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User:JayClark

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CACAO Spring 2019

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
acceptableCAUVC:Q9AAR62019-01-29 15:57:30 CSTGO:0000155 phosphorelay sensor kinase activity (F)PMID:16176121ECO:0001202 in vitro protein kinase assay evidence used in manual assertion

Fig. 5 shows that the cell envelope kinase (CenK, CC0530) strongly preferred phosphorylating in the presence of CenR (CC03743). This was accomplished using phosphotransfer profiling; comparing the activity of CenK and CenR relative to other substrates.

Organism: Caulobacter crescentus

challenge
acceptableLAMBD:FIBER2019-02-05 14:47:42 CSTGO:0098024 virus tail, fiber (C)PMID:1439823ECO:0007044 transmission electron microscopy evidence used in manual assertion

Fig. 3 shows that gene product stf produces a band on an SDS gel at approximately 78 kDa. Fig. 1 shows an electron microscopy image of Ur - lambda. Tail fibers are visible on the phage tail. The combine evidence shows that the stf gene product results in tail fiber formation at the virion tail.

Organism: Escherichia phage lambda

challenge
acceptableLAMBD:FIBER2019-02-05 15:26:56 CSTGO:0019062 virion attachment to host cell (P)PMID:1439823ECO:0007040 plaque assay evidence used in manual assertion

Fig. 4 demonstrates that Ur-lambda, which contains the tail fiber protein (stf), adsorbed to E. coli substantially faster than wild type lambda, which did not contain tail fiber proteins. Ur-lambda was capable of adsorbing in the presence of glucose, while wild type lambda was only capable of adsorbing in the presence of maltose. This evidence shows that the tail fiber proteins are involved in adsorption to the host cell.

Organism: Escherichia phage lambda

challenge
updatedbyinstructor9CAUD:H6X3Q12019-02-12 15:08:01 CSTGO:0019012 virion (C)PMID:23593293ECO:0007184 protein mass spectrometry evidence used in manual assertion

Fig. 5 shows that gp 094 (ORF 094), major capsid protein, of Klebsiella Phage vB_KleM-RaK2, produces a protein residue. Table S3 determines that gp 094 has a molecular mass of 42.725 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

challenge
acceptable9CAUD:H6X4Y92019-02-12 15:34:17 CSTGO:0019012 virion (C)PMID:23593293ECO:0007184 protein mass spectrometry evidence used in manual assertion

Fig. 5 shows that gp532 (ORF 532), Putative structural protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 532 has a molecular mass of 87.315 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

challenge
acceptable9CAUD:H6X3G72019-02-26 15:54:16 CSTGO:0019012 virion (C)PMID:23593293ECO:0007184 protein mass spectrometry evidence used in manual assertion

Fig. 5 shows that gp010 (ORF 010), Putative structural protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 010 has a molecular mass of 13.932 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

challenge
acceptable9CAUD:H6X3J92019-02-26 16:01:37 CSTGO:0019012 virion (C)PMID:23593293ECO:0007184 protein mass spectrometry evidence used in manual assertion

Fig. 5 shows that gp042 (ORF 042), uncharacterized protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 042 has a molecular mass of 24.950 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

challenge
acceptable9CAUD:H6X3K02019-02-26 16:05:00 CSTGO:0019012 virion (C)PMID:23593293ECO:0007184 protein mass spectrometry evidence used in manual assertion

Fig. 5 shows that gp043 (ORF 043), uncharacterized protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 043 has a molecular mass of 28.720 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

challenge
acceptable9CAUD:H6X3K42019-02-26 16:09:35 CSTGO:0019012 virion (C)PMID:23593293ECO:0007184 protein mass spectrometry evidence used in manual assertion

Fig. 5 shows that gp047 (ORF 047), uncharacterized protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 047 has a molecular mass of 23.356 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

challenge
acceptable9CAUD:H6X3K52019-02-26 16:15:33 CSTGO:0019012 virion (C)PMID:23593293ECO:0007184 protein mass spectrometry evidence used in manual assertion

