CpxA/CpxR

challenge
acceptableBACSU:SWRDZoe13, Catalyzers2019-04-11 22:21:17 CDTGO:0071978 bacterial-type flagellum-dependent swarming motility (P)PMID:29061663ECO:0007089 loss-of-function mutant phenotype evidence used in manual assertion

Protein required to increase flagellar power to increase swarming speed in Bacillus subtilis. Figure 3 shows quantitative swarm expansion assays. Cells mutated for swrD did not swarm.

Bacillus subtilis

challenge
acceptableTREPA:F7IUH9Zoe13, Catalyzers2019-04-11 22:01:08 CDTGO:0071978 bacterial-type flagellum-dependent swarming motility (P)PMID:29061663ECO:0000031 protein BLAST evidence used in manual assertion

Figure 7 (B) shows a swrD like swarming protein in Treponema pallidum (strain Nichols). Flagellar protein FlbD the protein. This swarming protein is located immediately upstream of the genes encoding MotA and MotB. This protein is related to flagellar stator activity in a way that could be bypassed by an excess of stators in the membrane.

Treponema pallidum (strain Nichols)

challenge
acceptablePEPD6:Q18CZ3Zoe13, Catalyzers2019-04-11 21:59:40 CDTGO:0071978 bacterial-type flagellum-dependent swarming motility (P)PMID:29061663ECO:0000031 protein BLAST evidence used in manual assertion

Figure 7 (B) shows a swrD like swarming protein in Clostridium difficile (strain 630). Flagellar protein FlbD is the protein. This swarming protein is located immediately upstream of the genes encoding MotA and MotB. This protein is related to flagellar stator activity in a way that could be bypassed by an excess of stators in the membrane.

Clostridium difficile (strain 630)

challenge
acceptableLEPBP:B0SK93Zoe13, Catalyzers2019-04-11 21:58:48 CDTGO:0071978 bacterial-type flagellum-dependent swarming motility (P)PMID:29061663ECO:0000031 protein BLAST evidence used in manual assertion

Figure 7 (B) shows a swrD like swarming protein in Leptospira biflexa (strain Patoc). Flagellar protein FlbD is the protein. This swarming protein is located immediately upstream of the genes encoding MotA and MotB. This protein is related to flagellar stator activity in a way that could be bypassed by an excess of stators in the membrane.

Leptospira biflexa serovar Patoc (strain Patoc 1)

challenge
acceptablePAESJ:C6D2W3Zoe13, Catalyzers2019-04-11 21:57:54 CDTGO:0071978 bacterial-type flagellum-dependent swarming motility (P)PMID:29061663ECO:0000031 protein BLAST evidence used in manual assertion

Figure 7 (B) shows a swrD like swarming protein in Paenibacillus sp. (strain JDR-2). Flagellar FlbD family protein is this protein. This swarming protein is located immediately upstream of the genes encoding MotA and MotB. This protein is related to flagellar stator activity in a way that could be bypassed by an excess of stators in the membrane.

Paenibacillus sp. (strain JDR-2)

challenge
acceptableARATH:A0A178USJ6Zoe13, Catalyzers2019-04-11 21:54:22 CDTGO:2001255 positive regulation of histone H3-K36 trimethylation (P)PMID:23899645ECO:0007129 chromatin immunoprecipitation-qPCR evidence used in manual assertion

Figure 3 (D) and Figure 6 (C) show the ChIP-qPCR results where H3K36 is being methylated by FLX4.

