Phage Hunters Spring 2017
My Annotations
| Status | Page | Date/Time | GO Term (Aspect) | Reference | Evidence | Notes | Links |
|---|
| unacceptable | 9CAUD:M1EAF4 | 2017-04-16 03:13:36 CDT | GO:0098024 virus tail, fiber (C) | PMID:23289425 | ECO:0000314 direct assay evidence used in manual assertion | In silico analysis was used to identify gp38 as a component of the putative long tail fibre (LTF) (Figure 3).
Sequence identity of S16 gp38 to the corresponding gene products in phages T4 and T2 is high (46%)(Figure 3).
A phylogenetic comparison of gp38 of S16 to homologues of other T4-like phages also clusters the S16 variant closer to T2 than to T4 (Figure S2).
SDS-PAGE of different S16 GFP-LTF protein synthesis variations in E.coli resulted in the production of functional GFP–LTF and
indicates trimerization of S16 gp37 and attachment of gp38 to S16 gp37 trimers (Figure 4 and S1)
The distal part of the S16 LTF likely has a putative structure closely related to what has been reported for phage T2 (Drexler et.al., 1986),
where gp38 acts as the actual adhesin while bound to the C-terminal (distal) tip of gp37.
The binding of purified S16 GFP–LTF fusion protein to wild-type and mutant Salmonella typhimurium cells (with mutated OmpC) were assessed. (Figure?5A and B)
The wild-type revealed an even decoration of the bacterial surface by the fluorescent LTF (Figure?5A and B).
Deletion of OmpC completely abolished decoration by S16 GFP–LTF (Fig.?5C and D).
The defective phenotype could be restored by in-trans complementation using ompC (Table?3, Figure?5E and F).
| challenge |
| unacceptable | 9CAUD:M1EAL7 | 2017-04-16 03:27:04 CDT | GO:0098024 virus tail, fiber (C) | PMID:23289425 | ECO:0000314 direct assay evidence used in manual assertion | In silico analysis was used to identify gp37 as a component of the putative long tail fibre (LTF)(Figure 3).
Sequence identity of S16 gp37 to the corresponding gene products in phages T4 and T2 is very low (T4: 20% and T2: 18%).
Because this homology is below the widely accepted threshold for relatedness (Tian and Skolnick, 2003),
hence might be considered orthologues rather than homologues.
SDS-PAGE of different S16 GFP-LTF protein synthesis variations in E.coli resulted in the production of functional GFP–LTF and
indicates trimerization of S16 gp37 and attachment of gp38 to S16 gp37 trimers (Figure 4 and S1)
The distal part of the S16 LTF likely has a putative structure closely related to what has been reported for phage T2 (Drexler et.al., 1986),
where gp38 acts as the actual adhesin while bound to the C-terminal (distal) tip of gp37.
The binding of purified S16 GFP–LTF fusion protein to wild-type and mutant Salmonella typhimurium cells (with mutated OmpC) were assessed. (Figure?5A and B)
The wild-type revealed an even decoration of the bacterial surface by the fluorescent LTF (Figure?5A and B).
Deletion of OmpC completely abolished decoration by S16 GFP–LTF (Figure?5C and D).
The defective phenotype could be restored by in-trans complementation using ompC (Table?3, Figure?5E and F).
| challenge |
| BPP22:RPC1 | 2017-04-23 07:10:41 CDT | GO:0044212 transcription regulatory region DNA binding (F) | PMID:1385814 | ECO:0000314 direct assay evidence used in manual assertion | Figure 4 shows that P22 C1 induces transcription and
Figure 6 shows the DNA binding sites of P22 c1
| challenge |
| 9CAUD:R9R488 | 2017-04-29 05:09:11 CDT | GO:0044659 cytolysis by virus of host cell (P) | PMID:26506338 | ECO:0000314 direct assay evidence used in manual assertion | Figure 2B shows LysB shares about 63% identity with another previously characterized LysB (gp12) in
mycobacteriophage D29, which has been proved to be a mycolylarabinogalactan esterase
(Payne et al., 2009). It cleaves the ester linkage joining the mycolic acid-rich outer membrane to
arabinogalactan, releasing free mycolic acids.
Figure 3B shows that LysB has antibacterial activity on M. smegmatis.
| challenge |
| 9CAUD:R9R591 | 2017-04-29 05:12:42 CDT | GO:0008233 peptidase activity (F) | PMID:26506338 | ECO:0000314 direct assay evidence used in manual assertion | Figure 2A suggests that LysA contains an N-terminal peptidase domain, a central catalytic GH19
(glycoside hydrolase family 19) domain, and a C-terminal cell wall binding domain.
Figure 3B shows that LysA has antibacterial activity on M. smegmatis.
| challenge |
acceptable:0
unacceptable:2
requires_changes:0
flagged:0
Annotations challenged by Bolu
| Status | Author,Group | Page | GO Term (Aspect) | Reference | Evidence | Links | Page history |
|---|
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