SUPERFAMILY 1.75 HMM library and genome assignments server

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

Coronavirus S2 glycoprotein alignments

These alignments are sequences aligned to the 0053539 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  
                                               |         |         |         |         |         |  
WP_002810835.1.77844:40-105 ladrveevrd-------------------------TQIEAKEQFQSALEQFSSVVNYDGGDLEDLYEELNGE

                                  70        80        90       100       110       120        
                                   |         |         |         |         |         |        
WP_002810835.1.77844:40-105 YQASQKKAEAVHDRIASV-----------------------------------------------e

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: 0053539 (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   Ictidomys tridecemlineatus 76_2 - Thirteen-lined ground squirrel
NoYes   Aspergillus acidus v1.0
NoYes   Aspergillus tubingensis v1.0
NoYes   Nocardia farcinica IFM 10152
NoYes   Desulfotalea psychrophila LSv54
NoYes   Shewanella piezotolerans WP3
NoYes   Shewanella loihica PV-4
NoYes   Shewanella halifaxensis HAW-EB4
NoYes   Shewanella sediminis HAW-EB3
NoYes   Shewanella pealeana ATCC 700345
NoYes   Shewanella oneidensis MR-1
NoYes   Shewanella baltica OS185
NoYes   Shewanella woodyi ATCC 51908
NoYes   Shewanella sp. MR-4
NoYes   Shewanella amazonensis SB2B
NoYes   Shewanella violacea DSS12
NoYes   Glaciecola nitratireducens FR1064
NoYes   Nitrosococcus watsonii C-113
NoYes   Nitrosococcus oceani ATCC 19707
NoYes   Bacillus thuringiensis MC28
NoYes   Desulfovibrio desulfuricans ND132
NoYes   Shewanella baltica BA175
NoYes   Shewanella baltica OS117
NoYes   Shewanella baltica OS223
NoYes   Shewanella baltica OS155
NoYes   Glaciecola psychrophila 170
NoYes   Ictidomys tridecemlineatus 69_2 - Thirteen-lined ground squirrel
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP7 from Chocolate Pots (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   simLC - Simulated Low Complexity Metagenome (meta-genome)
NoYes   Soil microbial communities from Minnesota Farm (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Termite Protist Endosymbiont Community (meta-genome)
NoYes   Uniprot 2018_03 genome
NoYes   Global Ocean Sampling Expedition (GOS)
NoYes   NCBI plasmid sequences (Plasmids)
NoYes   NCBI viral sequences (Viral)
NoYes   PDB chains (SCOP 1.75) (PDB)
NoYes   Protein Data Bank (all PDB sequenc)
NoYes   SCOP2 SCOPe CATH ECOD (all domain sequ)
NoYes   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)

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