SUPERFAMILY 1.75 HMM library and genome assignments server

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Perfringolysin alignments

These alignments are sequences aligned to the 0042290 model.

Sophisticated options are available for refining alignments:


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Alignments

The numbers along the top are the segment numbers of the HMM states, and each sequence is seperately aligned to the model.
The first sequence is the seed the model was built from.
Upper case letters are aligned, lower case letters are insertions, '-' signifies a deletion and '.' is nothing.

                                                10        20        30        40        50        60
                                                 |         |         |         |         |         |
d1pfoa_                                .DITDKNQSIDSGISSLSYNRNEVLASNGDKIESFVPKEGKKAGNKFIVVERQKRSLTTSP
gi|387627094|ref|YP_006063270.1|:3-468 n------KAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKKRSLSTNT


                                               70        80        90       100       110        120
                                                |         |         |         |         |          |
d1pfoa_                                VDISIIDSVNDRTYPGALQLADKALVENRPTILMVKRKPININIDLPGLKGENS.IKVDDP
gi|387627094|ref|YP_006063270.1|:3-468 SDISVTATNDSRLYPGALLVVDETLLENNPTLLAVDRAPMTYSIDLPGLASSDSfLQVEDP


                                              130       140       150       160       170       180 
                                                |         |         |         |         |         | 
d1pfoa_                                TYGKVSGAIDELVSKWNEKYSSTHTLPARTQYSESMVYSKSQISSALNVNAKVLENSLGVD
gi|387627094|ref|YP_006063270.1|:3-468 SNSSVRGAVNDLLAKWHQDYGQVNNVPARMQYEKITAHSMEQLKVKFGSDFEKTGNSLDID


                                             190       200       210       220       230       240  
                                               |         |         |         |         |         |  
d1pfoa_                                FNAVANNEKKVMILAYKQIFYTVSADLPKNPSDLFDDSVTFNDLKQKGVSNEAPPLMVSNV
gi|387627094|ref|YP_006063270.1|:3-468 FNSVHSGEKQIQIVNFKQIYYTVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSV


                                            250       260       270       280       290       300   
                                              |         |         |         |         |         |   
d1pfoa_                                AYGRTIYVKLETTSSSKDVQAAFKALIKNTDIKNSQQYKDIYENSSFTAVVLGGDAQEHNK
gi|387627094|ref|YP_006063270.1|:3-468 AYGRQVYLKLETTSKSDEVEAAFEALIKGVKVAPQTEWKQILDNTEVKAVILGGDPSSGAR


                                           310       320       330       340       350       360    
                                             |         |         |         |         |         |    
d1pfoa_                                VVTKDFDEIRKVIKDNATFSTKNPAYPISYTSVFLKDNSVAAVHNKTDYIETTSTEYSKGK
gi|387627094|ref|YP_006063270.1|:3-468 VVTGKVDMVEDLIQEGSRFTADHPGLPISYTTSFLRDNVVATFQNSTDYVETKVTAYRNGD


                                          370       380       390       400       410       420     
                                            |         |         |         |         |         |     
d1pfoa_                                INLDHSGAYVAQFEVAWDEVSYDKEGNEVLTHKTWDGNYQDKTAHYSTVIPLEANARNIRI
gi|387627094|ref|YP_006063270.1|:3-468 LLLDHSGAYVAQYYITWNELSYDHQGKEVLTPKAWDRNGQDLTAHFTTSIPLKGNVRNLSV


                                         430       440       450       460       470  
                                           |         |         |         |         |  
d1pfoa_                                KARECTGLAWEWWRDVISEYDVPLTNNINVSIWGTTLYPGSSITY-n
gi|387627094|ref|YP_006063270.1|:3-468 KIRECTGLAWEWWRTVYEKTDLPLVRKRTISIWGTTLYPQVEDK--v


Statistics on alignment.   Save alignment.

