SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from supfam.org. Please contact us if you experience any problems.

BLRF2-like alignments

These alignments are sequences aligned to the 0054351 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
                               |         |         |                 |         |         |         |
d2oa5a1             ..DKTYEEMVKEVERLKLENKTLKQKVKSSGAVS........SDDSILTAAKRESIIVSSSRALGAVAMRKIEAKVRSRA
FBpp0085929:146-199 dg-------------LRKENKTLKSQIQSMEGISailaagsaDADRLLKNEADPHVLANWVSTLK---------------


                            80        90        
                             |         |        
d2oa5a1             AKAVTEQELTSLLQSLTLRVDVSMEE..
FBpp0085929:146-199 --------------------------re


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: 0054351 (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   Sclerotinia sclerotiorum
NoYes   Aspergillus zonatus v1.0
NoYes   Anabaena variabilis ATCC 29413
NoYes   Streptococcus infantarius subsp. infantarius CJ18
NoYes   Bacillus clausii KSM-K16
NoYes   Candidatus Solibacter usitatus Ellin6076
NoYes   Sulfurovum sp. NBC37-1
NoYes   Pseudomonas sp. VLB120
NoYes   Streptococcus lutetiensis 033
NoYes   Streptococcus pneumoniae 70585
NoYes   Wolbachia endosymbiont of Drosophila melanogaster
NoYes   Wolbachia endosymbiont of Drosophila simulans wHa
NoYes   3_050719R (meta-genome)
NoYes   Dump top (Dump top) (meta-genome)
NoYes   Maize rhizosphere soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Soil sample from rhizosphere of corn (Zea mays))< (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   Soil microbial communities from sample at FACE Site 5 Oak Ridge CO2+ (Oak Ridge elevated CO2) (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   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)


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