SUPERFAMILY 1.75 HMM library and genome assignments server

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Cna protein B-type domain alignments

These alignments are sequences aligned to the 0036245 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   
                                                                 |         |         |          |   
d1d2oa1 ...............................................e-TTSSIGEKVWDDKDNQDGKRPEKVSVNLLANGEKV.KTLDVTS
d1d2oa2 ..............................................ge--TSATVTKNWDDNNNQDGKRPTEIKVELYQDGKATgKTAILNE
d1ti6b1 knyvtagilvqgdcfegakvvlksggkevasaetnffgefkfdaldng-----------------------EYTVEIDADGKSY.SDTVVID


             50        60        70         80        90        
              |         |         |          |         |        
d1d2oa1 ETNWKYEFKDLPKYDEGKKIEYTVTED.HVKDYTTDINGTTITNKYTP........
d1d2oa2 SNNWTHTWTGLDEKAKGQQVKYTVEELtKVKGYTTHVDNNDMGNL---ittnkytp
d1ti6b1 DKS------------------------.--------------------vdlgfikl


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: 0036245 (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   Atopobium parvulum DSM 20469
NoYes   Melissococcus plutonius DAT561
NoYes   Enterococcus faecium Aus0004
NoYes   Leuconostoc gasicomitatum LMG 18811
NoYes   Lactobacillus salivarius CECT 5713
NoYes   Streptococcus sp. I-P16
NoYes   Streptococcus sp. I-G2
NoYes   Streptococcus intermedius JTH08
NoYes   Streptococcus gallolyticus UCN34
NoYes   Streptococcus equi subsp. equi 4047
NoYes   Streptococcus parasanguinis ATCC 15912
NoYes   Streptococcus sanguinis SK36
NoYes   Clostridium sp. SY8519
NoYes   Melissococcus plutonius ATCC 35311
NoYes   Enterococcus casseliflavus EC20
NoYes   Enterococcus faecium Aus0085
NoYes   Enterococcus faecium NRRL B-2354
NoYes   Enterococcus faecium DO
NoYes   Leuconostoc gelidum JB7
NoYes   Lactobacillus casei str. Zhang
NoYes   Streptococcus intermedius B196
NoYes   Streptococcus anginosus C1051
NoYes   Streptococcus gallolyticus subsp. gallolyticus ATCC BAA-2069
NoYes   Streptococcus gallolyticus subsp. gallolyticus ATCC 43143
NoYes   Streptococcus equi subsp. zooepidemicus ATCC 35246
NoYes   Streptococcus equi subsp. zooepidemicus MGCS10565
NoYes   Streptococcus equi subsp. zooepidemicus
NoYes   Streptococcus parasanguinis FW213
NoYes   Staphylococcus aureus CA-347
NoYes   Staphylococcus aureus Bmb9393
NoYes   Staphylococcus aureus 08BA02176
NoYes   Staphylococcus aureus subsp. aureus Z172
NoYes   Staphylococcus aureus subsp. aureus 6850
NoYes   Staphylococcus aureus subsp. aureus HO 5096 0412
NoYes   Staphylococcus aureus subsp. aureus T0131
NoYes   Staphylococcus aureus subsp. aureus LGA251
NoYes   Staphylococcus aureus subsp. aureus TW20
NoYes   Staphylococcus aureus subsp. aureus 55/2053
NoYes   Staphylococcus aureus subsp. aureus TCH60
NoYes   Staphylococcus aureus subsp. aureus str. JKD6008
NoYes   Staphylococcus aureus subsp. aureus S0385
NoYes   Staphylococcus aureus subsp. aureus MSSA476
NoYes   Staphylococcus aureus subsp. aureus MRSA252
NoYes   Staphylococcus aureus subsp. aureus MW2
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Dump top (Dump top) (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden bottom (Fungus garden bottom) (meta-genome)
NoYes   Human Gut Community Subject 8 (meta-genome)
NoYes   Macropus eugenii forestomach microbiome from Canberra, Australia, sample Macropus_eugenii_combined (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
NoYes   NCBI plasmid sequences (Plasmids)
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)


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