FLX4 promotes FLC expression and activates histone modification at the FLC locus. Arabidopsis thaliana

challenge
acceptableYERPE:A0A3N4BLC7ADPowell, Catalyzers2019-04-11 00:15:57 CDTGO:0030254 protein secretion by the type III secretion system (P)PMID:23357388ECO:0007122 in vitro assay evidence used in manual assertion

Figure S1A shows the dependence on RfaL in the presence of calcium for secretion of late-phase type III secretion system proteins in Yersinia pestis through secretion assays followed by western blotting using anti YopD (early T3SS protein) and YopE (late T3SS protein) in WT, RfaL mutant, and RfaL complemented strains. YopD is still secreted in RfaL mutant in the absence of calcium, but to a lesser extent.

submitted a new term request for an evidence code describing secretion assays - waiting on term.

challenge
acceptableARATH:FRL1AZoe13, Catalyzers2019-04-10 20:27:52 CDTGO:2001255 positive regulation of histone H3-K36 trimethylation (P)PMID:23899645ECO:0007129 chromatin immunoprecipitation-qPCR evidence used in manual assertion

Figure 6 (C) shows that FLR1 methylates histone H3K36. FRL1 mutants showed a strong increase in H3K36 methylation that may account for the slight increase in FLC expression.

Arabidopsis thaliana

challenge
acceptableARATH:FLXZoe13, Catalyzers2019-04-10 20:26:02 CDTGO:0045944 positive regulation of transcription by RNA polymerase II (P)PMID:23899645ECO:0005805 yeast 2-hybrid evidence used in manual assertion

Figure 5 (A & E) shows that FLX grows by itself in -T and FLX+FLX4 grows. This shows FLX is involved in transcription activation.

Arabidopsis thaliana

challenge
acceptableARATH:SUF4Zoe13, Catalyzers2019-04-10 20:24:04 CDTGO:2001255 positive regulation of histone H3-K36 trimethylation (P)PMID:23899645ECO:0007129 chromatin immunoprecipitation-qPCR evidence used in manual assertion

Figure 6 (C) shows that SUF4 methylates histone H3-K36. This helps with promoting FLC expression.

Arabidopsis thaliana

challenge
acceptableARATH:SUF4Zoe13, Catalyzers2019-04-10 20:24:03 CDTGO:1905437 positive regulation of histone H3-K4 trimethylation (P)PMID:23899645ECO:0007129 chromatin immunoprecipitation-qPCR evidence used in manual assertion

Figure 6 (C) shows that SUF4 methylates histone H3-K4. This helps with promoting FLC expression.

Arabidopsis thaliana

challenge
acceptableARATH:FES1Zoe13, Catalyzers2019-04-10 20:20:29 CDTGO:2001255 positive regulation of histone H3-K36 trimethylation (P)PMID:23899645ECO:0007129 chromatin immunoprecipitation-qPCR evidence used in manual assertion

Figure 6 (C) shows that FES1 methylates histone H3-K36. This helps to promote FLC expression.

Arabidopsis thaliana

challenge
acceptableARATH:FES1Zoe13, Catalyzers2019-04-10 20:20:28 CDTGO:1905437 positive regulation of histone H3-K4 trimethylation (P)PMID:23899645ECO:0007129 chromatin immunoprecipitation-qPCR evidence used in manual assertion

Figure 6 (C) shows that FES1 methylates histone H3-K4. This helps to promote FLC expression.

Arabidopsis thaliana

challenge
unacceptableYERPU:A0A0N9NCT8ADPowell, Catalyzers2019-04-10 19:52:28 CDTGO:0044164 host cell cytosol (C)PMID:8112310ECO:0005804 immunofluorescence evidence used in manual assertion

Figure 5 shows the localization of the YopE protein to the host cytosol. Indirect immunofluorescence was used to visualize this localization in HeLa cells transfected with Yersinia pseudotuberculosis (serotype III did not have YopE protein listed). Used broader evidence code because indirect immunofluorescence microscopy was not a term.

challenge
updatedbyinstructorYERPU:A0A3G5IPC5ADPowell, Catalyzers2019-04-10 19:52:27 CDTGO:0044164 host cell cytosol (C)PMID:8112310ECO:0005804 immunofluorescence evidence used in manual assertion

Figure 5 shows the localization of the YopE protein to the host cytosol. Indirect immunofluorescence was used to visualize this localization in HeLa cells transfected with Yersinia pseudotuberculosis (serotype III did not have YopE protein listed). Used broader evidence code because indirect immunofluorescence microscopy was not a term.