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Refine alignments

Sophisticated options are available for refining alignments:

Add your sequences to the alignment:
Members of the same: including
Include all superfamily members: , or just those assigned by the selected model:
Initial T99 seed sequence: NoYes

You may enter many sequences at once using
FASTA format:

Upload a multiple sequence FASTA file:




Model: 0042290 (list models)
Initial SAMT99 seed:
Alignment:



Display Options:
Output in FASTA-like format: NoYes
Output column indices: NoYes
Sequence index (number) on each line: NoYes

Max number of insertions shown: (0 does not show insertions)
Characters per line:
Character to show inserts:
Maximum number of sequences:
Exclude sequences shorter than: residues



Jump to [ Top of page · Alignments · Refine alignments ]

Add alignments from genomes

Select below additional genomes you would like to see alignments for, then click on 'Re-Submit'. The genome assignments will be added to this page.


Select to display   Genome
NoYes   Pseudanabaena sp. PCC 7367
NoYes   Nostoc sp. PCC 7120
NoYes   Gardnerella vaginalis 409-05
NoYes   Arcanobacterium haemolyticum DSM 20595
NoYes   Deinococcus deserti VCD115
NoYes   Clostridium lentocellum DSM 5427
NoYes   Clostridium novyi NT
NoYes   Clostridium tetani E88
NoYes   Clostridium perfringens ATCC 13124
NoYes   Streptococcus intermedius JTH08
NoYes   Streptococcus pseudopneumoniae IS7493
NoYes   Streptococcus dysgalactiae subsp. equisimilis GGS_124
NoYes   Streptococcus pyogenes str. Manfredo
NoYes   Streptococcus pneumoniae P1031
NoYes   Streptococcus suis P1/7
NoYes   Brevibacillus brevis NBRC 100599
NoYes   Listeria seeligeri serovar 1/2b str. SLCC3954
NoYes   Listeria monocytogenes serotype 4b str. CLIP 80459
NoYes   Listeria ivanovii subsp. ivanovii PAM 55
NoYes   Lysinibacillus sphaericus C3-41
NoYes   Bacillus weihenstephanensis KBAB4
NoYes   Bacillus thuringiensis str. Al Hakam
NoYes   Bacillus cereus 03BB102
NoYes   Bacillus anthracis str. A0248
NoYes   Haliscomenobacter hydrossis DSM 1100
NoYes   Niastella koreensis GR20-10
NoYes   Parabacteroides distasonis ATCC 8503
NoYes   Prevotella melaninogenica ATCC 25845
NoYes   Prevotella intermedia 17
NoYes   Bacteroides helcogenes P 36-108
NoYes   Bacteroides vulgatus ATCC 8482
NoYes   Bacteroides fragilis YCH46
NoYes   Owenweeksia hongkongensis DSM 17368
NoYes   Maribacter sp. HTCC2170
NoYes   Cellulophaga algicola DSM 14237
NoYes   Cellulophaga lytica DSM 7489
NoYes   Capnocytophaga canimorsus Cc5
NoYes   Capnocytophaga ochracea DSM 7271
NoYes   Flavobacterium psychrophilum JIP02/86
NoYes   Flavobacterium columnare ATCC 49512
NoYes   Desulfobulbus propionicus DSM 2032
NoYes   Rubrivivax gelatinosus IL144
NoYes   Gardnerella vaginalis HMP9231
NoYes   Gardnerella vaginalis ATCC 14019
NoYes   Clostridium tetani genome 12124569
NoYes   Clostridium perfringens str. 13
NoYes   Clostridium botulinum BKT015925
NoYes   Clostridium botulinum E3 str. Alaska E43
NoYes   Streptococcus intermedius B196
NoYes   Streptococcus intermedius C270
NoYes   Streptococcus dysgalactiae subsp. equisimilis 167
NoYes   Streptococcus dysgalactiae subsp. equisimilis AC-2713
