SUPERFAMILY 1.75 HMM library and genome assignments server

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gp120 core alignments

These alignments are sequences aligned to the 0053728 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        40                                 50      
                            |         |         |         |                                  |      
d2b4cg1           v-VLENVTEHFNMWKNDMVEQMQEDIISLWDQSLKPCVKLTPLCVGA.........................GSCDTSVITQ
A0A023JAR6:82-431 v--LENVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLncdkqkkeyalfykldivplneytlINCNTSAVTQ


                    60        70        80        90       100       110       120       130       1
                     |         |         |         |         |         |         |         |        
d2b4cg1           ACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTII
A0A023JAR6:82-431 ACPKVSFDPIPIHYCAPAGYAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEKEIIVRSENITNNVKTII


                  40       150       160       170       180       190       200       210       220
                   |         |         |         |         |         |         |         |         |
d2b4cg1           VQLKESVEINCTRPNQNTRKSIHIGPGRAFYTTGEIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDP
A0A023JAR6:82-431 VHLNESVEIKCIRPGNNTSRSIRIGPGQTFYATGRIVGDIRQAHCNISEEAWNKTLQRVSRKLAEHFPNKTIKFEPHSGGDL


                         230       240       250       260       270       280       290       300  
                           |         |         |         |         |         |         |         |  
d2b4cg1           EIVMHSFNCGGEFFYCNSAQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLT
A0A023JAR6:82-431 EITMHSFNCRGEFFYCNTSRLFNSTYSNN-----------ITLQCKLKQIIRRWQGVGQAMYAPPIEGNITCNSNITGLLLV


                       310       320       330         
                         |         |         |         
d2b4cg1           RDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIE
A0A023JAR6:82-431 RDGGTN--DTETFRPGGGDMRDNWRSELYKYKVVEIK


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: 0053728 (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



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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   NCBI 2017_08 genome
NoYes   Uniprot 2018_03 genome
NoYes   Global Ocean Sampling Expedition (GOS)
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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