Fig. 5 shows that gp048 (ORF 048), uncharacterized protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 048 has a molecular mass of 20.374 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

challenge
acceptable9CAUD:H6X3K62019-02-26 16:21:15 CSTGO:0019012 virion (C)PMID:23593293ECO:0007184 protein mass spectrometry evidence used in manual assertion

Fig. 5 shows that gp049 (ORF 049), uncharacterized protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 049 has a molecular mass of 34.878 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

challenge
acceptable9CAUD:A0A2P1CKP92019-03-19 14:18:25 CDTGO:0019012 virion (C)PMID:30366363ECO:0007184 protein mass spectrometry evidence used in manual assertion

Pg. 583 shows that the portal protein (gp03, ORF03) was found in Pantoea phage vB_PagS_Vid5. LC MS/MS was run on protein, and a molecular weight of 54.818 kDa, with 48 amino acid residues was recorded. Supplementary Table 3 shows results of mass spectrometry.

challenge
acceptable9CAUD:A0A2P1CKJ42019-03-19 14:25:34 CDTGO:0019012 virion (C)PMID:30366363ECO:0007184 protein mass spectrometry evidence used in manual assertion

Pg. 583 shows that the tail fiber protein (gp22, ORF22) was found in Pantoea phage vB_PagS_Vid5. LC MS/MS was run on the protein, and a molecular weight of 98.324 kDa, with 7 amino acid residues was recorded. Supplementary Table 3 shows results of mass spectrometry.

challenge
acceptable9CAUD:H6X3Q12019-03-19 16:02:37 CDTGO:0098017 viral capsid, major subunit (C)PMID:23593293ECO:0000318 biological aspect of ancestor evidence used in manual assertion

Fig. 7 shows that gp 094, major capsid protein, of Klebsiella Phage vB_KleM-RaK2, shows phylogenetic similarity to Enterobacteria phage T4 major capsid protein gp23.

challenge
unacceptable9CAUD:H6X3Q12019-03-19 15:27:37 CDTGO:0019012 virion (C)PMID:23593293ECO:0007184 protein mass spectrometry evidence used in manual assertion

Fig. 5 shows that gp 094, major capsid protein, of Klebsiella Phage vB_KleM-RaK2, produces a protein residue. Table S3 determines that gp 094 has a molecular mass of 42.725 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

challenge
acceptable9CAUD:H6X4W32019-04-09 15:17:50 CDTGO:0019012 virion (C)PMID:23593293ECO:0007184 protein mass spectrometry evidence used in manual assertion

Table S3 show that gp506 (ORF 506), hypothetical protein, has a molecular mass of 53.675 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

challenge
acceptable9CAUD:H6X3V22019-04-09 15:27:20 CDTGO:0019012 virion (C)PMID:23593293ECO:0007184 protein mass spectrometry evidence used in manual assertion

Fig. 5 shows that gp145w (ORF145w), uncharacterized protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 145w has a molecular mass of 25.061 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

challenge
acceptable9CAUD:H6X4V32019-04-09 15:35:02 CDTGO:0019012 virion (C)PMID:23593293ECO:0007184 protein mass spectrometry evidence used in manual assertion

Fig. 5 shows that gp496 (ORF496), putative structural protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 496 has a molecular mass of 22.787 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

challenge
acceptable9CAUD:H6X3Y92019-04-09 15:39:43 CDTGO:0019012 virion (C)PMID:23593293ECO:0007184 protein mass spectrometry evidence used in manual assertion

Fig. 5 shows that gp182 (ORF182), putative structural protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 182 has a molecular mass of 13.142 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

challenge

acceptable:17
unacceptable:1
requires_changes:0
flagged:0

Annotations challenged by JayClark

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history

0 annotations fixed by JayClark

CACAO Fall 2018

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
acceptable9CAUD:U5PW982018-09-11 14:10:20 CDTGO:1900232 negative regulation of single-species biofilm formation on inanimate substrate (P)PMID:29298884ECO:0000314 direct assay evidence used in manual assertion

Figure 10 indicates that gp39/Dpo1 enzyme from acinetobacter phage Petty negatively regulates biofilm formation of acinetobacter calcoaeticus-baumannii strains.

