SUPERFAMILY 1.75 HMM library and genome assignments server

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Retroviral matrix proteins alignments

These alignments are sequences aligned to the 0039783 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        70   
                                    |         |         |         |         |         |         |   
EG:BRADI2G45870.2:406-456 v------------------------------------------------------HSTPIPPKDQKYSQVPQRI

                               80        90       100       110       120       130               
                                |         |         |         |         |         |               
EG:BRADI2G45870.2:406-456 PTGRPGRVVGPV---------------------IPFENSSTMDP--------------------ysqrrvar

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: 0039783 (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   Homo sapiens 76_38 - Human
NoYes   Pan troglodytes 76_2.1.4 - Chimpanzee
NoYes   Gorilla gorilla 76_3.1 - Western gorilla
NoYes   Pongo abelii 76_2 - Sumatran orangutan
NoYes   Nomascus leucogenys 76_1.0 - Northern white-cheeked gibbon
NoYes   Cavia porcellus 76_3 - Domestic guinea pig
NoYes   Oryctolagus cuniculus 76_2 - Rabbit
NoYes   Sus scrofa 76_10.2 - Pig
NoYes   Ovis aries 76_3.1 - Sheep
NoYes   Mustela putorius furo 76_1.0 - Domestic ferret
NoYes   Felis catus 76_6.2 - Domestic cat
NoYes   Dasypus novemcinctus 76_2 - Nine-banded armadillo
NoYes   Sarcophilus harrisii 76_7.0 - Tasmanian devil
NoYes   Anolis carolinensis 76_2.0 - Green anole
NoYes   Brugia malayi WS250 - Agent of lymphatic filariasis
NoYes   Trypanosoma congolense 2.4
NoYes   Theobroma cacao Matina 1-6 v0.9 - Cacao
NoYes   Homo sapiens 69_37 - Human
NoYes   Pan troglodytes 69_2.1.4 - Chimpanzee
NoYes   Gorilla gorilla 69_3.1 - Western gorilla
NoYes   Pongo abelii 69_2 - Sumatran orangutan
NoYes   Cavia porcellus 69_3 - Domestic guinea pig
NoYes   Sus scrofa 69_10.2 - Pig
NoYes   Mustela putorius furo 69_1.0 - Domestic ferret
NoYes   Sarcophilus harrisii 69_7.0 - Tasmanian devil
NoYes   Anolis carolinensis 69_2.0 - Green anole
NoYes   Homo sapiens 75_37 - Human
NoYes   Homo sapiens - Human
NoYes   NCBI 2017_08 genome
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
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   TargetDB (Targets)
NoYes   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)

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