SUPERFAMILY 1.75 HMM library and genome assignments server

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Leukocidin-like alignments

These alignments are sequences aligned to the 0042492 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      
                                                                         |         |         |      
d1pvla_ .......................................................a-QHITPVSEKKVDDKITLYKTTATSDSDKLKISQIL
d1t5ra_ .......................................................n--------IENIGDGAEVVKRTEDTSSDKWGVTQNI
d1uuna_ gldnelslvdgqdrtltvqqwdtflngvfpldrnrltrewfhsgrakyivagpgad------------------------------------
d3b07f_ .......................................................a----------------EIIKRTQDITSKRLAITQNI
d4i0na_ ...............................................sgeiikeng---------------KEAIKYTSSDTASHKGWKATL
d4tw1c_ .......................................................g--------------DTKMYTRTATTSDSQKNITQSL
d4tw1d_ ......................................................ta--------PDDIGKNGKITKRTETVYDEKTNILQNL
d7ahla_ ....................................................adsd--INIKTGTTDIGSNTTVKTGDLVTYDKENGMHKKV


          40        50        60        70         80        90        100       110       120      
           |         |         |         |          |         |          |         |         |      
d1pvla_ TFNFIKDKSYDKDTLILKAAGNIYSGYTKPNPKDTISS.QFYWGSKYNISINSDS.NDSVNVVDYAPKNQNEEFQVQQTVGYSYGGDINIS.
d1t5ra_ QFDFVKDKKYNKDALILKMQGFINSKTTYYNYKNTDHIkAMRWPFQYNIGLKTND.-PNVDLINYLPKNKIDSVNVSQTLGYNIGGNFN--.
d1uuna_ --------------------------------------.----------------.----------------E------------------.
d3b07f_ QFDFVKDKKYNKDALVVKMQGFISSRTTYSDLKKYPYIkRMIWPFQYNISLKTKD.-SNVDLINYLPKNKIDSADVSQKLGYNIGGNFQ--.
d4i0na_ SGTFIEDPHSDKKTALLNLEGFIPSDKQIFG--SKYYG.KMKWPETYRINVKSADvNNNIKIANSIPKNTIDKKDVSNSIGYSIGGNISVEg
d4tw1c_ QFNFLTEPNYDKETVFIKAKGTIGSGLRILDPNGYWNS.TLRWPGSYSVSIQNVDdNNNTNVTDFAPKNQDESREVKYTYGYKTGGDFSINr
d4tw1d_ QFDFIDDPTYDKNVLLVKKQGSIHSNLKFESHKEEKNSnWLKYPSEYHVDFQVKR.NRKTEILDQLPKNKISTAKVDSTFSYSSGGKFD--.
d7ahla_ FYSFIDDKNHNKKLLVIRTKGTIAGQYRVYSEEGANKS.GLAWPSAFKVQLQLPD.NEVAQISDYYPRNSIDTKEYMSTLTYGFNGNVTGD.


          130         140       150       160       170       180         190       200       210   
            |           |         |         |         |         |           |         |         |   
d1pvla_ NGLSGG..GNGSKSFSETINYKQESYRTSLDKRTNFKKIGWDVEAHKIMNNGWGPYGR..DSYHSTYGNEMFLGSRQSNLNAGQNFLEYHKM
d1t5ra_ SGPSTG..GNGSFNYSKTISYNQQNYISEVEHQNS-KSVQWGIKANSFITSLGK----..---MSGHDPNLFVGYKPYSQNPRDYFVPDNEL
d1uuna_ ------..--------------------------------------------------..--------------------------------
d3b07f_ SAPSIG..GSGSFNYSKTISYNQKNYVTEVESQNS-KGVKWGVKANSFVTPNGQ----..---VSAYDQYLFAQDPTGP-AARDYFVPDNQL
d4i0na_ KTAGAG..INASYNVQNTISYEQPDFRTIQRKDDA-NLASWDIKFVETK----DGYNI..DSYHAIYGNQLFMKSRLYN-NGDKNFTDDRDL
d4tw1c_ GGLTGN..ITKESNYSETISYQQPSYRTLLDQSTSHKGVGWKVEAHLINNMGHDHTRQltNDSDNRTKSEIFSLTRNGNLWAKDNFTPKDKM
d4tw1d_ STKGIG..RTSSNSYSKTISYNQQNYDTIASGKNNNWHVHWSVIANDLKYGG-EVKNR..NDELLFYRNTRIATVENPELS----FASKYRY
d7ahla_ DTGKIGglIGANVSIGHTLKYVQPDFKTILESPTD-KKVGWKVIFNNMVNQNWGPYDR..DSWNPVYGNQLFMKTRNGSMKAADNFLDPNKA