Uniprot name: Tail fiber protein

challenge
acceptable9CAUD:U5PVS92018-09-13 11:25:11 CDTGO:0019012 virion (C)PMID:29298884ECO:0000314 direct assay evidence used in manual assertion

Fig. 5 suggest that gp37 is a structural protein found in Acinetobacter phage Petty. Protein was identified as part of phage via mass spectroscopy.

challenge
acceptable9CAUD:A0A220GHA52018-09-15 20:55:04 CDTGO:0098672 evasion by virus of CRISPR-cas system (P)PMID:30046034ECO:0000314 direct assay evidence used in manual assertion

Fig. 5 demonstrates that acrIIA5 is capable of inhibiting the effects of CRISPR-stCas9 and spCas9 on sgRNA. Experiment was run on human cells which contained plasmid modifications.

challenge
acceptableBPT4:SOC2018-09-18 14:07:50 CDTGO:0098021 viral capsid, decoration (C)PMID:28893988ECO:0000315 mutant phenotype evidence used in manual assertion

Evidence for this the small outer capsid (Soc) protein of bacteriophage T4 comes from the sixth paragraph, “The outer surface of the expanded capsid is decorated by the small outer capsid (Soc) protein...”

Fig. 1 demonstrates where Soc is found on the capsid.

challenge
acceptable9CAUD:A0A2U7VJX72018-10-02 14:12:49 CDTGO:0098672 evasion by virus of CRISPR-cas system (P)PMID:30046034ECO:0000314 direct assay evidence used in manual assertion

Fig. 5 demonstrates that acrIIA6 protein in Streptococcus phage D1024 is capable of inhibiting the effects of CRISPR-st1Cas9 on sgRNA, but not spCas 9 system. Experiment was run on human cells which contained plasmid modifications.

challenge
flagged9GAMM:A0A0U2BNN72018-10-30 13:07:47 CDTGO:0099048 CRISPR-cas system (Fig. 3 demonstrates that acrVA1 from Moraxella bovoculi inhibits the effect of DNA modification by MbCas 12a, LbCas 12, and AsCas12 proteins. Note: NTR #16423 was submitted, waiting for reply. These proteins are negatively regulating this process.)PMID:30190307IDA: Inferred from Direct Assay
challenge
flagged9GAMM:A0A0U2BNN72018-10-30 13:13:19 CDTGO:0099048 CRISPR-cas system (Fig. 3 demonstrates that the acrVA1 protein effectively prevents various CRISPR Cas12a nucleases, including MbCas12a, Mb3Cas12a, AsCas12a, LbCas12a and FnCas12a from modifying DNA. NTR #16423, waiting for response. These proteins are negatively regulating this process.)PMID:30190308IDA: Inferred from Direct Assay
challenge
acceptable9CAUD:A0A2U7VKE82018-10-30 13:16:26 CDTGO:0098672 evasion by virus of CRISPR-cas system (P)PMID:30046034ECO:0000314 direct assay evidence used in manual assertion

Fig. 5 demonstrates that acrIIA6 protein in Streptococcus phage D1811 is capable of inhibiting the effects of CRISPR-st1Cas9 on sgRNA, but not spCas 9 system. Experiment was run on human cells which contained plasmid modifications.

challenge
acceptable9VIRU:A0A2D0TCG72018-10-30 13:19:48 CDTGO:0098672 evasion by virus of CRISPR-cas system (P)PMID:30046034ECO:0000314 direct assay evidence used in manual assertion

Fig. 5 demonstrates that acrIIA4 from Listeria monocytogenes prophage is capable of inhibiting the effects of CRISPR-stCas9, but not the effects of spCas9 on sgRNA. Experiment was run on human cells which contained plasmid modifications.

challenge
acceptable9CAUD:U5PZN72018-10-30 13:22:07 CDTGO:0019012 virion (C)PMID:29298884ECO:0000314 direct assay evidence used in manual assertion

Fig. 5 suggest that gp36 is an internal virion protein found in Acinetobacter phage Petty. Protein was identified as part of phage via mass spectroscopy.

challenge
acceptable9CAUD:U5PW932018-10-30 13:23:38 CDTGO:0019012 virion (C)PMID:29298884ECO:0000314 direct assay evidence used in manual assertion

