SUPERFAMILY 1.75 HMM library and genome assignments server

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Ribosome inactivating proteins (RIP) alignments

These alignments are sequences aligned to the 0034985 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         60             70  
                           |         |         |            |          |          |              |  
d1abra_ ........ed--RPIKFSTEGATSQSYKQFIEALRERLRGG...LIHDIPVLPDP.TTLQERNRYITVELSNS.DT.....ESIEVGIDVTN
d1ce7a_ yergdldvta----------QTTGAGYFSFITLLRDYVSSGs..FSNAIPLLSQS.GGGGEAGRFVLVELTNS.GG.....DGITVAIDVTN
d1cf5a_ .........d----VNFDLSTATAKTYTKFIEDFRATLPFSh..KVYDIPLLYS-.-TISDSRRFILLNLTSY.AY.....ETISVAIDVTN
d1ggpa_ .........s------------TDASYNADIKEERDAAEGP...MAHGIPALNA-.GALDEARAYATVDSAN-.TD.....EEVSVAVDVTN
d1hwma_ ........id-YPSVSFNLAGAKSTTYRDFLKNLRDRVATGty.EVNGLPVLRRE.SEVQVKNRFVLVRLTNY.NG.....DTVTSAVDVTN
d1j1qa_ ........in---TITFDAGNATINKYATFMESLRNEAKDPsl.KCYGIPMLP--.-NTNSTIKYLLVKLQGA.SL.....KTITLMLRRNN
d1qi7a_ .........v--TSITLDLVNPTAGQYSSFVDKIRNNVKDPn..LKYGGTDIAV-.IGPPSKEKFLRINFQS-.SR.....GTVSLGLKRDN
d1r4pa_ ........re------FTIDFSTQQSYVSSLNSIRTEISTPle.HISQGTTSVSV.INHTPPGSYFAVDIRGL.DVyqarfDHLRLIIEQNN
d1rzoa_ ........kq-YPIINFTTADATVESYTNFIRAVRSHLTTGad.VRHEIPVLPNR.VGLPISQRFILVELSNH.AE.....LSVTLALDVTN
d1uq5a_ .........q-YPIINFTTAGATVQSYTNFIRAVRGRLTTGad.VRHEIPVLPNR.VGLPINQRFILVELSNH.AE.....LSVTLALDVTN
d2g5xa_ ....rpswtv----------DSDSAKYSSFLDSLREEFGRGtp.KVCNIPVTKK-.---ANNDKFVLVNLVLPfNR.....NTITLAFRASD
d3bwha_ .........n----VRFDLSSATSSSYKTFIKNLREALPKDg..KVYDIPVLLS-.-TVMDSRRFILIDLVNY.DG.....QSITAAIDVLN
d3ctka1 ..........---TVSFNLG--EAYEYPTFIQDLRNELAKGt..PVCQLPVTLQ-.-TIADDKRFVLVDITTT.SK.....KTVKVAIDVTD
d3hitb_ .......vii----YELNLQGTTKAQYSTFLKQLRDDIKDPn..LHYGGTNLPVI.KRPVGPPKFLRVNLKA-.ST.....GTVSLAVQRSN
d3ktzb_ .......gld---TVSFSTKGATYITYVNFLNELRVKLKPEg..NSHGIPLLRKK.CD-DPGKCFVLVALSND.NG.....QLAEIAIDVTS
d3le7a_ ........in---TITYDAGNTTINKYATFMESLRNEAKDPsl.QCYGIPMLP--.-NNSSTIKYLLVKLQGA.SQ.....KTITLMLRRNN
d3mvga_ ........ie---TVEFRVTGTTRRSYSDFLQNLRNRLSSGt..SVHDIPLLPA-.-QSGSQQDLLFVRLFDW.GN.....RPITLVLNRVN
d4jkxa_ .yerlrlrvt---------HQTTGAEYFSFITLLRDYVSSGs..FSNQIPLLRQStIPVSEGQRFVLVELTNA.GG.....DSITAAIDVTN
d4za3a_ .......nls------LSQSNFSADTYKSFIKNLRKQLTIGasyGSAGIPILKH-.-SVPICERFLLVDLTNG.DN.....ETITLAINVED


