SUPERFAMILY 1.75 HMM library and genome assignments server

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

LigT-like alignments

These alignments are sequences aligned to the 0052753 model.

Sophisticated options are available for refining alignments:

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


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 
                  |         |         |         |         |         |         |         |         | 

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

            190       200       210       220       230   
              |         |         |         |         |   

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: 0052753 (list models)
Initial SAMT99 seed:

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   Jannaschia sp. CCS1
NoYes   Roseobacter litoralis Och 149
NoYes   Roseobacter denitrificans OCh 114
NoYes   Methylobacterium sp. 4-46
NoYes   Genome sequence of Rhizobium sp. strain IRBG74
NoYes   Rhizobium etli CIAT 652
NoYes   Rhizobium leguminosarum bv. viciae 3841
NoYes   Agrobacterium tumefaciens str. C58
NoYes   Agrobacterium sp. H13-3
NoYes   Agrobacterium vitis S4
NoYes   Mesorhizobium opportunistum WSM2075
NoYes   Mesorhizobium loti MAFF303099
NoYes   Dickeya zeae Ech1591
NoYes   Pantoea ananatis LMG 20103
NoYes   Rhizobium etli CFN 42
NoYes   Rhizobium etli bv. mimosae str. Mim1
NoYes   Rhizobium leguminosarum bv. trifolii WSM2304
NoYes   Rhizobium leguminosarum bv. trifolii WSM1325
NoYes   Mesorhizobium australicum WSM2073
NoYes   Dickeya dadantii Ech586
NoYes   Dickeya dadantii 3937
NoYes   Pantoea ananatis LMG 5342
NoYes   Pantoea ananatis PA13
NoYes   Pantoea ananatis AJ13355
NoYes   NCBI 2017_08 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   Global Ocean Sampling Expedition (GOS)
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 ]