SUPERFAMILY 1.75 HMM library and genome assignments server

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

Inovirus (filamentous phage) major coat protein alignments

These alignments are sequences aligned to the 0053498 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       
                                       |         |         |         |       
ENSECAP00000006952:526-555 tls------------TEGSGNMAVIGGVAVGVLLLLVLAGI--------g

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: 0053498 (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   Dechlorosoma suillum PS
NoYes   Ralstonia solanacearum CFBP2957
NoYes   Acidovorax ebreus TPSY
NoYes   Herminiimonas arsenicoxydans
NoYes   Collimonas fungivorans Ter331
NoYes   Nitrosomonas europaea ATCC 19718
NoYes   Vibrio sp. Ex25
NoYes   Methylomonas methanica MC09
NoYes   Xylella fastidiosa M23
NoYes   Xanthomonas albilineans GPE PC73
NoYes   Pseudomonas aeruginosa UCBPP-PA14
NoYes   Ralstonia pickettii 12J
NoYes   Nitrosomonas sp. AL212
NoYes   Xylella fastidiosa Temecula1
NoYes   Xanthomonas campestris pv. vesicatoria str. 85-10
NoYes   Xanthomonas oryzae pv. oryzae MAFF 311018
NoYes   Xanthomonas campestris pv. raphani 756C
NoYes   Yersinia enterocolitica subsp. palearctica 105.5R(r)
NoYes   Escherichia coli UM146
NoYes   Pseudomonas aeruginosa SCV20265
NoYes   Pseudomonas aeruginosa MTB-1
NoYes   Pseudomonas aeruginosa PA7
NoYes   Pseudomonas aeruginosa PAO1
NoYes   Acinetobacter baumannii ATCC 19606
NoYes   3_050719R (meta-genome)
NoYes   Atta cephalotes fungus garden (ACEF) (meta-genome)
NoYes   Bath Hot Springs, planktonic community (meta-genome)
NoYes   Combined (meta-genome)
NoYes   Endophytic microbiome from Rice (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 top (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Sludge/US, Phrap Assembly (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   Uranium Contaminated Groundwater FW106 (meta-genome)
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 ]