SUPERFAMILY 1.75 HMM library and genome assignments server

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Influenza hemagglutinin (stalk) alignments

These alignments are sequences aligned to the 0053413 model.

Sophisticated options are available for refining alignments:


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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 
                                                                              |         |         | 
d1flcf_                              ................................IDDLIIGVLFVAIVETGIGGYLLGSRKESGG
dx6_gi|384434916|ref|YP_005644274.1| eyaeknkkevidyvdktkkemldyvdkrfeai-------------------------------


                                            40        50        60        70        80        90    
                                             |         |         |         |         |         |    
d1flcf_                              GVTKESAEKGFEKIGNDIQILKSSINIAIEKLNDRISHDEQAIRDLTLEIENARSEALLGELG
dx6_gi|384434916|ref|YP_005644274.1| --------------DKRFEAID----KRFDDLNNRI---------------------------


                                        100       110       120       130       140       150       
                                          |         |         |         |         |         |       
d1flcf_                              IIRALLVGNISIGLQESLWELASEITNRAGDLAVEVSPGCWIIDNNICDQSCQNFIFKFNETA
dx6_gi|384434916|ref|YP_005644274.1| ---------------------------------------------------------------


                                     160         
                                       |         
d1flcf_                              PVPTI.......
dx6_gi|384434916|ref|YP_005644274.1| -----ddlreli


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: 0053413 (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   Astyanax mexicanus 76 - Mexican tetra
NoYes   Acromyrmex echinatior v3.8 - Panamanian leafcutter ant
NoYes   Caenorhabditis brenneri
NoYes   Volvox carteri f. nagariensis
NoYes   Synechococcus sp. PCC 6312
NoYes   Microcystis aeruginosa NIES-843
NoYes   Tepidanaerobacter acetatoxydans Re1
NoYes   Bacillus weihenstephanensis KBAB4
NoYes   Bacillus thuringiensis str. Al Hakam
NoYes   Bacillus cereus 03BB102
NoYes   Bacillus anthracis str. A0248
NoYes   Polaribacter sp. MED152
NoYes   Desulfurispirillum indicum S5
NoYes   Aquifex aeolicus VF5
NoYes   Babela massiliensis
NoYes   Nitrosomonas europaea ATCC 19718
NoYes   Methylomicrobium alcaliphilum
NoYes   Nitrosococcus halophilus Nc4
NoYes   Pantoea sp. At-9b
NoYes   Sulfolobus solfataricus P2
NoYes   Histoplasma capsulatum H88
NoYes   Chroococcidiopsis thermalis PCC 7203
NoYes   Chamaesiphon minutus PCC 6605
NoYes   Lactobacillus johnsonii NCC 533
NoYes   Bacillus toyonensis BCT-7112
NoYes   Bacillus thuringiensis HD-771
NoYes   Bacillus thuringiensis HD-789
NoYes   Bacillus thuringiensis MC28
NoYes   Bacillus thuringiensis serovar chinensis CT-43
NoYes   Bacillus thuringiensis YBT-1518
NoYes   Bacillus thuringiensis Bt407
NoYes   Bacillus thuringiensis serovar konkukian str. 97-27
NoYes   Bacillus thuringiensis serovar kurstaki str. HD73
NoYes   Bacillus thuringiensis BMB171
NoYes   Bacillus thuringiensis serovar finitimus YBT-020
NoYes   Bacillus thuringiensis serovar thuringiensis str. IS5056
NoYes   Bacillus cereus FRI-35
NoYes   Bacillus cereus biovar anthracis str. CI
NoYes   Bacillus cereus AH820
NoYes   Bacillus cereus AH187
NoYes   Bacillus cereus B4264
NoYes   Bacillus cereus G9842
NoYes   Bacillus cereus Q1
NoYes   Bacillus cereus F837/76
NoYes   Bacillus cereus NC7401
NoYes   Bacillus cereus E33L
NoYes   Bacillus cereus ATCC 14579
NoYes   Bacillus cereus ATCC 10987
NoYes   Bacillus anthracis str. H9401
NoYes   Bacillus anthracis str. CDC 684
NoYes   Bacillus anthracis str. 'Ames Ancestor'
NoYes   Bacillus anthracis str. Sterne
NoYes   Bacillus anthracis str. Ames
NoYes   Bacteroides xylanisolvens XB1A
NoYes   Candidatus Nitrososphaera gargensis Ga9.2
NoYes   Sulfolobus solfataricus 98/2
NoYes   Methanomethylovorans hollandica DSM 15978
NoYes   1_050719N (meta-genome)
NoYes   2_050719S (meta-genome)
NoYes   4_050719Q (meta-genome)
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Dump bottom (Dump bottom) (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   Freshwater propionate enrichment of Brocadia fulgida (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden top (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP11 from Octopus Springs (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP13 from Bechler Spring (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP15 from Mushroom Spring (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP18 from Washburn Springs #1 (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP5 from Bath Lake Vista Annex (meta-genome)
NoYes   Marine anammox bioreactor enriched for Scalindua species (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (meta-genome)
NoYes   Soil microbial communities from Minnesota Farm (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 1 Maryland Estuary CO2- (Maryland Estuary ambient) (meta-genome)
NoYes   STRING v9.0.5 (STRING)
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   TargetDB (Targets)
NoYes   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)


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