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User:Zoe13

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CACAO Spring 2019

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
updatedbyinstructorCAUVC:DIVJ2019-01-29 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
flaggedNEIME:A0A2D0TCG32019-02-26 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
unacceptableLISMN:A0A247D7112019-03-17 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
unacceptableNEIME:A0A2D0TCG32019-03-19 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
unacceptableNEIME:A0A2D0TCG32019-03-19 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
acceptableARATH:A0A178USJ62019-03-19 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
acceptableARATH:A0A178USJ62019-04-11 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
acceptableARATH:A0A178USJ62019-04-09 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
acceptableARATH:FLX2019-04-10 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:A0A178USJ62019-04-09 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:FES12019-04-10 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
acceptableARATH:FES12019-04-10 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:SUF42019-04-10 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:SUF42019-04-10 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:FRL1A2019-04-10 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
acceptablePAESJ:C6D2W32019-04-11 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
acceptablePEPD6:Q18CZ32019-04-11 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
acceptableTREPA:F7IUH92019-04-11 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
acceptableLEPBP:B0SK932019-04-11 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
acceptableBACSU:SWRD2019-04-11 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
acceptableECOLI:CPXA2019-04-14 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
acceptableECOLI:CPXR2019-04-14 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:CHEY2019-04-14 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:CHEA2019-04-14 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

acceptable:19
unacceptable:3
requires_changes:0
flagged:1

Annotations challenged by Zoe13

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history

0 annotations fixed by Zoe13