challenge
unacceptableRABIT:LBPADPowell, Catalyzers2019-04-09 22:06:53 CDTGO:0032760 positive regulation of tumor necrosis factor production (P)PMID:2402637ECO:0007070 crystal violet staining evidence used in manual assertion

Figure 2 A shows cytolytic activity of TNF pooled from cell-free supernatants from cultures of peritoneal exudate macrophages (PEM) with and without LPS binding protein (LBP) after being stimulated with LPS from E. coli. Although this TNF is being isolated from media, indicating it might be secreted, it is more logical to assume that LBP plays a role in TNF production rather than in the process of its secretion. L929 cells were incubated with purified TNF from PEM cell-free media, stained with crystal violet, and analyzed using spectrophotometry.

challenge
acceptableYERPU:A0A0N9NCT8ADPowell, Catalyzers2019-04-09 21:45:42 CDTGO:0030254 protein secretion by the type III secretion system (P)PMID:8112310ECO:0007042 epifluorescence microscopy evidence used in manual assertion

Figure 7 panels C and D show epifluorescence microscopy images of YopE localization in HeLa cells infected with the yopD mutant YPIII(pIB15) (Yersinia pseudotuberculosis serotype III). YopE was shown to not be dispersed throughout HeLa cells in YopD mutants in this imaging, indicating that YopD plays a role in the secretion of YopE.

challenge
acceptableYERPE:YOPMADPowell, Catalyzers2019-04-09 16:16:56 CDTGO:1990001 inhibition of cysteine-type endopeptidase activity involved in apoptotic process (P)PMID:27911947ECO:0000279 qualitative western immunoblotting evidence used in manual assertion

Figure 2D shows Western Blot data showing decreased pro-Caspase-1 and IL-1B, the inactive form of Caspase-1 that plays a role in Pyrin Inflammasome activation and the inactive form of IL-1B that is activated by Caspase-1, respectively, in the YopM mutants. This is indicative of more activation of Caspase-1 and IL-1B in the absence of YopM, which implies increased Pyrin Inflammasome activation. The figure also shows increased IL-1B in the YopM mutant, which inversely corresponds with the IL-1B protein expression data.

Yersinia pests

challenge
acceptableARATH:A0A178USJ6Zoe13, Catalyzers2019-04-09 16:06:02 CDTGO:0005634 nucleus (C)PMID:23899645ECO:0005589 confocal microscopy evidence used in manual assertion

Figure 1 (F) shows using confocal microscopy that YFP tagged FLX4 that has nuclear localization.

Arabidopsis thaliana

challenge
acceptableARATH:A0A178USJ6Zoe13, Catalyzers2019-04-09 16:06:01 CDTGO:1905437 positive regulation of histone H3-K4 trimethylation (P)PMID:23899645ECO:0007129 chromatin immunoprecipitation-qPCR evidence used in manual assertion

Figure 3 (D) and figure 6 (C) show the results from the ChIP-qPCR which shows H3-K4 being methylated by FLX4.

FLX4 promotes FLC expression and activates histone modifcations at the FLC locus. Arabidopsis thaliana

challenge
updatedbyinstructorYERPU:A0A0N9NCU6ADPowell, Catalyzers2019-03-26 16:04:05 CDTGO:0046329 negative regulation of JNK cascade (P)PMID:9535085ECO:0000279 qualitative western immunoblotting evidence used in manual assertion

CL:0000235 occurs in human macrophages. Figure 6c shows J774A.1 macrophages were infected with Yersinia pseudotuberculosis strains both able and unable to secrete full-length translocon YopJ for 1 hour. Cell lysates were taken for immunoblotting with a phosphospecific anti-JNK antibody. Blotting showed YopJ down regulated JNK in macrophages.