Fig. 5 suggest that gp34 is anTail tubular protein A found in Acinetobacter phage Petty. Protein was identified as part of phage via mass spectroscopy.

challenge
acceptableLAMBD:SPAN12018-11-13 12:57:44 CSTGO:0090680 disruption by virus of host outer membrane (P)PMID:22904283ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 2a,b,e and f demonstrates that Rz, a spanin inner membrane subunit of the Escherichia phage lambda is essential part of the RzRz1 spanin complex, which rapidly lyses the E. coli bacterium. When mutant was observed, the outer membrane was not ruptured, preventing lysis of the bacterium.

challenge
acceptableLAMBD:SPAN22018-11-13 13:07:57 CSTGO:0090680 disruption by virus of host outer membrane (P)PMID:22904283ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 2a,b,e and f demonstrates that Rz1, a spanin outer lipoprotein subunit of the Escherichia phage lambda is essential part of the RzRz1 spanin complex, which rapidly lyses the E. coli bacterium. When mutant was observed, the outer membrane was not ruptured, preventing lysis of the bacterium.

challenge
acceptableBPP21:SPAN12018-11-13 13:15:40 CSTGO:0090680 disruption by virus of host outer membrane (P)PMID:22904283ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 2c,d,g and h demonstrates that Rz, a spanin inner membrane subunit of the Enterobacteria phage P21 is essential part of the RzRz1 spanin complex, which rapidly lyses the E. coli bacterium. When mutant was observed, the outer membrane was not ruptured, preventing lysis of the bacterium.

challenge
flagged9GAMM:A0A0U2BNP22018-11-13 14:47:35 CSTGO:0099048 CRISPR-cas system (Fig. 2C and E demonstrates that acrVA2, an uncharacterized protein from Moraxella bovoculi, inhibits the effect of DNA modification by type V-A CRISPR, but not against Type I -C. NTR #16423, awaiting response.)PMID:30190308IDA: Inferred from Direct Assay
challenge
flagged9GAMM:A0A0U2B9832018-11-13 14:50:05 CSTGO:0099048 CRISPR-cas system (P)PMID:30190308ECO:0000314 direct assay evidence used in manual assertion

Fig. 2C and E demonstrates that acrVA2.1, an uncharacterized protein from Moraxella bovoculi, inhibits the effect of DNA modification by type V-A CRISPR, but not against Type I -C. NTR #16423, awaiting response.

challenge
flagged9GAMM:A0A0U2BNH12018-11-13 14:49:13 CSTGO:0099048 CRISPR-cas system (Fig. 2C and E demonstrates that acrIC1, an uncharacterized protein from Moraxella bovoculi, inhibits the effect of DNA modification by type I-C CRISPR, but not against Type V-A. NTR #16423, awaiting response.)PMID:30190308IDA: Inferred from Direct Assay
challenge
flagged9PSED:A0A1I0UR492018-11-20 14:09:31 CSTGO:0099048 CRISPR-cas system (P)PMID:30190308ECO:0000314 direct assay evidence used in manual assertion

Fig. 2B demonstrates that acrIE5, an uncharacterized protein from Pseudomonas otitidis, inhibits the effect of DNA modification by type I-E CRISPR, but not against Type I -F. NTR #16423, awaiting response.

challenge
flaggedPSEAI:A6N5E22018-11-20 14:20:29 CSTGO:0099048 CRISPR-cas system (P)PMID:30190308ECO:0000314 direct assay evidence used in manual assertion

Fig. 2B demonstrates that acrIF12, an uncharacterized protein from Pseudomonas aeruginosa, inhibits the effect of DNA modification by type I-F CRISPR, but not against Type I-E. NTR #16423, awaiting response.

challenge

acceptable:12
unacceptable:0
requires_changes:0
flagged:7

Annotations challenged by JayClark

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history
acceptableVanessaDoan,
Team Mighty Chondria
STAAN:A0A0H3JN63GO:0140282 - carbon-nitrogen ligase activity on lipid II (F)PMID:22291598ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
acceptableKhuramMamji,
Team N4 Avengers
STAAU:Q79LN3GO:0098609 - cell-cell adhesion (P)PMID:11292810ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1

0 annotations fixed by JayClark