T2SS available
T4P available
Tad available

Performing HMMER search for T2SS

---------
- gspC -
---------
- profile: ./profiles/gspC.fasta-aln_edit.hmm
- length: 76
Hmmer search done. 
- outfile: ./datatest/res_search/gspC.search_hmm.out
Hits extracted to: ./datatest/res_search/gspC.res_hmm_extract
---------
- gspD -
---------
- profile: ./profiles/gspD.fasta-aln_edit.hmm
- length: 596
Hmmer search done. 
- outfile: ./datatest/res_search/gspD.search_hmm.out
Hits extracted to: ./datatest/res_search/gspD.res_hmm_extract
---------
- gspE -
---------
- profile: ./profiles/gspE.fasta-aln_edit.hmm
- length: 378
Hmmer search done. 
- outfile: ./datatest/res_search/gspE.search_hmm.out
Hits extracted to: ./datatest/res_search/gspE.res_hmm_extract
---------
- gspF -
---------
- profile: ./profiles/gspF.fasta-aln_edit.hmm
- length: 394
Hmmer search done. 
- outfile: ./datatest/res_search/gspF.search_hmm.out
Hits extracted to: ./datatest/res_search/gspF.res_hmm_extract
---------
- gspG -
---------
- profile: ./profiles/gspG.fasta-aln_edit.hmm
- length: 131
Hmmer search done. 
- outfile: ./datatest/res_search/gspG.search_hmm.out
Hits extracted to: ./datatest/res_search/gspG.res_hmm_extract
---------
- gspH -
---------
- profile: ./profiles/gspH.fasta-aln_edit.hmm
- length: 153
Hmmer search done. 
- outfile: ./datatest/res_search/gspH.search_hmm.out
Hits extracted to: ./datatest/res_search/gspH.res_hmm_extract
---------
- gspI -
---------
- profile: ./profiles/gspI.fasta-aln_edit.hmm
- length: 109
Hmmer search done. 
- outfile: ./datatest/res_search/gspI.search_hmm.out
Hits extracted to: ./datatest/res_search/gspI.res_hmm_extract
---------
- gspJ -
---------
- profile: ./profiles/gspJ.fasta-aln_edit.hmm
- length: 123
Hmmer search done. 
- outfile: ./datatest/res_search/gspJ.search_hmm.out
Hits extracted to: ./datatest/res_search/gspJ.res_hmm_extract
---------
- gspK -
---------
- profile: ./profiles/gspK.fasta-aln_edit.hmm
- length: 247
Hmmer search done. 
- outfile: ./datatest/res_search/gspK.search_hmm.out
Hits extracted to: ./datatest/res_search/gspK.res_hmm_extract
---------
- gspL -
---------
- profile: ./profiles/gspL.fasta-aln_edit.hmm
- length: 254
Hmmer search done. 
- outfile: ./datatest/res_search/gspL.search_hmm.out
Hits extracted to: ./datatest/res_search/gspL.res_hmm_extract
---------
- gspM -
---------
- profile: ./profiles/gspM.fasta-aln_edit.hmm
- length: 134
Hmmer search done. 
- outfile: ./datatest/res_search/gspM.search_hmm.out
Hits extracted to: ./datatest/res_search/gspM.res_hmm_extract
---------
- gspO -
---------
- profile: ./profiles/gspO.fasta-aln_edit.hmm
- length: 233
Hmmer search done. 
- outfile: ./datatest/res_search/gspO.search_hmm.out
Hits extracted to: ./datatest/res_search/gspO.res_hmm_extract