Yersinia pseudotuberculosis

challenge
updatedbyinstructorYERPU:A0A0N9NCU6ADPowell, Catalyzers2019-03-26 16:00:08 CDTGO:1903753 negative regulation of p38MAPK cascade (P)PMID:9535085ECO:0000279 qualitative western immunoblotting evidence used in manual assertion

CL:0000235 occurs in human macrophages. Figure 6 shows J774A.1 macrophages infected with Yersinia pseudotuberculosis strains both able and unable to secrete full-length translocon YopJ for 1 hour, and protein samples were taken to be analyzed by immunoblotting with anti-P38, indicating down-regulation of P38 by YopJ.

Yersinia pseudotuberculosis

challenge
updatedbyinstructorYERPS:YOPJADPowell, Catalyzers2019-03-26 15:52:44 CDTGO:0042536 negative regulation of tumor necrosis factor biosynthetic process (P)PMID:9535085ECO:0000335 substance quantification evidence

Figure 3b shows that strain YP25, defective for secretion of effector YopJ, had increased macrophage TNF-alpha production after J774A.1 macrophages were infected with Yersinia pseudotuberculosis strains both able and unable to secrete YopJ.

Yersinia pseudotuberculosis accuring in human macrophages.

challenge
acceptableYERPS:YOPBADPowell, Catalyzers2019-03-26 15:44:08 CDTGO:0042536 negative regulation of tumor necrosis factor biosynthetic process (P)PMID:9535085ECO:0000335 substance quantification evidence

CL:0000235 occurs in human macrophages. Figure 1B shows J774A.1 macrophages were infected with Yersinia pseudotuberculosis strains both able and unable to secrete full-length translocon YopB for 1 hour. Levels of TNF-alpha in media were quantified, with YopB mutants consistently producing twofold more TNF-alpha.

Yersinia pseudotuberculosis

A0A0N9NJG3 should be the protein ID. This is described as an Uncharacterized protein, I chose this protein designation because there is no YopB for Yersinia pseudotuberculosis.

challenge
acceptableARATH:A0A178USJ6Zoe13, Catalyzers2019-03-19 16:12:00 CDTGO:0010228 vegetative to reproductive phase transition of meristem (P)PMID:23899645ECO:0005027 genetic transformation evidence

Microarray found that FLX4 is required for the proper expression of a relatively small number of genes.

Detected mutations in FLX4 are responsible for early-flowering. Supplemental Table S1 shows microarray results. Arabidopsis thaliana

challenge
acceptableYERPE:O68704ADPowell, Catalyzers2019-03-19 15:46:56 CDTGO:1900226 negative regulation of NLRP3 inflammasome complex assembly (P)PMID:27911947ECO:0005581 enzyme-linked immunoabsorbent assay evidence used in manual assertion

Figure 3E,G YopK mutants showed a sharp increase in IL-1B production in 3E. 3G shows the independence of this effect on Pyrin, but its dependence on NLRP3/NLRC4 pathway.

Yersinia pestis

challenge
unacceptableNEIME:A0A2D0TCG3Zoe13, Catalyzers2019-03-19 15:02:11 CDTGO:0110133 negative regulation of CRISPR-cas system (P)PMID:27984730ECO:0005027 genetic transformation evidence

Figure 1 (C) shows that acrIIC3 inhibits CRISPR interference in N. meningitidis using the transformation assay of N. meningitidis

acrIIC3Nme

challenge
unacceptableNEIME:A0A2D0TCG3Zoe13, Catalyzers2019-03-19 15:02:10 CDTGO:0110133 negative regulation of CRISPR-cas system (P)PMID:27984730ECO:0005027 genetic transformation evidence

Figure 1 (C) shows that acrIIC2 inhibits CRISPR interference in N. meningitidis using the transformation assay of N. meningitidis

acrIIC2Nme

challenge
unacceptableLISMN:A0A247D711Zoe13, Catalyzers2019-03-17 18:25:43 CDTGO:0110133 negative regulation of CRISPR-cas system (P)PMID:28041849ECO:0007150 plasmid maintenance assay evidence used in manual assertion

