ORFs file "does not exist" in HHyeast, even though the file exists - may overlap with previous issue

[timlevine]

I found that the file of all HHyeast hits (HHpry_hits_171010) hd nothing from a particular ORF in it. Also that ORF is shown by HHyeast as "does not exist" Yet I have the file which was made by HHyeast - see attached. This has 34 Pram hits with pSS≥50%

YFL007W.0.ssw11.hhr.txt

Maybe this issue overlaps with the previous one!

Was this excluded because of the 2nd hit:
No 2

PF16507.4 ; BLM10_mid ; Proteasome-substrate-size regulator, mid region
Probab=100.00 E-value=6e-73 Score=745.17 Aligned_cols=512 Identities=46% Similarity=0.855 Sum_probs=459.9 Template_Neff=8.400

This is very strong (pSS=100%), full length and contains the name of the protein.

[timlevine]

Further to this:
I looked for ORFs that have Pfam hits in the InterPro list used by SGD. There are 4964. Of these 87 have no Pfam hit in HHyeast

These fall into three classes:

1. hits too short (n=26): all hits less than 30 aligned columns

2. pseudogenes (n=3) - no confidence in gene's reality at SGD. For one of these we have a file, but it's OK to not show any of these results.

3. file dropped out for no clear reason (n=58 - list below): the files have been made for all of these in the HHyeast dataset, and the website know the ORFs exist, i.e. when I put in the systematic name (e.g. YAL008W) the website uses the non-systematic name (e.g. Fun14) to tell me that files do not exist.

This final 1% of files (some of which have gaps/inserts files) should be put back in the HHyeast data set! List here:

Q0050
YAL008W
YAL026C
YAR019C
YBL088C
YBL099W
YBR084W
YBR276C
YCL011C
YDL040C
YDR145W
YDR359C
YDR406W
YDR422C
YDR484W
YEL060C
YER132C
YER164W
YFL007W
YGL062W
YGL086W
YGL097W
YGL100W
YGL197W
YGR003W
YGR061C
YGR199W
YGR204W
YGR240C
YGR245C
YGR281W
YIL147C
YJR066W
YKL164C
YKL188C
YKL203C
YKL209C
YLL001W
YLR096W
YLR163C
YLR398C
YMR176W
YMR284W
YMR296C
YNL163C
YNR033W
YNR047W
YOL021C
YOL123W
YOL152W
YOR116C
YOR162C
YOR251C
YOR343W-B
YOR393W
YPL226W
YPL249C
YPR032W

[tamuri]

We have results for all in that list. I think this is related to #6. Will fix now.

[tamuri]

I've uploaded those missing data files - you should be able to see them on the website now.

[tamuri]

PF16507.4 ; BLM10_mid ; Proteasome-substrate-size regulator, mid region
Probab=100.00 E-value=6e-73 Score=745.17 Aligned_cols=512 Identities=46% Similarity=0.855 Sum_probs=459.9 Template_Neff=8.400

This is very strong (pSS=100%), full length and contains the name of the protein.

Any Pfam hits that contain the name of the protein are not shown.

[timlevine]

Great - thanks for putting up those 58
T