SUPERFAMILY 1.75 HMM library and genome assignments server

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Clostridium neurotoxins, "coiled-coil" domain alignments

These alignments are sequences aligned to the 0053509 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        
                                                   |         |         |         |         |        
d1s0ba4                 .................n-TIFQYLYSQTFPLDIRDISLTSSFDDALLFSNKVYSFFSMDYIKTANKVVEAGLFAG
jCVI|EIN_044600:109-174 qntqldaakknmksglsk----------------------------------------------------------


                        60        70        80        90       100       110       120       130    
                         |         |         |         |         |         |         |         |    
d1s0ba4                 WVKQIVNDFVIEANKSNTMDKIADISLIVPYIGLALNVGNETAKGNFENAFEIAGASILLEFIPELLIPVVGAFLL
jCVI|EIN_044600:109-174 ----------------------------------------------------------------------------


                           140       150       160       170       180       190       200       210
                             |         |         |         |         |         |         |         |
d1s0ba4                 ESYIDNKNKIIKTIDNALTKRNEKWSDMYGLIVAQWLSTVNTQFYTIKEGMYKALNYQAQALEEIIKYRYNIYSEK
jCVI|EIN_044600:109-174 ---------------------------------------------------TQTLNAQVSSLKVQVSAPASVAQEE


                               220       230       240       250       260       270       280      
                                 |         |         |         |         |         |         |      
d1s0ba4                 EKSNINIDFNDINSKLNEGINQAIDNINNFINGCSVSYLMKKMIPLAVEKLLDFDNTLKKNLLNYIDENKLYLIGS
jCVI|EIN_044600:109-174 EKNMLNARIAEIQAQLDEERQKA-----------------------------------------------------


                         290       300       310       320         
                           |         |         |         |         
d1s0ba4                 AEYEKSKVNKYLKTIMPFDLSIYTNDTILIEMFNKYNSEIL-n
jCVI|EIN_044600:109-174 ------------------------------------------.


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: 0053509 (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   Clostridium tetani E88
NoYes   Clostridium botulinum A str. ATCC 3502
NoYes   Clostridium tetani genome 12124569
NoYes   Clostridium botulinum H04402 065
NoYes   Clostridium botulinum BKT015925
NoYes   Clostridium botulinum F str. 230613
NoYes   Clostridium botulinum F str. Langeland
NoYes   Clostridium botulinum E3 str. Alaska E43
NoYes   Clostridium botulinum B1 str. Okra
NoYes   Clostridium botulinum Ba4 str. 657
NoYes   Clostridium botulinum A2 str. Kyoto
NoYes   Clostridium botulinum A3 str. Loch Maree
NoYes   Clostridium botulinum A str. Hall
NoYes   Clostridium botulinum A str. ATCC 19397
NoYes   Clostridium botulinum B str. Eklund 17B
NoYes   Mouse Gut Community lean1 (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (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   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)


Jump to [ Top of page · Alignments · Refine alignments · Add alignments from genomes ]