SUPERFAMILY 1.75 HMM library and genome assignments server

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L-A virus major coat protein alignments

These alignments are sequences aligned to the 0040728 model.

Sophisticated options are available for refining alignments:


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

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        40        50        60        70        80        90  
                 |         |         |         |         |         |         |         |         |  
d1m1ca_ MLRFVTKNSQDKSSDLFSICSDRGTFVAHNRVRTDFKFDNLVFNRVYGVSQKFTLVGNPTVCFNEGSSYLEGIAKKYLTLDGGLAIDNVLNE


             100       110       120       130       140       150       160       170       180    
               |         |         |         |         |         |         |         |         |    
d1m1ca_ LRSTCGIPGNAVASHAYNITSWRWYDNHVALLMNMLRAYHLQVLTEQGQYSAGDIPMYHDGHVKIKLPVTIDDTAGPTQFAWPSDRSTDSYP


           190       200       210       220       230       240       250       260       270      
             |         |         |         |         |         |         |         |         |      
d1m1ca_ DWAQFSESFPSIDVPYLDVRPLTVTEVNFVLMMMSKWHRRTNLAIDYEAPQLADKFAYRHALTVQDADEWIEGDRTDDQFRPPSSKVMLSAL


         280       290       300       310       320       330       340       350       360       3
           |         |         |         |         |         |         |         |         |        
d1m1ca_ RKYVNHNRLYNQFYTAAQLLAQIMMKPVPNCAEGYAWLMHDALVNIPKFGSIRGRYPFLLSGDAALIQATALEDWSAIMAKPELVFTYAMQV


        70       380       390       400       410       420       430       440       450       460
         |         |         |         |         |         |         |         |         |         |
d1m1ca_ SVALNTGLYLRRVKKTGFGTTIDDSYEDGAFLQPETFVQAALACCTGQDAPLNGMSDVYVTYPDLLEFDAVTQVPITVIEPAGYNIVDDHLV


               470       480       490       500       510       520       530       540       550  
                 |         |         |         |         |         |         |         |         |  
d1m1ca_ VVGVPVACSPYMIFPVAAFDTANPYCGNFVIKAANKYLRKGAVYDKLEAWKLAWALRVAGYDTHFKVYGDTHGLTKFYADNGDTWTHIPEFV


             560       570       580       590       600       610       620       630       640    
               |         |         |         |         |         |         |         |         |    
d1m1ca_ TDGDVMEVFVTAIERRARHFVELPRLNSPAFFRSVEVSTTIYDTHVQAGAHAVYHASRINLDYVKPVSTGIQVINAGELKNYWGSVRRTQQG


           650 
             | 
d1m1ca_ LGVVGLT


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: 0040728 (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   Penicillium marneffei ATCC 18224
NoYes   Candida parapsilosis
NoYes   Debaromyces hansenii
NoYes   Schizosaccharomyces pombe - Fission yeast
NoYes   Schizosaccharomyces pombe 972h-
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   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)


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