Conserved Protein Domain Family
CLN3

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pfam02487: CLN3 (This model is not part of the current CDD release)
CLN3 protein
This is a family of proteins from the CLN3 gene. A mis-sense mutation of glutamic acid (E) to lysine (K) at position 295 in the human protein has been implicated in Juvenile neuronal ceroid lipofuscinosis (Batten disease). Batten disease is characterised by the accumulation of autofluorescent material in the lysosomes of most cells. Members of this family are transmembrane proteins functional in pre-vacuolar compartments. The protein in Sch.pombe is found to be localised to the vacuolar membrane, and a lack of functional protein clearly affects the size and pH of the vacuole. Thus the protein is necessary for vacuolar homeostasis. It is important for localisation of late endosomal/lysosomal compartments, and it interacts with motor components driving both plus and minus end microtubular trafficking: tubulin, dynactin, dynein and kinesin-2.
Statistics
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PSSM-Id: 514959
Aligned: 86 rows
Threshold Bit Score: 366.838
Created: 13-Feb-2025
Updated: 28-Apr-2025
Structure
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Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
EMD36899       17 LSFFLFGLINNVLYVIILSAALDLVPPST------------------------------------------PKGIIAFCN 54 
XP_015781750   61 IGFWILGLCNNYGYVIMLSAAFDILSRNFnenedkktdq-----------------------ddepfcnpmSTGAILIAD 117
XP_046464081   39 IAYWLLGLCNNYAYVIMLSAAHDILSEDFqgnstvptpsp--------------------vtnntrdcnpvSTGAILLAD 98 
XP_008200233   25 VSYWILGLCNNYGYVVMLTAASDIIGESEgakste------------------------------rnctymSTGAILLAD 74 
EDS31304       29 VAYWILGLCNNYGYVVMLTAAHDILKELGggdhgddgksmmmldpfaenstllrsgdpaafayekrpcnklSTGAILLAD 108
12_pfamImport   1 VAYWILGLCNNYGYVVMLTAAHDILKELEggdghaksaspldgydvakt---taraddvtfgyearpcnklSTGAILLAD 77 
3_pfamImport    1 ASFWILGLCNNFGYVVMLSSAHDILKSNSaalggnetvsiss-----------------tqdvfkrecnylSTGVILLAD 63 
XP_011253723   30 LAFWILGLCNNYGYVVMLSAAHDILDIKFsdkdnstlntng------------------tnmtgirmcntvSTGAILLAD 91 
XP_011053297   30 IAFWILGLCNNYGYVVMLSAAHDILQSKFgeqkdipstnn---------------------tnttrtcntvSTGAILLAD 88 
NP_649011      39 TSYWILGLCNNYGYVVMLSAAHDIIKQFNpndeseess-------------------------sgrnchlvSTGAILLAD 93  fruit fly
EMD36899       55 IFPALLAKLGWPYVlkgRIRYAKRLMGCTVISISGMIVVAFFDGLTMRLLGICCASFSSGLGELTFLQLSTRYhppqvAG 134
