Phage Hunters Spring 2016
My Annotations
| Status | Page | Date/Time | GO Term (Aspect) | Reference | Evidence | Notes | Links |
|---|
| updatedbyinstructor | BACAN:Q81WA9 | 2016-04-06 12:23:13 CDT | GO:0008745 N-acetylmuramoyl-L-alanine amidase activity (F) | PMID:16103125 | ECO:0000314 direct assay evidence used in manual assertion | PlyL is an endolysin enzyme with 2 separate domains, an N-terminal catalytic domain, and a C-terminal cell wall binding domain. This annotation is for the N-terminal domain of PlyL.
Peptidoglycan from B. subtilis was subjected to both the full-length PlyL and the N-terminal domain only. In supplemental figure 1, (see link: http://www.jbc.org/content/suppl/2005/08/16/M502723200.DC1/Suppdata.pdf) the amount of 2,4-dinitrophenyl-alanine is shown to increase sharply, indicating that PlyL is an N-acetylmuramoyl-L-alanine amidase. Additionally, the figure shows that alanine is increased even more when the N-terminal domain alone is used, compared to the full-length protein.
As additional support that PlyL is an amidase, figure 2 compares the crystal structure of PlyL to other known amidase enzymes.
Figure 4 shows a time course assay where the purified endolysin (PlyL) was able to lyse 4 different bacillus species cultures within 400 seconds.
In 4a, the lysing capabilities of the full-length version of PlyL are shown. In 4b, the lysing capabilities of the N-terminal portion only are shown. The N-terminal domain by itself is more effective at cleaving Bacillus species than the entirety of PlyL.
| challenge |
| updatedbyinstructor | BACAN:Q81WA9 | 2016-04-06 12:23:13 CDT | GO:0051672 catabolism by organism of cell wall peptidoglycan in other organism (P) | PMID:16103125 | ECO:0000314 direct assay evidence used in manual assertion | Peptidoglycan from B. subtilis was subjected to both the full-length PlyL and the N-terminal domain only. In supplemental figure 1, (see link: http://www.jbc.org/content/suppl/2005/08/16/M502723200.DC1/Suppdata.pdf) the amount of 2,4-dinitrophenyl-alanine is shown to increase sharply, indicating that PlyL is an N-acetylmuramoyl-L-alanine amidase. Additionally, the figure shows that alanine is increased even more when the N-terminal domain alone is used, compared to the full-length protein.
| challenge |
| updatedbyinstructor | 9CAUD:A0A024B2H2 | 2016-04-11 09:24:42 CDT | GO:0008745 N-acetylmuramoyl-L-alanine amidase activity (F) | GO_REF:0000100 | ECO:0000250 sequence similarity evidence used in manual assertion | Fulfilling the minimum requirements for using GO_REF:0000100, the probability from hhpred is 100% and the e-value is 1e-33.
The e-value from blastp is 1e-50.
Note that I am annotating the catalytic domain and for this domain the blastp and hhpred criteria are achieved.
The domain for the peptidoglycan should be annotated separately.
| challenge |
| updatedbyinstructor | 9CAUD:A0A024B2H2 | 2016-04-11 09:29:30 CDT | GO:0051672 catabolism by organism of cell wall peptidoglycan in other organism (P) | GO_REF:0000100 | ECO:0000250 sequence similarity evidence used in manual assertion | Fulfilling the minimum requirements for using GO_REF:0000100, the probability from hhpred is 100% and the e-value is 1e-33.
The e-value from blastp is 1e-50.
Note that I am annotating the catalytic domain and for this domain the blastp and hhpred criteria are achieved.
The domain for the peptidoglycan should be annotated separately.
| challenge |
| unacceptable | 9CAUD:A0A0K2FL53 | 2016-04-24 01:34:01 CDT | GO:0008745 N-acetylmuramoyl-L-alanine amidase activity (F) | other:GO_REF:0000100 | ECO:0000250 sequence similarity evidence used in manual assertion | This is a transfer annotation made from a bacillus anthracis gene with a regular annotation previously made on it, see: http://gowiki.tamu.edu/wiki/index.php/BACAN:Q81WA9
Fulfilling the minimum requirements for using GO_REF:0000100, the probability from hhpred is 100% and the e-value is 6.2e-34.
The e-value from blastp is 2e-50. Note that I am annotating the catalytic domain and for this domain the blastp and hhpred criteria are achieved.
| challenge |
| updatedbyinstructor | 9CAUD:A0A024B0U5 | 2016-04-24 01:41:58 CDT | GO:0008745 N-acetylmuramoyl-L-alanine amidase activity (F) | GO_REF:0000100 | ECO:0000250 sequence similarity evidence used in manual assertion | This is a transfer annotation made from a bacillus anthracis gene with a regular annotation previously made on it, see: http://gowiki.tamu.edu/wiki/index.php/BACAN:Q81WA9 Fulfilling the minimum requirements for using GO_REF:0000100, the probability from hhpred is 100% and the e-value is 6.2e-34. The e-value from blastp is 2e-50. Note that I am annotating the catalytic domain and for this domain the blastp and hhpred criteria are achieved.
| challenge |
| updatedbyinstructor | BPT7:DPOL | 2016-04-27 10:45:56 CDT | GO:0004529 exodeoxyribonuclease activity (F) | PMID:1846298 | ECO:0000315 mutant phenotype evidence used in manual assertion | Table 3 (specifically k_exo) compares the rates of exonuclease activity between the wild-type enzyme (105 1/s) and mutant enzyme (6.9e-4 1/s), revealing that the wild-type exonuclease rates are dramatically higher than that of the mutant enzyme's exonuclease rates. This shows that this domain of DNA polymerase has exonuclease activity.
| challenge |
acceptable:0
unacceptable:1
requires_changes:0
flagged:0
Annotations challenged by Strandquistg
0 annotations fixed by Strandquistg
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