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.


PMT central region-like alignments

These alignments are sequences aligned to the 0053875 model.

Sophisticated options are available for refining alignments:


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

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        80        90
                   |         |         |         |         |         |         |         |         |
d2ebfx1 lg--GSPYSPFRIGLEGVWTPEVLKARASVIGKPIGESYKRILAKLQRIHNSNILDERQGLMHELMELIDLYEESQPSSERLNAFRELRTQL


               100       110       120       130       140       150       160       170       180  
                 |         |         |         |         |         |         |         |         |  
d2ebfx1 EKALYLPEMEALKKQILQIPNKGSGAARFLLRTAMNEMAGKTSESTADLIRFALQDTVISAPFRGYAGAIPEAIDFPVKYVIEDISVFDKIQ


             190       200       210       220       230       240       250       260       270    
               |         |         |         |         |         |         |         |         |    
d2ebfx1 TNYWELPAYESWNEGSNSALLPGLLRESQSKGMLSKCRIIENSLYIGHSYEEMFYSISPYSNQVGGPYELYPFTFFSMLQEVQGDLGFEQAF


           280       290       300  
             |         |         |  
d2ebfx1 ATRNFFNTLVSDRLSLMENTMLLT--es


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: 0053875 (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   Pasteurella multocida subsp. multocida str. HN06
NoYes   NCBI 2017_08 genome
NoYes   Uniprot 2018_03 genome
NoYes   PDB chains (SCOP 1.75) (PDB)
NoYes   Protein Data Bank (all PDB sequenc)
NoYes   SCOP2 SCOPe CATH ECOD (all domain sequ)
NoYes   ALL (only advised for small superfamilies)


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