SUPERFAMILY 1.75 HMM library and genome assignments server

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Apolipophorin-III alignments

These alignments are sequences aligned to the 0037127 model.

Sophisticated options are available for refining alignments:

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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       100       110   
                                              |         |         |         |         |         |   
POPTR_0001s14820.1|PACid:18234441:7-77 QLQQVNSQMQAWVS-----------------------------------------------

                                           120       130       140       150       160           
                                             |         |         |         |         |           
POPTR_0001s14820.1|PACid:18234441:7-77 -----------------------------------------------------sggse

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: 0037127 (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

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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   Danaus plexippus OGS1.0 - Monarch butterfly
NoYes   Heliconius melpomene - Postman butterfly
NoYes   Bombyx mori - Domestic silkworm
NoYes   Nasonia vitripennis - Jewel wasp
NoYes   Apis mellifera 38.2d - Honey bee
NoYes   Linepithema humile v1.1 - Argentine ant
NoYes   Pogonomyrmex barbatus v1.2 - Red harvester ant
NoYes   Solenopsis invicta v.2.2.3 - Red fire ant
NoYes   Acromyrmex echinatior v3.8 - Panamanian leafcutter ant
NoYes   Atta cephalotes v1.1
NoYes   Drosophila suzukii
NoYes   Drosophila simulans 1.3
NoYes   Drosophila sechellia 1.3
NoYes   Drosophila melanogaster 76_5 - Fruit fly
NoYes   Megaselia scalaris 22
NoYes   Aedes aegypti 55 - Yellow fever mosquito
NoYes   Anopheles darlingi 22 - American malaria mosquito
NoYes   Pediculus humanus corporis - Human body louse
NoYes   Acropora digitifera v1.0
NoYes   Trichoplax adhaerens
NoYes   Tetrahymena thermophila SB210 1
NoYes   Clostridium clariflavum DSM 19732
NoYes   Tepidanaerobacter acetatoxydans Re1
NoYes   Marinobacter adhaerens HP15
NoYes   Marinobacter hydrocarbonoclasticus ATCC 49840
NoYes   Marinobacter aquaeolei VT8
NoYes   Acidianus hospitalis W1
NoYes   Drosophila melanogaster FlyBase 5.12 - Fruit fly
NoYes   Anopheles gambiae VectorBase AgamP3.6 - African malaria mosquito
NoYes   Crinalium epipsammum PCC 9333
NoYes   Cyanothece sp. PCC 7822
NoYes   Mycoplasma ovis str. Michigan
NoYes   Streptomyces venezuelae ATCC 10712
NoYes   Amphibacillus xylanus NBRC 15112
NoYes   Candidatus Liberibacter solanacearum CLso-ZC1
NoYes   Drosophila melanogaster 69_5 - Fruit fly
NoYes   Heliconius numata
NoYes   1_050719N (meta-genome)
NoYes   Bath Hot Springs, planktonic community (meta-genome)
NoYes   Endophytic microbiome from Rice (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP1 from Alice Springs, Crater Hills (meta-genome)
NoYes   Macropus eugenii forestomach microbiome from Canberra, Australia, sample Macropus_eugenii_combined (meta-genome)
NoYes   Mountain Pine Beetle microbial communities from Grand Prairie, Alberta, sample from Hybrid pine (MPB hybrid beetle) (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (meta-genome)
NoYes   simLC - Simulated Low 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   Wastewater Terephthalate-degrading communities from Bioreactor (meta-genome)
NoYes   Global Ocean Sampling Expedition (GOS)
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)

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