Performing HMMER search for T4P

---------
- pilAE -
---------
- profile: ./profiles/pilAE.fasta-aln_edit.hmm
- length: 165
Hmmer search done. 
- outfile: ./datatest/res_search/pilAE.search_hmm.out
Hits extracted to: ./datatest/res_search/pilAE.res_hmm_extract
---------
- pilB -
---------
- profile: ./profiles/pilB.fasta-aln_edit.hmm
- length: 383
Hmmer search done. 
- outfile: ./datatest/res_search/pilB.search_hmm.out
Hits extracted to: ./datatest/res_search/pilB.res_hmm_extract
---------
- pilC -
---------
- profile: ./profiles/pilC.fasta-aln_edit.hmm
- length: 339
Hmmer search done. 
- outfile: ./datatest/res_search/pilC.search_hmm.out
Hits extracted to: ./datatest/res_search/pilC.res_hmm_extract
---------
- pilD -
---------
- profile: ./profiles/pilD.fasta-aln_edit.hmm
- length: 232
Hmmer search done. 
- outfile: ./datatest/res_search/pilD.search_hmm.out
Hits extracted to: ./datatest/res_search/pilD.res_hmm_extract
---------
- pilI_pilV -
---------
- profile: ./profiles/pilI_pilV.fasta-aln_edit.hmm
- length: 171
Hmmer search done. 
- outfile: ./datatest/res_search/pilI_pilV.search_hmm.out
Hits extracted to: ./datatest/res_search/pilI_pilV.res_hmm_extract
---------
- pilM -
---------
- profile: ./profiles/pilM.fasta-aln_edit.hmm
- length: 338
Hmmer search done. 
- outfile: ./datatest/res_search/pilM.search_hmm.out
Hits extracted to: ./datatest/res_search/pilM.res_hmm_extract
---------
- pilN -
---------
- profile: ./profiles/pilN.fasta-aln_edit.hmm
- length: 193
Hmmer search done. 
- outfile: ./datatest/res_search/pilN.search_hmm.out
Hits extracted to: ./datatest/res_search/pilN.res_hmm_extract
---------
- pilO -
---------
- profile: ./profiles/pilO.fasta-aln_edit.hmm
- length: 187
Hmmer search done. 
- outfile: ./datatest/res_search/pilO.search_hmm.out
Hits extracted to: ./datatest/res_search/pilO.res_hmm_extract
---------
- pilP -
---------
- profile: ./profiles/pilP.fasta-aln_edit.hmm
- length: 143
Hmmer search done. 
- outfile: ./datatest/res_search/pilP.search_hmm.out
Hits extracted to: ./datatest/res_search/pilP.res_hmm_extract
---------
- pilQ -
---------
- profile: ./profiles/pilQ.fasta-aln_edit.hmm
- length: 279
Hmmer search done. 
- outfile: ./datatest/res_search/pilQ.search_hmm.out
Hits extracted to: ./datatest/res_search/pilQ.res_hmm_extract
---------
- pilT_pilU -
---------
- profile: ./profiles/pilT_pilU.fasta-aln_edit.hmm
- length: 333
Hmmer search done. 
- outfile: ./datatest/res_search/pilT_pilU.search_hmm.out
Hits extracted to: ./datatest/res_search/pilT_pilU.res_hmm_extract

Performing HMMER search for Tad

---------
- flp -
---------
- profile: ./profiles/flp.fasta-aln_edit.hmm
- length: 56
Hmmer search done. 
- outfile: ./datatest/res_search/flp.search_hmm.out
Hits extracted to: ./datatest/res_search/flp.res_hmm_extract
---------
- rcpA -
---------
- profile: ./profiles/rcpA.fasta-aln_edit.hmm
- length: 405
Hmmer search done. 
- outfile: ./datatest/res_search/rcpA.search_hmm.out
Hits extracted to: ./datatest/res_search/rcpA.res_hmm_extract
---------
- tadA -
---------
- profile: ./profiles/tadA.fasta-aln_edit.hmm
- length: 291
Hmmer search done. 
- outfile: ./datatest/res_search/tadA.search_hmm.out
Hits extracted to: ./datatest/res_search/tadA.res_hmm_extract
---------
- tadB -
---------
- profile: ./profiles/tadB.fasta-aln_edit.hmm
- length: 220
Hmmer search done. 
- outfile: ./datatest/res_search/tadB.search_hmm.out
Hits extracted to: ./datatest/res_search/tadB.res_hmm_extract
---------
- tadC -
---------
- profile: ./profiles/tadC.fasta-aln_edit.hmm
- length: 295
Hmmer search done. 
- outfile: ./datatest/res_search/tadC.search_hmm.out
Hits extracted to: ./datatest/res_search/tadC.res_hmm_extract
---------
- tadD -
---------
- profile: ./profiles/tadD.fasta-aln_edit.hmm
- length: 237
Hmmer search done. 
- outfile: ./datatest/res_search/tadD.search_hmm.out
Hits extracted to: ./datatest/res_search/tadD.res_hmm_extract
---------
- tadE -
---------
- profile: ./profiles/tadE.fasta-aln_edit.hmm
- length: 152
Hmmer search done. 
- outfile: ./datatest/res_search/tadE.search_hmm.out
Hits extracted to: ./datatest/res_search/tadE.res_hmm_extract
---------
- tadF -
---------
- profile: ./profiles/tadF.fasta-aln_edit.hmm
- length: 196
Hmmer search done. 
- outfile: ./datatest/res_search/tadF.search_hmm.out
Hits extracted to: ./datatest/res_search/tadF.res_hmm_extract
---------
- tadV -
---------
- profile: ./profiles/tadV.fasta-aln_edit.hmm
- length: 152
Hmmer search done. 
- outfile: ./datatest/res_search/tadV.search_hmm.out
Hits extracted to: ./datatest/res_search/tadV.res_hmm_extract
---------
- tadZ -
---------
- profile: ./profiles/tadZ.fasta-aln_edit.hmm
- length: 416
Hmmer search done. 
- outfile: ./datatest/res_search/tadZ.search_hmm.out
Hits extracted to: ./datatest/res_search/tadZ.res_hmm_extract