XP_015781750  118 IIPSLCIKLLSPVL---PLGANLRVILVVIFSVLSYLMTALSFARWVSFLGVIFASASSGLGEATFLSYSSRFs----DS 190
XP_046464081   99 VLPSLAMKLTMPFL---LTHIRLRVLIVILLSSASFLMVSFSTAQWQAFLGVVFAAISGGLGEVTFLQYSSHY-----DK 170
XP_008200233   75 IIPSLLVKLLAPFL---PFFVNVRVAVCILCSSAGFLLVAFSQNITMSLLGVVATSFCSGLGEVTYLQYSSFY-----DK 146
EDS31304      109 ILPALSIKLVASFL---PLWKHVRVAGCVSLAAAGFLLVAFATSDWVLFLGVICTSFSSGLGEATFLAYASYF-----NK 180
12_pfamImport  78 ILPALAVKSIASFL---PLAKHVRIFLCVAAAAAGFLLTAFATVEWVLFVGVIATSFSSGLGEATFLAYATYF-----NK 149
3_pfamImport   64 IMPGLIIKIFSPFF---GLYINRRLSLCIALTTASFITVAKADTELVAAFGVALTSMASGLGETTLLSYMVNY-----ER 135
XP_011253723   92 ILPSLAIKMIAPFL---PFLVHARLATCVLFSAAGFLMVSLSTVEWLALLGVVITSLSSGLGEATLLGYSNQF-----SK 163
XP_011053297   89 ILPALAIKITAPFL---PFLVHARLATCVLFSAAGFLMVSLSMIEWVAIMGVVLTSLSSGLGEVTLLSYSNQF-----SK 160
NP_649011      94 VLPSLFVKILMPFF---PFWVNFRIALAVAFSAAGFLLVGFANAEWMALLGVIITSASSGIGETTFLAYSSRY-----NK 165 fruit fly
EMD36899      135 HSVGYFASGTGAAGLVGAFLWWELR---NLGVRVGVGLSSVLPLVIPLAYYFLLPLPPAFVGLGIPe-eA---------- 200
XP_015781750  191 DTISFWSSGTGGAGLIGSISYAGLTq-lGLSPRVTLLVMLIVPVIMAITFWIVLAPPKIDVATITPlmqPnepstgdeii 269
XP_046464081  171 DVVSTWSSGTGGSGLFGALSFAALTt-aGLSARKTVLLMLVIPALMAITFFFILDHEKRRVKTNDSdadTeplmeenqp- 248
XP_008200233  147 NVVSTWSSGTGGAGVIGAVSYSLLQq---LGLKTTLLVMLLVPGMMAVTFYIILPSPEVMDENDIqadvnn--------- 214
EDS31304      181 NVISTWSSGTGGAGVIGSLSYTGLTa-aGLSPKATMLVMLVVPALEACSFWVLLRHKDTSKDALVe---Tadsakqaidy 256
12_pfamImport 150 NVISTWSSGTGGAGIAGSLSYTGLTg-lGLTPKTTILIMLVVPGLEAAAFWLLLRHKDTDKPADISeqeAgsekpeeidy 228
3_pfamImport  136 TVITSWASGTGAAGILGALTYAGLTgvfHLSPSTTMYLMLSVPFLMGVSFWVLLEHPKKDEIPTMPsisPdpst------ 209
XP_011253723  164 QVISTWSSGTGGAGVIGALSYASLAt--VLSVENTLLVMLIVPLLQGITFWCVLKHPVHTKISIng--vEnqeqii---- 235
XP_011053297  161 QVISTWSSGTGGAGVIGAVSYAGLTl--VLSIENTLLVMLIVPFLQAVTFWVILKHPTHIRIPITKngiDsqeqii---- 234
NP_649011     166 NVISTWSSGTGGAGVIGSLSYASLRs-lDFSPRDTMLIMLIFPAIEAFAFWLLLRRPQVDILPVTTvesTevlisd---- 240 fruit fly
EMD36899      201 ------------RsssappspytpymplpeddaetdvsvnaqigmgddmqsgkghvaLtAQDKWKLAKPLIMKYMMPLFC 268
XP_015781750  270 syqtvrepeiglT----------------------------------------------LREKSILMKGLLG-FMIPLAV 302
XP_046464081  249 ---sfkghiapiS----------------------------------------------MRSKCRMLPRM-ArFIVPLGS 278
XP_008200233  215 ------eeiknpK--------------------------------------------EaFMKKLKHVPSL-FKYMIPFGL 243
EDS31304      257 s-tlpederpleN----------------------------------------------WRQKLGYIPALFI-FMIPLIL 288
