SUPERFAMILY 1.75 HMM library and genome assignments server

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Variable surface antigen VlsE alignments

These alignments are sequences aligned to the 0040421 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        70     
                                  |         |         |         |         |         |         |     
d1l8wd_              ....KFYQSVIQLGNGFLDVFTSFGGLVAEAFGFKSDPKKSDVKTYFTTVAAKLEKTKTDLNSLPKEKSDISSTTGKPD
JGI_V11_91744:15-117 annt---------------------------------------------------------------------------


                        80        90       100       110       120       130       140       150    
                         |         |         |         |         |         |         |         |    
d1l8wd_              STGSVGTAVEGAIKEVSELLDKLVKAVKTAEGASSGTAAIGEVVADADAAKVADKASVKGIAKGIKEIVEAAGGSEKLK
JGI_V11_91744:15-117 ---ITSNKTKSVFDTPSTVIGPLFGSSSSSSSHSAGSKKNGSSLTEARGGGGDDKRKVESE----DEVVEVIEKY----


                        160       170       180       190       200       210       220       230   
                          |         |         |         |         |         |         |         |   
d1l8wd_              AVAAAKGENNKGAGKLFGKAGAAAHGDSEAASKAAGAVSAVSGEQILSAIVTAADAAEQDGKKPEEAKNPIAAAIGDKD
JGI_V11_91744:15-117 ----EEGQAEKGGGALVADSKNDTGGAAVAA------------------------------------------------


                         240       250       260       270       280       290       300       310  
                           |         |         |         |         |         |         |         |  
d1l8wd_              GGAEFGQDEMKKDDQIAAAIALRGMAKDGKFAVKDGEKEKAEGAIKGAAESAVRKVLGAITGLIGDAVSSGLRKVGDSV
JGI_V11_91744:15-117 -------------------------------------------------------------------------------


                          320      
                            |      
d1l8wd_              KAASKET---ppa.
JGI_V11_91744:15-117 ----------nnss


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: 0040421 (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   Borrelia afzelii PKo
NoYes   Borrelia burgdorferi B31
NoYes   Borrelia recurrentis A1
NoYes   Borrelia duttonii Ly
NoYes   Borrelia crocidurae str. Achema
NoYes   Borrelia hermsii DAH
NoYes   Halalkalicoccus jeotgali B3
NoYes   Lactococcus lactis subsp. lactis KLDS 4.0325
NoYes   Lactococcus lactis subsp. lactis Il1403
NoYes   Lactococcus lactis subsp. cremoris A76
NoYes   Borrelia valaisiana VS116
NoYes   Borrelia afzelii PKo
NoYes   Borrelia burgdorferi JD1
NoYes   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (meta-genome)
NoYes   Sludge/Australian, Phrap Assembly (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
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   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)


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