Building a joint resfile
./datatest/res_search/gspC.res_hmm_extract
./datatest/res_search/gspD.res_hmm_extract
./datatest/res_search/gspE.res_hmm_extract
./datatest/res_search/gspF.res_hmm_extract
./datatest/res_search/gspG.res_hmm_extract
./datatest/res_search/gspH.res_hmm_extract
./datatest/res_search/gspI.res_hmm_extract
./datatest/res_search/gspJ.res_hmm_extract
./datatest/res_search/gspK.res_hmm_extract
./datatest/res_search/gspL.res_hmm_extract
./datatest/res_search/gspM.res_hmm_extract
./datatest/res_search/gspO.res_hmm_extract
./datatest/res_search/pilAE.res_hmm_extract
./datatest/res_search/pilB.res_hmm_extract
./datatest/res_search/pilC.res_hmm_extract
./datatest/res_search/pilD.res_hmm_extract
./datatest/res_search/pilI_pilV.res_hmm_extract
./datatest/res_search/pilM.res_hmm_extract
./datatest/res_search/pilN.res_hmm_extract
./datatest/res_search/pilO.res_hmm_extract
./datatest/res_search/pilP.res_hmm_extract
./datatest/res_search/pilQ.res_hmm_extract
./datatest/res_search/pilT_pilU.res_hmm_extract
./datatest/res_search/flp.res_hmm_extract
./datatest/res_search/rcpA.res_hmm_extract
./datatest/res_search/tadA.res_hmm_extract
./datatest/res_search/tadB.res_hmm_extract
./datatest/res_search/tadC.res_hmm_extract
./datatest/res_search/tadD.res_hmm_extract
./datatest/res_search/tadE.res_hmm_extract
./datatest/res_search/tadF.res_hmm_extract
./datatest/res_search/tadV.res_hmm_extract
./datatest/res_search/tadZ.res_hmm_extract
***** PSAE001c01 *****
['PSAE001c01_003970', 'PSAE001c01_003980']
['pilT_pilU', 'pilT_pilU']
[397, 398]
['PSAE001c01_006860', 'PSAE001c01_006870', 'PSAE001c01_006880', 'PSAE001c01_006890', 'PSAE001c01_006900', 'PSAE001c01_006910', 'PSAE001c01_006920', 'PSAE001c01_006930', 'PSAE001c01_006940', 'PSAE001c01_006950', 'PSAE001c01_006960']
['gspJ', 'gspH', 'gspC', 'gspI', 'gspG', 'gspK', 'gspL', 'gspM', 'gspD', 'gspE', 'gspF']
[686, 687, 688, 689, 690, 691, 692, 693, 694, 695, 696]
['PSAE001c01_018910', 'PSAE001c01_018920']
['gspC', 'gspD']
[1891, 1892]
['PSAE001c01_027020', 'PSAE001c01_027030', 'PSAE001c01_027040']
['gspG', 'gspF', 'pilB']
[2702, 2703, 2704]
['PSAE001c01_031320', 'PSAE001c01_031330', 'PSAE001c01_031340', 'PSAE001c01_031350', 'PSAE001c01_031360', 'PSAE001c01_031370', 'PSAE001c01_031380', 'PSAE001c01_031390', 'PSAE001c01_031400', 'PSAE001c01_031410', 'PSAE001c01_031420']
['gspM', 'gspL', 'gspK', 'gspJ', 'gspI', 'gspH', 'gspG', 'gspF', 'gspE', 'gspC', 'gspD']
[3132, 3133, 3134, 3135, 3136, 3137, 3138, 3139, 3140, 3141, 3142]
['PSAE001c01_043490', 'PSAE001c01_043540', 'PSAE001c01_043550', 'PSAE001c01_043560', 'PSAE001c01_043570', 'PSAE001c01_043580', 'PSAE001c01_043600']
['tadV', 'tadC', 'tadB', 'tadA', 'tadZ', 'rcpA', 'flp']
[4349, 4354, 4355, 4356, 4357, 4358, 4360]
['PSAE001c01_045800', 'PSAE001c01_045810', 'PSAE001c01_045820']
['pilAE', 'pilB', 'pilD']
[4580, 4581, 4582]
['PSAE001c01_046060', 'PSAE001c01_046070', 'PSAE001c01_046080', 'PSAE001c01_046130']
['pilAE', 'pilAE', 'pilI_pilV', 'pilAE']
[4606, 4607, 4608, 4613]
['PSAE001c01_051090', 'PSAE001c01_051100', 'PSAE001c01_051110', 'PSAE001c01_051120', 'PSAE001c01_051130']
['pilQ', 'pilP', 'pilO', 'pilN', 'pilM']
[5109, 5110, 5111, 5112, 5113]