              80              90           100           110       120            130       140     
               |               |             |             |         |              |         |     
d1abra_ AYVVAYRA......GTQSYFLRDAPS....SASDYLFTGT....DQHSLPFYGTYGDLERWAH.....QSRQQIPLGLQALTHGISFFRSG.
d1ce7a_ LYVVAYQA......GSQSYFLSGPGG....---RHGFTGT....TRSSLPFNGSYPDLEQYGG.....-QRKQIPLGIDQLIQSVTALKFP.
d1cf5a_ VYVVAYRT......RDVSYFFKESPP....EAYNILFKGT....RKITLPYTGNYENLQTAAH.....KIRENIDLGLPALSSAITTLFYY.
d1ggpa_ LAVVAYRA......GSNSYFHAAAPG....SSLSHLFSRS....SQHTLGFDNTYGDMAQAAG.....SNRKAIPLGAAALESGIASLNSK.
d1hwma_ LYLVAFSA......NGNSYFFKDATE....LQKSNLFLGT....TQHTLSFTGNYDNLETAAG.....TRRESIELGPNPLDGAITSLWYD.
d1j1qa_ LYVMGYSDpydn..KCRYHIFNDIKGteysDVENTLCPSSnpr.VAKPINYNGLYPTLEKKAGv....TSRNEVQLGIQILSSDIGKISGQ.
d1qi7a_ LYVVAYLAmdntnvNRAYYFKSEITS....AELTALFPEAtta.NQKALEYTEDYQSIEKNAQitqgdKSRKELGLGIDLLLTFMEAVNKK.
d1r4pa_ LYVAGFVNta....TNTFYRFSDFTH....----ISVPGV....TTVSMTTDSSYTTLQRVAA.....LERSGMQISRHSLVSSYLALMEFs
d1rzoa_ AYVVGCRAg.....NSAYFFHPDNQEda..EAITHLFTDVq...NSFTFAFGGNYDRLEQLGG.....-LRENIELGTGPLEDAISALYYY.
d1uq5a_ AYVVGYRAg.....NSAYFFHPDNQEda..EAITHLFTDVq...NRYTFAFGGAYDRLEQLAG.....NLRENIELGNGPLEEAISALYYY.
d2g5xa_ AYLVGFQDrdsktnKLRANFFSDEYRals.GKYKSIFTDAev..LAPALPCASTYTDLQNKAG.....VSREKLSLGVSSLQTAFTAVYGK.
d3bwha_ VYIVAYST......GTVSYFFQQVPA....QAPKLLFKGT....QQRTLPYTGNYENLQTAAK.....KLRENIELGLPALDSAITTLFHY.
d3ctka1 VYVVGYQDkwdg..KDRAVFLDKVPT....VATSKLFPGVt...NRVTLTFDGSYQKLVNAAK.....VDRKDLELGVYKLEFSIEAIHGK.
d3hitb_ LYVAAYLAknnnk.QFRAYYFKGFQItt..NQLNNLFPEAtgvsNQQELGYGESYPQIQNAAG.....VTRQQAGLGIKKLAESMTKVNGV.
d3ktzb_ VYVVGYQV......RNRSYFFKDAPD....AAYEGLFKNT....IKTRLHFGGSYPSLEGEKA.....-YRETTDLGIEPLRIGIKKLDENa
d3le7a_ LYVMGYSDpfng..NCRYHIFNDITGtertNVENTLCSSSssr.DAKPINYNSLYSTLEKKAEv....NSRSQVQLGIQILSSDIGKISGQ.
d3mvga_ AYVVAYQA......QNRFYLLSDTPA....---NPQVYGN....NPHRLTFTGSYGALQNVAK.....SNRENIDLGINPLATAITTLHNW.
d4jkxa_ LYVVAYQA......GDQSYFLKDAPA....GAETQDFTGT....TRSSLPFNGSYPDLERYAG.....-HRDQIPLGIDQLIQSVTALRFP.
d4za3a_ AGFAAYRA......ADRSYFFQNAPP....IASYVIFTDT....NQNIMNFNNTFESIEIVGG.....TTRSETPLGIMHFEASIFHLFVH.


