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.


HAD-like alignments

These alignments are sequences aligned to the 0051058 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        80        90  
                 |         |         |         |         |         |         |         |         |  
d1xpja_ MKKLIVDLDGTLTQANTSDYRNVLPRLDVIEQLREYHQLGFEIVISTARNMRTYEGNVGKINIHTLPIITEWLDKHQVPYDEILVGKPWCGH


             100       110       120                
               |         |         |                
d1xpja_ DGFYIDDRAVRPSEFASMNL------------eeihqlfekeks


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: 0051058 (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   Campylobacter jejuni subsp. doylei 269.97
NoYes   Ralstonia eutropha JMP134
NoYes   Ramlibacter tataouinensis TTB310
NoYes   Phenylobacterium zucineum HLK1
NoYes   Acetobacter pasteurianus IFO 3283-01
NoYes   Vibrio fischeri MJ11
NoYes   Vibrio cholerae O395
NoYes   Shewanella sp. MR-4
NoYes   Shewanella amazonensis SB2B
NoYes   Alteromonas sp. SN2
NoYes   Frateuria aurantia DSM 6220
NoYes   Campylobacter jejuni subsp. jejuni PT14
NoYes   Campylobacter jejuni subsp. jejuni IA3902
NoYes   Variovorax paradoxus B4
NoYes   Zymomonas mobilis subsp. mobilis ATCC 29191
NoYes   Zymomonas mobilis subsp. mobilis ZM4
NoYes   Acetobacter pasteurianus IFO 3283-12
NoYes   Acetobacter pasteurianus IFO 3283-01-42C
NoYes   Acetobacter pasteurianus IFO 3283-32
NoYes   Acetobacter pasteurianus IFO 3283-26
NoYes   Acetobacter pasteurianus IFO 3283-22
NoYes   Acetobacter pasteurianus IFO 3283-07
NoYes   Acetobacter pasteurianus IFO 3283-03
NoYes   Bibersteinia trehalosi USDA-ARS-USMARC-192
NoYes   Actinobacillus suis H91-0380
NoYes   Vibrio cholerae LMA3984-4
NoYes   Vibrio cholerae M66-2
NoYes   Vibrio cholerae O395
NoYes   Vibrio cholerae IEC224
NoYes   Vibrio cholerae O1 str. 2010EL-1786
NoYes   Vibrio cholerae MJ-1236
NoYes   Vibrio cholerae O1 biovar El Tor str. N16961
NoYes   Shewanella sp. ANA-3
NoYes   Thalassolituus oleivorans MIL-1
NoYes   Escherichia coli APEC O78
NoYes   Escherichia coli UMN026
NoYes   Escherichia coli ETEC H10407
NoYes   Air microbial communities Singapore indoor air filters 2 (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #3 (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden bottom (Fungus garden bottom) (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   STRING v9.0.5 (STRING)
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 ]