SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from supfam.org. Please contact us if you experience any problems.

gp120 core alignments

These alignments are sequences aligned to the 0038012 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                                         
                            |         |         |         |                                         
d1g9mg_           .EVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVGAGS................................
A0A075VQQ6:68-505 a----LNVTESFDAWDNTVTEQAIEDVWNLFETSIKPCVKLTPLCIAMRCnktetdkwrltgtaptttttlttrttpdkvvn


                                                                                50        60        
                                                                                 |         |        
d1g9mg_           ...............................................................CNTSVITQACPKVSFEPIP
A0A075VQQ6:68-505 estlciknnscagleqepmvsctfnmtglkrdkkkeynetwysrdlvceqstngseskcymnhCNTSVIQESCDKHYWDAIR


                  70        80        90        100       110       120       130       140       15
                   |         |         |          |         |         |         |         |         
d1g9mg_           IHYCAPAGFAILKCNNKTFNGTGP.CTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSVNFTDNAKTIIVQLNTSVEIN
A0A075VQQ6:68-505 FRYCAPPGYALLRCNDSNYSGFAPnCSKVVVSSCTRMMETQTSTWFGFNGTRAENRTYIYWHG-KRNSTIISLNKYYNLTMR


                  0                                 160       170            180       190       200
                  |                                   |         |              |         |         |
d1g9mg_           CTGAGH..........................CNISRAKWNNTLKQIASKLREQFG.....NNKTIIFKQSSGGDPEIVTHS
A0A075VQQ6:68-505 CRRPGNktvlpvatmsgfffhlqqinerprqaWCRFGGSWREAIQEVKETIVKHPRytgtnDTKKINLTAPGGGDPEVTFMW


                         210       220         230       240       250       260       270       280
                           |         |           |         |         |         |         |         |
d1g9mg_           FNCGGEFFYCNSTQLFNSTWFNSTWS..TEGSNNTEGSDTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLT
A0A075VQQ6:68-505 TNCRGEFLYCKMNWFLNWVEDRNTSHprWKKQTPKEKHKRNYVPCHIRQIINTWHKVGKNVYLPPREGDLTCNSTVTSLIAT


                         290       300       310       
                           |         |         |       
d1g9mg_           RDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIE
A0A075VQQ6:68-505 MEWIDNDETNITM---GADVAELYRLELGDYKLVEI-


Statistics on alignment.   Save alignment.

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

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: 0038012 (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   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)


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