Figure 3 (C)

acrIIA4 often occurred in the absence of acrIIA1 homologs in phages and mobile elements of Listeria monocytogenes

challenge
flaggedNEIME:A0A2D0TCG3Zoe13, Catalyzers2019-02-26 16:27:16 CSTGO:0110133 negative regulation of CRISPR-cas system (P)PMID:27984730ECO:0005027 genetic transformation evidence

Figure 1 (C) shows that acrIIC1 inhibits CRISPR interference in N. meningitidis using the transformation assay of N. meningitidis

acrIIC1Nme

challenge
unacceptableBORBU:O50835ADPowell, Catalyzers2019-02-12 16:18:37 CSTGO:0048519 negative regulation of biological process (P)PMID:26808924ECO:0001258 spectrophotometry evidence used in manual assertion

Figure 4A-C shows use of classical pathway (CP)-mediated hemolysis assays using absorbance to measure cell lysis. Performed with BBK32 N-terminal, C-termainl, and full-length protein

Waiting on new GO term Borrelia burgdorferi

challenge
unacceptableBORBU:O50835Mason.Tomas, Catalyzers2019-02-12 15:48:12 CSTGO:0045959 negative regulation of complement activation, classical pathway (P)PMID:26808924ECO:0000279 qualitative western immunoblotting evidence used in manual assertion

Fig. 7A-D BBK32 from Borrelia burgdorferi is shown to inhibit autocatalysis of C1r and subsequent C1r cleavage of C1s within the C1 complex.

challenge
unacceptableBORBG:C5J482ADPowell, Catalyzers2019-02-05 21:28:17 CSTGO:0004867 complement binding (F)PMID:26808924ECO:0001269 surface plasmon resonance evidence used in manual assertion

C1r binding protein. Figure 5A-E shows C1r binding to BBK32 Full-length and the C-terminal of BBK32 through surface plasmon resonance assays. Far Western blot analysis was used to confirm this interaction.

Waiting on new GO term - Complement component C1r binding. Borrelia burgdorferi

challenge
acceptableCAUVN:A0A0H3C9D0Mason.Tomas, Catalyzers2019-02-05 14:39:18 CSTGO:0000160 phosphorelay signal transduction system (P)PMID:16176121ECO:0001202 in vitro protein kinase assay evidence used in manual assertion

Fig. 5C-D. It is shown that DivK is a phosphorylation target of the histidine kinase DivJ in Caulobacter crescentus.

challenge
acceptableCAUVC:DIVJADPowell, Catalyzers2019-02-05 14:30:54 CSTGO:0000160 phosphorelay signal transduction system (P)PMID:16176121ECO:0001202 in vitro protein kinase assay evidence used in manual assertion

Cell cycle regulator

Figure 5C-D Ten-second time point phosphotransfer profile of DivJ demonstrating phosphorylation of PleD and DivK Caulobacter vibrioides

challenge
updatedbyinstructorCAUVC:DIVJZoe13, Catalyzers2019-01-29 16:09:12 CSTGO:0000155 phosphorelay sensor kinase activity (F)PMID:16176121ECO:0001202 in vitro protein kinase assay evidence used in manual assertion

Figure 5C displays the phosphotransfer profiling of Caulobacter crescentus, particularly the phosphorylation of PleD and DivK by the orphan kinase DivJ (Uniprot: histidine protein kinase DivJ).

challenge
unacceptableCAUVN:A0A0H3C9D0Mason.Tomas, Catalyzers2019-01-29 15:54:35 CSTGO:0000156 phosphorelay response regulator activity (F)PMID:16176121ECO:0001202 in vitro protein kinase assay evidence used in manual assertion

Fig. 5C-D. It is shown that DivK is a phosphorylation target of the histidine kinase DivJ in Caulobacter crescentus.

challenge

Pages in category "Catalyzers"

The following 3 pages are in this category, out of 3 total.


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