NoYes   Streptococcus dysgalactiae subsp. equisimilis ATCC 12394
NoYes   Streptococcus dysgalactiae subsp. equisimilis RE378
NoYes   Streptococcus pyogenes HSC5
NoYes   Streptococcus pyogenes A20
NoYes   Streptococcus pyogenes MGAS1882
NoYes   Streptococcus pyogenes MGAS15252
NoYes   Streptococcus pyogenes Alab49
NoYes   Streptococcus pyogenes MGAS10750
NoYes   Streptococcus pyogenes MGAS10270
NoYes   Streptococcus pyogenes MGAS2096
NoYes   Streptococcus pyogenes MGAS9429
NoYes   Streptococcus pyogenes MGAS6180
NoYes   Clostridium botulinum B str. Eklund 17B
NoYes   Streptococcus pyogenes NZ131
NoYes   Streptococcus pyogenes MGAS8232
NoYes   Streptococcus pyogenes MGAS10394
NoYes   Streptococcus pyogenes MGAS315
NoYes   Streptococcus pyogenes SSI-1
NoYes   Streptococcus pyogenes M1 476
NoYes   Streptococcus pyogenes MGAS5005
NoYes   Streptococcus pyogenes M1 GAS
NoYes   Streptococcus pneumoniae A026
NoYes   Streptococcus pneumoniae ST556
NoYes   Streptococcus pneumoniae SPNA45
NoYes   Streptococcus pneumoniae SPN994039
NoYes   Streptococcus pneumoniae SPN994038
NoYes   Streptococcus pneumoniae SPN034183
NoYes   Streptococcus pneumoniae SPN034156
NoYes   Streptococcus pneumoniae INV104
NoYes   Streptococcus pneumoniae INV200
NoYes   Streptococcus pneumoniae OXC141
NoYes   Streptococcus pneumoniae gamPNI0373
NoYes   Streptococcus pneumoniae AP200
NoYes   Streptococcus pneumoniae ATCC 700669
NoYes   Streptococcus pneumoniae TCH8431/19A
NoYes   Streptococcus pneumoniae CGSP14
NoYes   Streptococcus pneumoniae G54
NoYes   Streptococcus pneumoniae JJA
NoYes   Streptococcus pneumoniae 70585
NoYes   Streptococcus pneumoniae Hungary19A-6
NoYes   Streptococcus pneumoniae Taiwan19F-14
NoYes   Streptococcus pneumoniae D39
NoYes   Streptococcus pneumoniae 670-6B
NoYes   Streptococcus pneumoniae R6
NoYes   Streptococcus pneumoniae TIGR4
NoYes   Streptococcus suis T15
NoYes   Streptococcus suis SC070731
NoYes   Streptococcus suis S735
NoYes   Streptococcus suis SS12
NoYes   Streptococcus suis ST1
NoYes   Streptococcus suis A7
NoYes   Streptococcus suis JS14
NoYes   Streptococcus suis BM407
NoYes   Streptococcus suis SC84
NoYes   Streptococcus suis GZ1
NoYes   Streptococcus suis 98HAH33
NoYes   Streptococcus suis 05ZYH33
NoYes   Listeria monocytogenes EGD sequence
NoYes   Listeria monocytogenes N53-1
NoYes   Listeria monocytogenes La111
NoYes   Listeria monocytogenes serotype 4b str. LL195
NoYes   Listeria monocytogenes 07PF0776
NoYes   Listeria monocytogenes M7
NoYes   Listeria monocytogenes J1-220
NoYes   Listeria monocytogenes J1816
NoYes   Listeria monocytogenes SLCC2376
NoYes   Listeria monocytogenes SLCC5850
NoYes   Listeria monocytogenes ATCC 19117
NoYes   Listeria monocytogenes L312
NoYes   Listeria monocytogenes SLCC2479
NoYes   Listeria monocytogenes SLCC7179
NoYes   Listeria monocytogenes SLCC2540
NoYes   Listeria monocytogenes SLCC2378
NoYes   Listeria monocytogenes serotype 1/2b str. SLCC2755
NoYes   Listeria monocytogenes serotype 1/2c str. SLCC2372
NoYes   Listeria monocytogenes serotype 7 str. SLCC2482
NoYes   Listeria monocytogenes 08-5578
NoYes   Listeria monocytogenes 08-5923
NoYes   Listeria monocytogenes L99
NoYes   Listeria monocytogenes HCC23
NoYes   Listeria monocytogenes 10403S
NoYes   Listeria monocytogenes J0161
