Cysteines are the least abundant amino acids in any genome (even humans) because it has such specialized behaviors due to the sulfhydryl group. It can allow for very strong bonds between metal ions, especially iron in the case of WhiB transcription factors, and sulfur side chains. With that being said, the cysteine motif is very common in proteins that involve redox reactions which tend to include transcription factors. So, cysteines are more typical for transcription factor proteins in general. But the WhiB transcription factor has the more specified to cysteine motif that can be seen in my poster.
The gene could be isolated from the Auspice genome and recombined with another genome that previously had its known/functioning WhiB transcription factor removed. If the phage still undergoes the appropriate processes then the gene is considered a functioning WhiB transcription factor. Otherwise, it would either be a non-functioning WhiB transcription factor (psuedolog) or it may not be a WhiB factor at all. To determine if it is a psuedolog it would be necessary to do a deep dive into the ancestry of the gene and the Auspice genome.
You mentioned how understanding different motifs like CXC could be beneficial, in what ways do these proteins allow for classification of Whi-B-like proteins in the Auspice Genome?
You mentioned how understanding different motifs like CXC could be beneficial, in what ways do these proteins allow for classification of Whi-B-like proteins in the Auspice Genome?
I am not sure if I understand your question but, the CXC motif is not typical for WhiB transcription factors (CXXC is more typical) but it does not mean that the CXC motif can not ever be in a WhiB transcription factor. It simply is indicative of the gene needing further investigation. The gene may still be a functioning WhiB protein with a cysteine mutation but it may also mean it is a non-functioning WhiB protein. It could also mean the gene isn’t related to WhiB proteins at all. CXC is simply a way of identifying a gene that is likely involved in binding to metal ions or compounds. It also suggests that the protein may be involved in some kind of redox reaction.
Phamerator includes tRNAs in the overall count of the genes whereas DNA Mastering does not. So, the count is just slightly higher in phamerator as the genes are interrupted by tRNAs.
Are cysteine groups typical for transcription factor proteins? Or are they more specific to WhibB proteins?
Cysteines are the least abundant amino acids in any genome (even humans) because it has such specialized behaviors due to the sulfhydryl group. It can allow for very strong bonds between metal ions, especially iron in the case of WhiB transcription factors, and sulfur side chains. With that being said, the cysteine motif is very common in proteins that involve redox reactions which tend to include transcription factors. So, cysteines are more typical for transcription factor proteins in general. But the WhiB transcription factor has the more specified to cysteine motif that can be seen in my poster.
What kind of experiments could be done to confirm whether Gene 69 is a pseudolog or not?
The gene could be isolated from the Auspice genome and recombined with another genome that previously had its known/functioning WhiB transcription factor removed. If the phage still undergoes the appropriate processes then the gene is considered a functioning WhiB transcription factor. Otherwise, it would either be a non-functioning WhiB transcription factor (psuedolog) or it may not be a WhiB factor at all. To determine if it is a psuedolog it would be necessary to do a deep dive into the ancestry of the gene and the Auspice genome.
You mentioned how understanding different motifs like CXC could be beneficial, in what ways do these proteins allow for classification of Whi-B-like proteins in the Auspice Genome?
You mentioned how understanding different motifs like CXC could be beneficial, in what ways do these proteins allow for classification of Whi-B-like proteins in the Auspice Genome?
I am not sure if I understand your question but, the CXC motif is not typical for WhiB transcription factors (CXXC is more typical) but it does not mean that the CXC motif can not ever be in a WhiB transcription factor. It simply is indicative of the gene needing further investigation. The gene may still be a functioning WhiB protein with a cysteine mutation but it may also mean it is a non-functioning WhiB protein. It could also mean the gene isn’t related to WhiB proteins at all. CXC is simply a way of identifying a gene that is likely involved in binding to metal ions or compounds. It also suggests that the protein may be involved in some kind of redox reaction.
What about phamerator naming conventions caused it to identify genes 69 and 71 as different numbers?
Phamerator includes tRNAs in the overall count of the genes whereas DNA Mastering does not. So, the count is just slightly higher in phamerator as the genes are interrupted by tRNAs.