            220       230        240       250           260             270       280       290    
              |         |          |         |             |               |         |         |    
d1pvla_ PVLSRGNFNPEFIGVLSRK.QNAAKKSKITVTYQREMDRYTNFWN....QLHWIG......NNYKDENRATHTSIYEVDWENHTVKLIDTQS
d1t5ra_ PPLVHSGFNPSFIATVSHE.KGSGDTSEFEITYGRNMDVTHATRR....TTHYGNsylegsRIHNAFVNRNYTVKYEVNWKTHEIKVKGH--
d1uuna_ -------------------.-------------------------....------......-------------------------------
d3b07f_ PPLIQSGFNPSFITTLSHE.RGKGDKSEFEITYGRNMDATYAYVTr...HRLAVD......RKHDAFKNRNVTVKYEVNWKTHEVKIKS---
d4i0na_ STLISGGFSPNMALALTAP.K-NAKESVIIVEYQRFDNDYILNWE....TTQWRG......TNKLSSTSEYNEFMFKINWQDHKIEY-----
d4tw1c_ PVTVSEGFNPEFLAVMSHD.KKDKGKSQFVVHYKRSMDEFKIDWNrhgfWGYWSG......ENHVDKKEEKLSALYEVDWKTHNVKFVKVLN
d4tw1d_ PALVRSGFNPEFLTYLSNE.K-SNEKTQFEVTYTRNQDILKNRPG....IHYAPP......ILEKNKDGQRLIVTYEVDWKNKTVKVVDKYS
d7ahla_ SSLLSSGFSPDFATVITMDrKASKQQTNIDVIYERVRDDYQLHWT....STNWKG......TNTKDKWTDRSSERYKIDWEKEEMT------


           300                                                                                      
             |                                                                                      
d1pvla_ KEKNPM-s....................................................................................
d1t5ra_ -------n....................................................................................
d1uuna_ -------fegtlelgyqigfpwslgvginfsyttpniliddgditrppfglnsvitpnlfpgvsisadlgngpgiqevatfsvdvsgaeggv
d3b07f_ -------itpk.................................................................................
d4i0na_ -------yl...................................................................................
d4tw1c_ -------d....................................................................................
d4tw1d_ DDNKPY-ke...................................................................................
d7ahla_ -------n....................................................................................


                                                  
                                                  
d1pvla_ ..........................................
d1t5ra_ ..........................................
d1uuna_ avsnahgtvtgaaggvllrpfarliastgdsvttygepwnmn
d3b07f_ ..........................................
d4i0na_ ..........................................
d4tw1c_ ..........................................
d4tw1d_ ..........................................
d7ahla_ ..........................................


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: 0042492 (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