NoYes   Listeria monocytogenes Finland 1998
NoYes   Listeria monocytogenes FSL R2-561
NoYes   Listeria monocytogenes serotype 4b str. F2365
NoYes   Listeria monocytogenes EGD-e
NoYes   Bacillus thuringiensis HD-771
NoYes   Bacillus thuringiensis HD-789
NoYes   Bacillus thuringiensis MC28
NoYes   Bacillus thuringiensis serovar chinensis CT-43
NoYes   Bacillus thuringiensis YBT-1518
NoYes   Bacillus thuringiensis Bt407
NoYes   Bacillus thuringiensis serovar konkukian str. 97-27
NoYes   Bacillus thuringiensis serovar kurstaki str. HD73
NoYes   Bacillus thuringiensis BMB171
NoYes   Bacillus thuringiensis serovar finitimus YBT-020
NoYes   Bacillus thuringiensis serovar thuringiensis str. IS5056
NoYes   Bacillus cereus FRI-35
NoYes   Bacillus cereus biovar anthracis str. CI
NoYes   Bacillus cereus AH820
NoYes   Bacillus cereus AH187
NoYes   Bacillus cereus B4264
NoYes   Bacillus cereus G9842
NoYes   Bacillus cereus Q1
NoYes   Bacillus cereus F837/76
NoYes   Bacillus cereus NC7401
NoYes   Bacillus cereus E33L
NoYes   Bacillus cereus ATCC 14579
NoYes   Bacillus cereus ATCC 10987
NoYes   Bacillus anthracis str. H9401
NoYes   Bacillus anthracis str. CDC 684
NoYes   Bacillus anthracis str. 'Ames Ancestor'
NoYes   Bacillus anthracis str. Sterne
NoYes   Bacillus anthracis str. Ames
NoYes   Enterobacter cloacae SCF1
NoYes   Combined (meta-genome)
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Dump top (Dump top) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 03(I) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 04(N) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 05(O) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 07(S) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 09(Y) (meta-genome)
NoYes   Macropus eugenii forestomach microbiome from Canberra, Australia, sample Macropus_eugenii_combined (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment combined (v2) (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methanol enrichment (meta-genome)
NoYes   Miscanthus field bulk soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Bulk soil sample from field growing Miscanthu (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (meta-genome)
NoYes   Sludge/US, Jazz Assembly (meta-genome)
NoYes   Sludge/US, Phrap Assembly (meta-genome)
NoYes   Soil microbial communities from Minnesota Farm (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 1 Maryland Estuary CO2- (Maryland Estuary ambient) (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 3 Nevada Test Site Creosote CO2- (meta-genome)
NoYes   Soil microbial community from bioreactor at Alameda Naval Air Station, CA, contaminated with Chloroethene, Sample 196 (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Switchgrass rhizosphere microbial community from Michigan, US, sample from East Lansing bulk soil (meta-genome)
NoYes   Uniprot 2018_03 genome
NoYes   Global Ocean Sampling Expedition (GOS)
NoYes   NCBI plasmid sequences (Plasmids)
NoYes   PDB chains (SCOP 1.75) (PDB)
NoYes   Protein Data Bank (all PDB sequenc)
NoYes   SCOP2 SCOPe CATH ECOD (all domain sequ)
NoYes   TargetDB (Targets)
NoYes   ALL (only advised for small superfamilies)


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