              150          160       170             180        190       200          210       220
                |            |         |               |          |         |            |         |
d1abra_ .GND..NEE...KARTLIVIIQMVAEAARFRYISNRVRVSI......QTGTAFQ.PDAAMISLENNWDNLSRGVQES...VQDTFPNQVTLT
d1ce7a_ .GS-..TRT...GARSILILIQMISEAARFNPILWRARQYI......NSGASFL.PDVYMLELETSWGQQSTQVQHS...TDGVFNNPIALA
d1cf5a_ .NA-..-QS...APSALLVLIQTTAEAARFKYIERHVAKYV......--ATNFK.PNLAIISLENQWSALSKQIFLAqn.QGGKFRNPVDLI
d1ggpa_ .NP-..---...LARTLMVIIQMLVEAARFRYIQNNVDVSI......ETQSAFA.ADAAMISLENNWANLSALVQGSsg.GQGTFASSATLQ
d1hwma_ .GG-..---...VARSLLVLIQMVPEAARFRYIEQEVRRSL......QQLTSFT.PNALMLSMENNWSSMSLEVQLSgd.NVSPFSGTVQLQ
d1j1qa_ .GSFt.EKI...EAKFLLVAIQMVSEAARFKYIENQVKTNF......--NRDFS.PNDKVLDLEENWGKISTAIHNS...KNGALPKPLELK
d1qi7a_ .ARV..VKN...EARFLLIAIQMTAEVARFRYIQNLVTKNF......--PNKFD.SDNKVIQFEVSWRKISTAIYGDa..KNGVFNKDYD--
d1r4pa_ gNTM..TRD...ASRAVLRFVTVTAEALRFRQIQREFRQALs.....ETAPVYT.MTPGDVDLTLNWGRISNVLPEY...RGE--------D
d1rzoa_ .STC..GTQiptLARSFMVCIQMISEAARFQYIEGEMRTRI......RYNRRSA.PDPSVITLENSWGRLSTAIQES...NQGAFASPIQLQ
d1uq5a_ .STG..GTQlptLARSFIICIQMISEAARFQYIEGEMRTRI......RYNRRSA.PDPSVITLENSWGRLSTAIQES...NQGAFASPIQLQ
d2g5xa_ .VFT..GKN...VAKFALISIQMVAEAARFKYIEDQVINRG......M-YSSFE.AGARITLLENNWSKISEQYHKScklGGGQF-------
d3bwha_ .NA-..-EA...AASALLVLIQTTSEAARFRYIELQIANNV......--GTKFK.PSQTIISLENNWSALSKQIQIAkn.KNGQFETPVILI
d3ctka1 .TIN..GQE...IAKFFLIVIQMVSEAARFKYIETEVVDRG......L-YGSFK.PNFKVLNLENNWGDISDAIHKSsp.QCTTINPALQLI
d3hitb_ .ARV..EKD...EALFLLIVVQMVGEAARFKYIENLVLNNF......DTAKEVEpVPDRVIILENNWGLLSRAAKTA...NNGVFQTPLVLT
d3ktzb_ iDNYk.PTE...IASSLLVVIQMVSEAARFTFIENQIRNNF......--QQRIR.PANNTISLENKWGKLSFQIRTSg..ANGMFSEAVELE
d3le7a_ .SSFt.DKT...EAKFLLVAIQMVSEAARFKYIENQVKTNF......--NRDFS.PNDKILDLEENWGKISTAIHDA...TNGALPKPLELK
d3mvga_ .SPPtvETS...VARSLIVLIQLVSETARFRAIEQRVTNNIidqvtpIRYDNFR.PRVGIIDLQTNWQTLSTEVQRA...EGGRFLQPVKLQ
d4jkxa_ .GGS..TRT...QARSILILIQMISEAARFNPILWRARQYI......NSGASFL.PDVYMLELETSWGQQSTQVQHS...TDGVFNNPIRLA
d4za3a_ .DE-..-NY...VPTSFLVLIQMVLEAAKFKFIEQKVIHSI......MDMEDFT.PGLAMLSLEENWTQLSLQLQASes.LNGVFGDSVSLY


               230       240       250                                                      
                 |         |         |                                                      
d1abra_ NIRNEPVIVDSLSHPTVAVLALMLFVCNP--pn...................................................
d1ce7a_ DPG-GGVTLTNVRDVIASLAIMLFV------c....................................................
d1cf5a_ KPTGQRFQVTNVDSDVVKGNIKLLL------nsrastaden...........................................
d1ggpa_ NAEDEPIIVDAVYHPTVAAVLALML------rkac.................................................
d1hwma_ NYDHTPRLVDNFEELYKITGIAILLFRC---va...................................................
d1j1qa_ NADGTKWIVLRVDEIKPDVGLLNYVNGTC--qat..................................................
d1qi7a_ ------FGFGKVRQVKDLQMGLLMYLG----kpk..................................................
d1r4pa_ GVRVGRISFNNISAILGTVAVILNCHHQ---garsvravneesqpecqitgdrpvikinntlwesntaaaflnrksqflyttgk
d1rzoa_ RRNGSKFNVYDVSILIPIIALMVYRCAPP--p....................................................
d1uq5a_ RRNGSKFSVYDVSILIPIIALMVYRCAPP--pssqf................................................
d2g5xa_ -------------------------------teeemklglllyn........................................
d3bwha_ DPQGNRVQITNVTSNVVTQNIQLLL------nigat................................................
d3ctka1 SPSNDPWVVNKVSQISPDMGILKF-------ks...................................................
d3hitb_ SYAVPG-------------------------vewrvttvaeveigiflnvd.................................
d3ktzb_ RANGKKYYVTAVDQVKPKIALLKFV------dkdpk................................................
d3le7a_ NADGTKWIVLRVDEIKPDMGLLNYVNGTC--qtt..................................................
d3mvga_ VSVQQTVVISDVEKARTFCGLALLL------rwr..................................................
d4jkxa_ LAPANIVTLTNVRDVIASLAIMLFVC-----ge...................................................
d4za3a_ NSMDEPIGVDSMYYPILTANMAFQL------yqcp.................................................


