When I use the server HHpred and search against PDB70 I get different results when I run it locally (run HHblits, add ss then HHsearch). I use the same setting as the server (I copy these from the raw output tab on the results from the server). I do, however, get the same results when I search against pfam. Can anyone help?
HHpred Server Results
Query sp|Q5BJD5|TM41B_HUMAN Transmembrane protein 41B OS=Homo sapiens OX=9606
GN=TMEM41B PE=1 SV=1
Match_columns 291
No_of_seqs 260 out of 1755
Neff 8.62981
Searched_HMMs 46150
Date Thu Nov 1 17:25:23 2018
Command hhsearch -cpu 8 -i ../results/full.a3m -d /cluster/toolkit/production/databases/hh-suite/mmcif70/pdb70 -o ../results/1206399.hhr -oa3m ../results/1206399.a3m -p 20 -Z 250 -loc -z 1 -b 1 -B 250 -ssm 2 -sc 1 -seq 1 -dbstrlen 10000 -norealign -maxres 32000 -contxt /cluster/toolkit/production/bioprogs/tools/hh-suite-build/data/context_data.crf
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3D31_D Sulfate/molybdate ABC t 91.3 7.9 0.00017 33.9 19.9 272 9-291 1-294 (295)
2 3B5X_B Lipid A export ATP-bind 66.9 1.5E+02 0.0032 28.5 14.3 188 89-291 7-194 (582)
3 2ONK_C membrane protein; membr 60.4 1.4E+02 0.003 25.8 17.8 264 25-291 1-282 (284)
4 6BPL_A Lipid A export ATP-bind 59.8 2E+02 0.0044 27.6 13.3 188 89-291 7-194 (582)
5 2KS1_A Receptor tyrosine-prote 53.8 47 0.001 19.4 4.2 27 265-291 18-44 (44)
HHsearch local results
Query sp|Q5BJD5|TM41B_HUMAN Transmembrane protein 41B OS=Homo sapiens OX=9606
GN=TMEM41B PE=1 SV=1
Match_columns 291
No_of_seqs 256 out of 1602
Neff 6.9
Searched_HMMs 60862
Date Tue Nov 20 10:57:43 2018
Command hhsearch -i /home/shah/seq/tests/test_addss/tmem41b_human_w_ss.a3m -d /home/shah/db/pdb70/pdb70_hhm.ffdata -o /home/shah/seq/tests/test_addss/tmem41b_ss_test4.hhr -p 20 -Z 250 -loc -z 1 -b 1 -B 250 -ssm 2 -sc 1 -seq 1 -dbstrlen 10000 -norealign -maxres 32000 -contxt /home/shah/hh/hh-suite-3.0-beta.3/data/context_data.lib
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 6B87_C TMHC2_E; De novo design 63.5 84 0.0014 24.6 8.4 74 53-126 15-89 (111)
2 6B87_D TMHC2_E; De novo design 61.8 84 0.0014 24.6 7.4 74 53-126 15-89 (111)
3 4HUQ_S Energy-coupling factor 53.4 62 0.001 27.5 6.3 65 98-162 1-72 (174)
4 3RLB_A Putative uncharacterize 31.1 2E+02 0.0032 25.0 6.1 70 83-161 2-79 (192)
5 4Z7F_E Folate ECF transporter; 24.4 2E+02 0.0032 25.4 4.9 64 99-162 19-90 (199)
The difference in "Searched_HMMs" means that the searches are performed against different (versions of) databases, i think.
BTW, hhpred uses hhblits to construct input a3m before the final search. Did you surely turn it off with the "Parameters" tab?