Joseph Perez, Myrielis Rivera, Dr. Michael Rubin
University of Puerto Rico at Cayey
Mycobacteriophage Myxus
List of Problematic Genes

Myxus_gp9
SSC:6006-6146
CP: YES
SD: NO
SCS:Glimmer
Gap (or overlap):1 overlap
Blast:gp10 myco_phage Packman q1:s46	e = 4.3E-23
LO (Longest ORF):NO
F (Function):NKF
FS (Function source):-
Anything else you think is important.
Size 141bp. Another start site offers 168bp but starts with TTG. Another start is ATG offers 300bp but overlaps with a tRNA and 21bp of Myxus_gp7.

Myxus_gp25
SSC:17045-17461
CP: NO
SD:NO
SCS:GeneMark
Gap (or overlap):129
Blast:gp26 myco_phage Packman q8:s166	e=0
LO (Longest ORF):NO
F (Function):Tail assembly chaperone
FS (Function source):myco_phage Jobu08 e = 0
Anything else you think is important.
Does not include all coding potential. Query to subject does not line up 1 to 1. Chose Genemark call that is different than Glimmer call. Glimmer call had a big overlap (more than 30bp). 

Myxus_gp34
SSC:26524-26946
CP: YES for available ORF
SD: YES
SCS:Not called by glimmer or GeneMark, manually added
Gap (or overlap):22
Blast:gp35 myco_phage Alma q1:s98	e=1E-56
LO (Longest ORF):YES
F (Function):NKF
FS (Function source):-
Anything else you think is important.
Gene not called by Glimmer or Genemark in DNA master. Without this gene there would be a large gap (more than 300pb) between myxus gp32 and gp33. The product for this squence matches q to s 1 to 1 with gp35 of Bacteriophage Alma. It has a decent ORF length and SD score. 

Myxus_gp51
SSC:35873-35670
CP: YES
SD: NO
SCS:Glimmer (genemark called different)
Gap (or overlap):29 overlap ***
Blast:gp51 myco_phage Packman q1:s67	e=1.6E-39
LO (Longest ORF):YES
F (Function):NKF
FS (Function source):-
Anything else you think is important.
Best open reading frame called by glimmer that is q to s 1 to 1 with many blast alignments, but has a 29 bp overlap with Myxus_gp50

Myxus_gp59
SSC:39071-38688
CP: YES
SD: YES
SCS:GeneMark
Gap (or overlap):8 overlap ***
Blast:gp59 myco_phage Packman q1:s127	e=0
LO (Longest ORF):NO
F (Function):DNA primase
FS (Function source):myco_phage Odin e = 0
Anything else you think is important.
Blast calls possible functions as DNA primase compared to myco phage Odin. Myxus_gp56 also called possible function as DNA primase compared to myco phage Chy4.

Myxus_gp WAS DELETED
SSC:39195-39064
CP: 
SD: 
SCS:
Gap (or overlap):4 overlap
Blast:
LO (Longest ORF):
F (Function):
FS (Function source):
Anything else you think is important.
MARKED FOR DELETION. Small ORF with no significant blast hits to other phages. Blastp of protein product results in low homology to a protein from a tree.

Myxus_gp62
SSC:40037-39573
CP: YES
SD: YES
SCS:Glimmer
Gap (or overlap):56 overlap ***
Blast:gp62 myco_phage Alma q1:s154	e=5E-109
LO (Longest ORF):YES
F (Function):Endo VII
FS (Function source):myco_phage AnnaL29 e = 0
Anything else you think is important.
This product does not line up 1 to 1 with blast hits. Careful reviewing required. 
This gene was extended to the best ORF and had a 1to1 q to s with myco Alma, better results than the blast if left at the lower ORF. 

Myxus_gp63
SSC:40137-39982
CP: 
SD: 
SCS:
Gap (or overlap):4 overlap
Blast:
LO (Longest ORF):
F (Function):
FS (Function source):
Anything else you think is important.
This gp is probably not real for Myco Myxus. The blast shows that the only similarity to other phages is only Packman and Alma. The product is only 52 amino acids and the next blast hits are low and are not phages. Also if this gene is left as a feature, it will overlap more then 30bp with Myxus_gp61. Conclusion: Eligible to be deleted. 

Myxus_gp83
SSC:46898-46383
CP: YES
SD: NO
SCS: Glimmer 
Gap (or overlap):50 overlap ***
Blast:gp82 myco_phage Alma q1:s171	e=0
LO (Longest ORF):NO
F (Function):DNA methylase
FS (Function source):myco_phage Severus e = 0
Anything else you think is important.
Large overlap

Myxus_gp84
SSC:47397-46849
CP: YES
SD: YES
SCS:Glimmer
Gap (or overlap):4
Blast:gp83 myco_phage Alma q3:s184	e=0
LO (Longest ORF):YES
F (Function):NKF
FS (Function source):-
Anything else you think is important.
Gene has an overlap of more than 30bp with Myxus_gp82, but if ORF shorten it would be significantly and won’t have a good blast result. 

Myxus_gp99
SSC:51621-51538
CP: YES
SD: NO
SCS:Glimmer
Gap (or overlap):31
Blast:gp96 myco_phage Alma q1:s27	e=2E-10
LO (Longest ORF):YES
F (Function):NKF
FS (Function source):-
Anything else you think is important.
Very small gene ~80bp. Carefully inspect.