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User:Nmcdon1

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Phage Hunters Spring 2016

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
unacceptable9CAUD:A0A0K2D0E32016-04-10 07:40:45 CDTGO:0030541 plasmid partitioning (P)GO_REF:0000100ECO:0000317 genomic context evidence used in manual assertion

BLASTP result indicates that the protein encoded by TSARBOMBA_192 is a homolog of ParM protein, the plasmid segregation actin-like motor protein in Bacteria (PMID:12065424, PMID:20844556), of Bacillus phage Troll orf220 (S5Y097) and Bacillus phage Riley orf215 (A0A075M4S3) with 95% Quer cover, 63% identity with e-value of 6e-166.

Several other closely related Bacillus phages were also found to contain genes that encode for plasmid segregation protein as shown on phylogeny tree based on the amino acid sequences in Figure 7A (PMID:25344242).

Examples of these include Plasmid segregation protein coded by Bacillus phage Spock orf209 (U5PXI1), Bacillus phage BigBertha orf214 (U5PVU6), and Putative plasmid segregation proteins coded by Bacillus phage Bp8p-T orf27 (A0A0A0PJ25), Bacillus phage Bp8p-C orf27 (A0A0A0PKY3).

challenge
unacceptableECOLX:PARM2016-04-10 06:42:41 CDTGO:0030541 plasmid partitioning (P)PMID:12065424ECO:0000315 mutant phenotype evidence used in manual assertion

ParM is an actin-like protein which generates dynamic filaments that are necessary for Plasmid DNA segregation. The filament polymerization is activated only with the presence of ATP-bound form of ParM protein (PMID:20550930). Using the combined phase-contrast and immunofluorescence microscopy, figure 2C demonstrates the cells with mutation of ParM proteins fail to bind and hydrolyse ATP, leading to incorrect segregation of plasmid DNA.

challenge
updatedbyinstructor9CAUD:A0A0A0PKY32016-04-10 07:24:59 CDTGO:0030541 plasmid partitioning (P)PMID:25344242ECO:0000315 mutant phenotype evidence used in manual assertion

This protein is the only one affected by the 3nt sequence differences (1 missense and 2 bp indel) between Bp8p-T (turbid) and Bp8p-C (clear) phages, which were separate isolates, but are essentially a mutant and wt version of the same phage.

The result from Figure 7 indicates that truncation of putative plasmid segregation proteins coded by Bacillus phage Bp8p-C orf27 leads to changing in phage phenotype, decreasing in protein function, and higher rate of genome-packaging into phage capsid. These results imply direct relationship between the protein itself and lysogenic ability of the phage.

challenge
updatedbyinstructor9CAUD:A0A0A0PJ252016-04-10 07:34:27 CDTGO:0030541 plasmid partitioning (P)PMID:25344242ECO:0000315 mutant phenotype evidence used in manual assertion

This protein is the only one affected by the 3nt sequence differences (1 missense and 2 bp indel) between Bp8p-T (turbid) and Bp8p-C (clear) phages, which were separate isolates, but are essentially a mutant and wt version of the same phage.

The result from figure 7 indicates that truncation of putative plasmid segregation proteins coded by Bacillus phage Bp8p-T orf27 leads to decrease of the ATPase and polymerization abilities.

challenge

acceptable:0
unacceptable:2
requires_changes:0
flagged:0

Annotations challenged by Nmcdon1

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history
updatedbyinstructorAmariam1,
Team You can't B. cereus
PYRFU:HJCGO:0048476 - Holliday junction resolvase complex (C)PMID:11286886ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 4

fixed by Mnguy1
unacceptableLian2,
Team Purple B
9CAUD:A0A0K2D0M5GO:0003677 - DNA binding (F)PMID:3092189ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2
unacceptableLian2,
Team Purple B
9CAUD:A0A0K2D0M7GO:0005524 - ATP binding (F)PMID:8444794ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2
unacceptableLian2,
Team Purple B
9CAUD:A0A0K2D0E0GO:0008193 - tRNA guanylyltransferase activity (F)PMID:14633974ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
unacceptableLian2,
Team Purple B
9CAUD:A0A0K2D065GO:0006281 - DNA repair (P)PMID:1896024ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
unacceptableLian2,
Team Purple B
9CAUD:A0A0K2D065GO:0006281 - DNA repair (P)PMID:1896024ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1

0 annotations fixed by Nmcdon1

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