SUPERFAMILY 1.75 HMM library and genome assignments server

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Retrovirus capsid protein, N-terminal core domain alignments

These alignments are sequences aligned to the 0037867 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.

                                                                                                    
                                                                                                    
d1g03a_ ............................................................................................
d1l6na2 nypivqnlqgqmvhqaisprtlnawvkvveekafspevipmfsalse.............................................
d1p7na_ gptspgpaltdwarvreelastgppvvampvviktegpawtplepk..............................................
d1u7ka_ plrmggngqlqywpfsssdlynwknnnpsfsedpgklta.....................................................
d2eiaa2 prgyttwvntiqtngllneasqnlfgilsvdctseemnafldvvpgqagqkqilldaidkiaddwdnrhplpnaplvappqgpipmtarfir
d2xgva_ pvvnrgqgwayepmstrtvaawirqtgekgltspetitywglisqdlssreqvqllevvpglqadkdmlgayleera...............
d2xgya_ pimlrggrqeyepvgpgliaawlkqvqehglthpatityfgvisinftsvdinmllnvtpgfaaekqlvidkikekaiawdemhppppadaa
d4htwa_ pvqqi.......................................................................................


                                           10        20        30        40        50        60     
                                            |         |         |         |         |         |     
d1g03a_ ...........................PVMHPHGAPPNHRPWQMKDLQAIKQEVSQAAPGSPQFMQTIRLAVQQFDPTAKDLQDLLQYLCSS
d1l6na2 ...........................------------------------------------------------GATPQDLNTMLNTVGG-
d1p7na_ ...........................-------------------------------------------------------------LITR
d1u7ka_ ...........................---------------------------------------LIESVLTTHQPTWDDCQQLLGTLLTG
d2eiaa2 ...................glgvprer-----------------------------------------------------------------
d2xgva_ ...........................------------R----------------------------------------------------
d2xgya_ gpvpltsdqirgiglspeeaagprfad-------ARTLYRTWVLEALQ--------------------------------------------
d4htwa_ ...........................------GGNYVHLPLSPRTLNAWVKLIEEKKFGAEVVPG---FQALSEGCTPYDINQMLNCVGD-


           70        80        90       100       110       120       130                           
            |         |         |         |         |         |         |                           
d1g03a_ LVASLHHQQLDSLISEAETRGITSYNPLAGPLRVQANNPQQQGLRREYQQLWLAAFAALPGSAKDPSWA.......................
d1l6na2 ---------------------------------------------------------------------hqaamqmlketineeaaewdrlh
d1p7na_ LADTVRTKGLRSPITMAEVEAL-----------------------------------------------msspllphdvtnlmrvilgpapy
d1u7ka_ ---------------------------------------------------------------------eekqrvllearkavrgndgrptq
d2eiaa2 -----------------------------------QMEPAFDQFRQTYRQWIIE---------------amsegikvmigk...........
d2xgva_ ---------------------------------------------------------------------ewdaqpqqplpytsahirgltgd
d2xgya_ ---------------------------------------------------------------------ecqr...................
d4htwa_ --HQAAMQIIRDIINEE---------AADWDLQHPQPAPQQGQLRE-----------------------psgsdiagttssvdeqiqwmyrq


                                                                                         
                                                                                         
d1g03a_ .................................................................................
d1l6na2 pvhagpiapgqmreprgsdiagttstlqeqigwmthnppipvgeiykrwiilglnkivrmysptsilhhhhhh........
d1p7na_ alwmdawgvqlqtviaaatrdprhpangqgrgertnlnrlkgladgmvgnpqgqaallrpgelvaitasalqafrevarla
d1u7ka_ lpnevdaafplerpdwdyttqrgrnhlvlyrqlllagmqnagr......................................
d2eiaa2 .................................................................................
d2xgva_ qafaisaqgreaaqvfrawitqglmnlaqlra.................................................
d2xgya_ .................................................................................
d4htwa_ qnpipvgniyrrwiqlglqkcvrmy........................................................


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: 0037867 (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   Mus musculus 56 (pseudogenes) - House mouse
NoYes   Gorilla gorilla 76_3.1 - Western gorilla
NoYes   Nomascus leucogenys 76_1.0 - Northern white-cheeked gibbon
NoYes   Heterocephalus glaber v1.7-2 - Naked mole-rat
NoYes   Cavia porcellus 76_3 - Domestic guinea pig
NoYes   Oryctolagus cuniculus 76_2 - Rabbit
NoYes   Sus scrofa 76_10.2 - Pig
NoYes   Ovis aries 76_3.1 - Sheep
NoYes   Mustela putorius furo 76_1.0 - Domestic ferret
NoYes   Felis catus 76_6.2 - Domestic cat
NoYes   Dasypus novemcinctus 76_2 - Nine-banded armadillo
NoYes   Sarcophilus harrisii 76_7.0 - Tasmanian devil
NoYes   Monodelphis domestica 76_5 - Gray short-tailed opossum
NoYes   Ornithorhynchus anatinus 76_5 - Platypus
NoYes   Gallus gallus 76_4 - Chicken
NoYes   Anas platyrhynchos 76_1.0 - Mallard
NoYes   Taeniopygia guttata 76_3.2.4 - Zebra finch
NoYes   Ficedula albicollis 76_1.0 - Collared flycatcher
NoYes   Pelodiscus sinensis 76_1.0 - Chinese soft-shelled turtle
NoYes   Anolis carolinensis 76_2.0 - Green anole
NoYes   Brugia malayi WS250 - Agent of lymphatic filariasis
NoYes   Trypanosoma congolense 2.4
NoYes   Gorilla gorilla 69_3.1 - Western gorilla
NoYes   Cavia porcellus 69_3 - Domestic guinea pig
NoYes   Sus scrofa 69_10.2 - Pig
NoYes   Mustela putorius furo 69_1.0 - Domestic ferret
NoYes   Sarcophilus harrisii 69_7.0 - Tasmanian devil
NoYes   Monodelphis domestica 69_5 - Gray short-tailed opossum
NoYes   Ornithorhynchus anatinus 69_5 - Platypus
NoYes   Gallus gallus 69_2 - Chicken
NoYes   Taeniopygia guttata 69_3.2.4 - Zebra finch
NoYes   Pelodiscus sinensis 69_1.0 - Chinese soft-shelled turtle
NoYes   Anolis carolinensis 69_2.0 - Green anole
NoYes   Groundwater dechlorinating community (KB-1) from synthetic mineral medium in Toronto, ON, sample from Site contaminated with chlorinated ethenes
NoYes   Mouse Gut Community ob2 (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Protozoadb 2010_08 (Protozoadb)
NoYes   STRING v9.0.5 (STRING)
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   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)


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