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All posts created by Wabush

| posted 25 Mar, 2021 21:18
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Wabush
Hi Chris,

Thank-you so much for the explanation. It was very nice of you to write such a nice detailed response. Very helpful indeed. Much appreciated!

Kieran
Posted in: Functional Annotation → Phage gene annotation has matching phage genes have 4 different proteins - which one is a match?
| posted 06 Mar, 2021 02:01
default avatar
Wabush
Wabush
I am annotating the phage Crewmate (gene '28'smile in PECAAN and I would like some guidance as to which protein function I should assign to the gene.

- The NCBI BlastP of the gene returns several matching phages and their proteins.
- (See the attached image for details) The first 9 phages returned have high coverage (99.28%-100%), high alignment (>96%), low e-values (0), and high identity (>90%). (see the attached image for details)but they have annotated 4 different proteins and I am unsure which one is a good reference for the Crewmate gene 28? The proteins assigned to the 9 phages are:

- Cas4 family exonuclease (4 of 9 phages called this)
- Exonuclease (3 of 9 phages called this)
- RepA-like helicase (1 of 9 phages called this)
- Hypothetical protein (1 of 9 phages called this)

Thank-you kindly for reading and for any help offered,
Kieran

References:
A. Attached to this post is a screen shot of NCBI Blastp in PECAAN
B. Protein Sequence:
MTTPKVSTIKRGGARFYVDPDDGKIKVPGVTSIIGMLPKEFLRYWAAKEVAQTAVDSLPTVLQMILNDQSDAAVDFLKKSPDRNTRKAADTGTAAHDLFERMAKGETVGRVHPDLEPFVRHFDEFLTVAKPEYHFLEETVWSDKHAYAGSFDAYATIGGERLWLDNKTTRSGIHEEVGIQLAAYRFADSIIRADGGRVPMPTADGGAVLHVRPEGWKLVPVRCDEELFEVFLHLREVFKYEKEIKSTIVGREVFSGPAEDAPTGPKRRTPRARKAAE
Posted in: Functional Annotation → Phage gene annotation has matching phage genes have 4 different proteins - which one is a match?
| posted 06 Mar, 2021 02:01
default avatar
Wabush
I am annotating the phage Crewmate (gene 2smile in PECAAN and I would like some guidance as to which protein function I should assign to the gene.

- The NCBI BlastP of the gene returns several matching phages and their proteins.
- (See the attached image for details) The first 9 phages returned have high coverage (99.28%-100%), high alignment (>96%), low e-values (0), and high identity (>90%). (see the attached image for details)but they have annotated 4 different proteins and I am unsure which one is a good reference for the Crewmate gene 28? The proteins assigned to the 9 phages are:

- Cas4 family exonuclease (4 of 9 phages called this)
- Exonuclease (3 of 9 phages called this)
- RepA-like helicase (1 of 9 phages called this)
- Hypothetical protein (1 of 9 phages called this)

Thank-you kindly for reading and for any help offered,
Kieran

References:
A. Attached to this post is a screen shot of NCBI Blastp in PECAAN
B. Protein Sequence:
MTTPKVSTIKRGGARFYVDPDDGKIKVPGVTSIIGMLPKEFLRYWAAKEVAQTAVDSLPTVLQMILNDQSDAAVDFLKKSPDRNTRKAADTGTAAHDLFERMAKGETVGRVHPDLEPFVRHFDEFLTVAKPEYHFLEETVWSDKHAYAGSFDAYATIGGERLWLDNKTTRSGIHEEVGIQLAAYRFADSIIRADGGRVPMPTADGGAVLHVRPEGWKLVPVRCDEELFEVFLHLREVFKYEKEIKSTIVGREVFSGPAEDAPTGPKRRTPRARKAAE
67Kb
Posted in: Functional Annotation → Phage gene annotation has matching phage genes have 4 different proteins - which one is a match?