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.


Galactose-binding domain-like alignments

These alignments are sequences aligned to the 0054314 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 
                  |         |         |         |         |         |         |         |         | 
d2o14a1 k-VYQFDFGSGSMEPGYIGVRASDRYDRSKGYGFQTPENMRDVAASGAGVKSDAVEFLAYGTKSNNTFNVDLPNGLYEVKVTLGNTARASVA


              100       110       120       130       140       
                |         |         |         |         |       
d2o14a1 AEGVFQVINMTGDGAEDTFQIPVTDGQLNLLVTEGKAGTAFTLSALKIKKLSDQ-p


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: 0054314 (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   Arthrobacter chlorophenolicus A6
NoYes   Clostridium clariflavum DSM 19732
NoYes   Clostridium thermocellum ATCC 27405
NoYes   Ruminococcus albus 7
NoYes   Paenibacillus terrae HPL-003
NoYes   Paenibacillus mucilaginosus 3016
NoYes   Paenibacillus polymyxa M1
NoYes   Bacillus sp. JS
NoYes   Bacillus atrophaeus 1942
NoYes   Bacillus subtilis subsp. subtilis str. 168
NoYes   Clostridium thermocellum DSM 1313
NoYes   Ruminococcus champanellensis 18P13
NoYes   Paenibacillus mucilaginosus KNP414
NoYes   Paenibacillus mucilaginosus K02
NoYes   Paenibacillus polymyxa CR1
NoYes   Paenibacillus polymyxa SC2
NoYes   Paenibacillus polymyxa E681
NoYes   Bacillus subtilis PY79
NoYes   Bacillus subtilis XF-1
NoYes   Bacillus subtilis QB928
NoYes   Bacillus subtilis BSn5
NoYes   Bacillus subtilis subsp. subtilis str. BAB-1
NoYes   Bacillus subtilis subsp. subtilis str. BSP1
NoYes   Bacillus subtilis subsp. subtilis str. RO-NN-1
NoYes   Bacillus subtilis subsp. subtilis 6051-HGW
NoYes   Bacillus subtilis subsp. spizizenii TU-B-10
NoYes   Bacillus subtilis subsp. spizizenii str. W23
NoYes   Bacillus subtilis subsp. natto BEST195
NoYes   NCBI 2017_08 genome
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 3 Nevada Test Site Creosote CO2- (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 ]