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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   Aspergillus zonatus v1.0
NoYes   Segniliparus rotundus DSM 44985
NoYes   Tsukamurella paurometabola DSM 20162
NoYes   Gordonia sp. KTR9
NoYes   Gordonia polyisoprenivorans VH2
NoYes   Gordonia bronchialis DSM 43247
NoYes   Rhodococcus jostii RHA1
NoYes   Rhodococcus equi 103S
NoYes   Rhodococcus opacus B4
NoYes   Rhodococcus erythropolis PR4
NoYes   Nocardia farcinica IFM 10152
NoYes   Mycobacterium massiliense str. GO 06
NoYes   Mycobacterium abscessus ATCC 19977
NoYes   Mycobacterium sp. JLS
NoYes   Mycobacterium intracellulare ATCC 13950
NoYes   Mycobacterium avium 104
NoYes   Mycobacterium vanbaalenii PYR-1
NoYes   Mycobacterium rhodesiae NBB3
NoYes   Mycobacterium ulcerans Agy99
NoYes   Mycobacterium gilvum PYR-GCK
NoYes   Mycobacterium chubuense NBB4
NoYes   Mycobacterium marinum M
NoYes   Mycobacterium smegmatis str. MC2 155
NoYes   Bacillus thuringiensis str. Al Hakam
NoYes   Bacillus cereus 03BB102
NoYes   Staphylococcus pseudintermedius HKU10-03
NoYes   Staphylococcus aureus subsp. aureus JH1
NoYes   Staphylococcus aureus
NoYes   Aeromonas salmonicida subsp. salmonicida A449
NoYes   Aeromonas hydrophila subsp. hydrophila ATCC 7966
NoYes   Vibrio sp. Ex25
NoYes   Vibrio parahaemolyticus RIMD 2210633
NoYes   Vibrio anguillarum 775
NoYes   Vibrio vulnificus MO6-24/O
NoYes   Vibrio cholerae O395
NoYes   Hahella chejuensis KCTC 2396
NoYes   Rhodococcus pyridinivorans SB3094
NoYes   Rhodococcus erythropolis CCM2595
NoYes   Nocardia brasiliensis ATCC 700358
NoYes   Mycobacterium sp. MOTT36Y
NoYes   Mycobacterium abscessus subsp. bolletii 50594
NoYes   Mycobacterium liflandii 128FXT
NoYes   Mycobacterium sp. KMS
NoYes   Mycobacterium sp. MCS
NoYes   Mycobacterium yongonense 05-1390
NoYes   Mycobacterium intracellulare MOTT-64
NoYes   Mycobacterium indicus pranii MTCC 9506
NoYes   Mycobacterium intracellulare MOTT-02
NoYes   Mycobacterium avium subsp. paratuberculosis MAP4
NoYes   Mycobacterium avium subsp. paratuberculosis K-10
NoYes   Mycobacterium gilvum Spyr1
NoYes   Mycobacterium smegmatis str. MC2 155
NoYes   Mycobacterium kansasii ATCC 12478
NoYes   Mycobacterium smegmatis JS623
NoYes   Corynebacterium terpenotabidum Y-11
NoYes   Clostridium botulinum BKT015925
NoYes   Clostridium botulinum Ba4 str. 657
NoYes   Bacillus cereus subsp. cytotoxis NVH 391-98
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 B4264
NoYes   Bacillus cereus G9842
NoYes   Bacillus cereus F837/76
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   Staphylococcus aureus subsp. aureus MSHR1132
NoYes   Staphylococcus pseudintermedius ED99
NoYes   Staphylococcus aureus CA-347
NoYes   Staphylococcus aureus Bmb9393
NoYes   Staphylococcus aureus M1
NoYes   Staphylococcus aureus 08BA02176
NoYes   Staphylococcus aureus ST228/18412
NoYes   Staphylococcus aureus ST228/18341
NoYes   Staphylococcus aureus ST228/16125
NoYes   Staphylococcus aureus ST228/16035
NoYes   Staphylococcus aureus ST228/15532
NoYes   Staphylococcus aureus ST228/10497
NoYes   Staphylococcus aureus ST228/10388
NoYes   Staphylococcus aureus 04-02981
NoYes   Staphylococcus aureus RF122
NoYes   Staphylococcus aureus subsp. aureus Z172
NoYes   Staphylococcus aureus subsp. aureus 6850
NoYes   Staphylococcus aureus subsp. aureus SA957
NoYes   Staphylococcus aureus subsp. aureus CN1
NoYes   Staphylococcus aureus subsp. aureus SA40
NoYes   Staphylococcus aureus subsp. aureus 11819-97
NoYes   Staphylococcus aureus subsp. aureus M013
NoYes   Staphylococcus aureus subsp. aureus HO 5096 0412
NoYes   Staphylococcus aureus subsp. aureus VC40
NoYes   Staphylococcus aureus subsp. aureus T0131
NoYes   Staphylococcus aureus subsp. aureus LGA251
NoYes   Staphylococcus aureus subsp. aureus ECT-R 2
NoYes   Staphylococcus aureus subsp. aureus JKD6159
NoYes   Staphylococcus aureus subsp. aureus ED133
NoYes   Staphylococcus aureus subsp. aureus ED98
NoYes   Staphylococcus aureus subsp. aureus TW20
NoYes   Staphylococcus aureus subsp. aureus 55/2053
NoYes   Staphylococcus aureus subsp. aureus TCH60
NoYes   Staphylococcus aureus subsp. aureus str. JKD6008
NoYes   Staphylococcus aureus subsp. aureus 71193
NoYes   Staphylococcus aureus subsp. aureus S0385
NoYes   Staphylococcus aureus subsp. aureus str. Newman
NoYes   Staphylococcus aureus subsp. aureus Mu3
NoYes   Staphylococcus aureus subsp. aureus USA300_TCH1516
NoYes   Staphylococcus aureus subsp. aureus USA300_FPR3757
NoYes   Staphylococcus aureus subsp. aureus JH9
NoYes   Staphylococcus aureus subsp. aureus MSSA476
NoYes   Staphylococcus aureus subsp. aureus MRSA252
NoYes   Staphylococcus aureus subsp. aureus MW2
NoYes   Staphylococcus aureus subsp. aureus N315
NoYes   Staphylococcus aureus subsp. aureus Mu50
NoYes   Staphylococcus aureus subsp. aureus COL
NoYes   Staphylococcus aureus subsp. aureus NCTC 8325
NoYes   Aeromonas hydrophila ML09-119
NoYes   Vibrio parahaemolyticus BB22OP
NoYes   Vibrio alginolyticus NBRC 15630 = ATCC 17749
NoYes   Vibrio anguillarum Listonella anguillarum M3
NoYes   Vibrio vulnificus CMCP6
NoYes   Vibrio vulnificus YJ016
NoYes   Vibrio cholerae LMA3984-4
NoYes   Vibrio cholerae M66-2
NoYes   Vibrio cholerae O395
NoYes   Vibrio cholerae IEC224
NoYes   Vibrio cholerae O1 str. 2010EL-1786
NoYes   Vibrio cholerae MJ-1236
NoYes   Vibrio cholerae O1 biovar El Tor str. N16961
NoYes   Activated sludge plasmid pool Morges-2009 (Newbler) (meta-genome)
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #2 (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   simLC - Simulated Low Complexity Metagenome (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 communities from sample at FACE Site 3 Nevada Test Site Creosote CO2- (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 5 Oak Ridge CO2+ (Oak Ridge elevated CO2) (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 5 Oak Ridge CO2- (Oak Ridge ambient) (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
NoYes   Global Ocean Sampling Expedition (GOS)
NoYes   NCBI plasmid sequences (Plasmids)
NoYes   NCBI viral sequences (Viral)
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   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)


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