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.


AF2212/PG0164-like alignments

These alignments are sequences aligned to the 0052412 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       
                   |         |         |         |         |         |         |         |       
d2d9ra1 sp--IEFDAIIRQVPDMDAAYVEIPFDVKTVYGKGRVRVNATFDGYPYTGYIVRMGLPCHILGLRQDIRRAIGKQPGDSVYVTLL--pl


Statistics on alignment.   Save alignment.

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

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: 0052412 (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   Desulfitobacterium hafniense Y51
NoYes   Desulfitobacterium dehalogenans ATCC 51507
NoYes   Eubacterium limosum KIST612
NoYes   Clostridium phytofermentans ISDg
NoYes   Alkaliphilus oremlandii OhILAs
NoYes   Clostridium sp. BNL1100
NoYes   Porphyromonas gingivalis ATCC 33277
NoYes   Sphaerochaeta globus str. Buddy
NoYes   Mesotoga prima MesG1.Ag.4.2
NoYes   Desulfitobacterium dichloroeliminans LMG P-21439
NoYes   Desulfitobacterium hafniense DCB-2
NoYes   Porphyromonas gingivalis TDC60
NoYes   Porphyromonas gingivalis W83
NoYes   NCBI 2017_08 genome
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   STRING v9.0.5 (STRING)
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   TargetDB (Targets)
NoYes   ALL (only advised for small superfamilies)


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