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: 0034985 (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   Aedes aegypti 55 - Yellow fever mosquito
NoYes   Culex pipiens quinquefasciatus - Southern house mosquito
NoYes   Sphaerobolus stellatus v1.0
NoYes   Daldinia eschscholzii EC12 v1.0
NoYes   Magnaporthe poae ATCC 64411 22
NoYes   Theobroma cacao B97-61/B2 v1 - Cacao
NoYes   Gossypium raimondii v221
NoYes   Cucumis sativus v122 - Cucumber
NoYes   Malus domestica v196 - Apple
NoYes   Prunus persica v139 - Peach
NoYes   Manihot esculenta v147 - Cassava
NoYes   Populus trichocarpa v156 - Black cottonwood
NoYes   Triticum urartu 22
NoYes   Triticum aestivum 22 - Bread wheat
NoYes   Aegilops tauschii 22
NoYes   Brachypodium distachyon - Stiff brome
NoYes   Oryza barthii 22 - African wild rice
NoYes   Oryza meridionalis 22
NoYes   Oryza glumaepatula 22
NoYes   Oryza glaberrima - African rice
NoYes   Oryza punctata 22
NoYes   Oryza nivara 22
NoYes   Oryza brachyantha 22 - Malo sina
NoYes   Oryza sativa ssp. japonica 5.0 - Japanese rice
NoYes   Oryza sativa v193 - Rice
NoYes   Phyllostachys heterocyclavar. pubescens - Mosochiku
NoYes   Panicum virgatum v202 - Switchgrass
NoYes   Setaria italica v164 - Foxtail millet
NoYes   Zea mays subsp. mays - Maize
NoYes   Zea mays v181 - Maize
NoYes   Sorghum bicolor - Sorghum
NoYes   Streptomyces coelicolor A3(2)
NoYes   Streptomyces scabiei 87.22
NoYes   Melioribacter roseus P3M
NoYes   Flavobacterium columnare ATCC 49512
NoYes   Burkholderia sp. CCGE1002
NoYes   Xanthomonas axonopodis pv. citri str. 306
NoYes   Shigella dysenteriae Sd197
NoYes   Theobroma cacao Matina 1-6 v0.9 - Cacao
NoYes   Hordeum vulgare 22 - Domesticated barley
NoYes   Oryza sativa ssp. Indica - Long-grained rice
NoYes   Oscillatoria nigro-viridis PCC 7112
NoYes   Calothrix parietina Calothrix sp. PCC 6303
NoYes   Corynebacterium ulcerans 809
NoYes   Corynebacterium diphtheriae BH8
NoYes   Corynebacterium diphtheriae INCA 402
NoYes   Corynebacterium diphtheriae VA01
NoYes   Corynebacterium diphtheriae HC04
NoYes   Corynebacterium diphtheriae HC03
NoYes   Corynebacterium diphtheriae HC02
NoYes   Corynebacterium diphtheriae HC01
NoYes   Corynebacterium diphtheriae 241
NoYes   Corynebacterium diphtheriae CDCE 8392
NoYes   Corynebacterium diphtheriae PW8
NoYes   Corynebacterium diphtheriae C7 (beta)
NoYes   Corynebacterium diphtheriae 31A
NoYes   Burkholderia ambifaria MC40-6
NoYes   Burkholderia cenocepacia J2315
NoYes   Xanthomonas citri subsp. citri Aw12879
NoYes   Xanthomonas axonopodis Xac29-1
NoYes   Shigella dysenteriae 1617
NoYes   Escherichia coli O104:H4 str. 2009EL-2050
NoYes   Escherichia coli O104:H4 str. 2009EL-2071
NoYes   Escherichia coli O104:H4 str. 2011C-3493
NoYes   Escherichia coli Xuzhou21
NoYes   Escherichia coli O103:H2 str. 12009
NoYes   Escherichia coli O26:H11 str. 11368
NoYes   Escherichia coli O111:H- str. 11128
NoYes   Escherichia coli O157:H7 str. TW14359
NoYes   Escherichia coli O157:H7 str. EC4115
NoYes   Escherichia coli O157:H7 str. Sakai
NoYes   Escherichia coli O157:H7 str. EDL933
NoYes   Malus x domestica - Apple
NoYes   Ricinus communis - Castor bean
NoYes   Combined (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   Guerrero Negro salt ponds hypersaline mat 09(Y) (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
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   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)


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