12_pfamImport 229 n-tlpederpleN----------------------------------------------WNQRLRYIPSLFI-FMIPLIL 260
3_pfamImport  210 -------------------------------------------------------nnqsFSNKFSYIPKL-LkFMIPLGL 233
XP_011253723  236 -----------------------------------------------------kvpeksIRDKFKLIPGL-LkYMIPLGL 261
XP_011053297  235 -----------------------------------------------------kvpektFRDKINLVPGL-LkYMIPLGL 260
NP_649011     241 -----------------------------------------------------ekplvgFKEKLFYIKHL-FkYMLPLCL 266 fruit fly
EMD36899      269 VYLFEYTINQGIAPTLIYP-VpssseawlmpkIVHSIRDYYPLWQLVYQTTVFFSRSSIS-IGIpplpsRLLFLPALLQG 346
XP_015781750  303 VYFAEYLINQALFELVYFPgI------------WLSHNEQYRWYQVDYQLGVLISRSSVKwIKI-----KALWILPLLQI 365
XP_046464081  279 VYLFEYFINQGVFELIYFEnI------------WLDHHSQYRWLQVDYQLGVFLSRSSVNlFRI-----NAVWFLAVLQF 341
XP_008200233  244 VYFLEYYINQGTFELINFE-N-----------TFLAPSDQYRWLQVAYQIGVFVSRSSVNfFHI-----RHIWVMSVLQA 306
EDS31304      289 VYLFEYFINQGMFELVYFPgI------------SLSQSEQYRWYQVLYQVGVFISRSSVNiVHF-----RHVWVMALLQF 351
12_pfamImport 261 VYLLEYYINQGLFELVYFPgI------------WLSQSAQYRWYQVIYQIGVFISRSSVNlIQF-----RQVWIMAVFQF 323
3_pfamImport  234 VYFFEYLINQGLFELVYFEkI------------WLTHSEQYRWYQVIYQLGVFTSRTSVSlFPI-----EKIWILTILQG 296
XP_011253723  262 VYLFEYFINQGLYELIEFDnI------------WLTQHEQYRWLQVDYQIGVFISRSSVNvVTI-----NKIWIMSVFQL 324
XP_011053297  261 VYLFEYFINQGLYELIEFKdI------------WLTHSEQYRWLQVDYQIGVFISRSSVNlVTI-----NKIWIMSVLQF 323
NP_649011     267 VYFFEYFINQGLFELVYFEdI------------FLDKDSQYRWLNVDYQIGVFISRSSVNlFQL-----DKIWLMSIFQF 329 fruit fly
EMD36899      347 FILLFLGFESavgvsGDnSpVTSFWMVFWLVALEGTCGGLAYINAYYRVGQDHRVssgvdgdesdaerarQEREFRIGSI 426
XP_015781750  366 INLLLVFVEA-----LK-NyLPNIWIMLLIVFYEGLLGGAAYVNTFDQIYRKYED---------------RVRGFCLGAA 424
XP_046464081  342 VNVILLTTEA-----VF-LyIPSIWIVFTIVFWEGLLAGAAYVNTFYRVAFETIP---------------QEKAFAMGIT 400
XP_008200233  307 VNVVIFTTEV-----IY-YyMPSFWIILALTLWEGLLGGAAYVNTFYRISTEVRE---------------ENKQFSMAIT 365
EDS31304      352 INMVFFIFEA-----IY-MfTPSIWIIFVLILWEGLLGGGGYVNTFYRMQIEVPE---------------ARREYAMMIT 410
12_pfamImport 324 LNVVYFTFEA-----VY-YfTPSIWIIFVLILWEGLLGGGGYVNTFYRIQTDVPA---------------ARREYAMMVT 382
3_pfamImport  297 LNVVYFLIET-----LY-SfTPNIYIIFALIGYEGLLGGGSYANTYHNIMKKVPK---------------ERQEYAMAMT 355
XP_011253723  325 INVIILLFET-----LF-YyIPNIWIVFALVLWEGLLGGGAYVNTFFRISTEIPK---------------TDRETSLEIA 383
XP_011053297  324 FNVILFFFET-----LY-YyIPNIWIIFALVLWEGLLGGGAYVNTFYRMSTEIPK---------------VDREASLGIA 382
NP_649011     330 VNVVYFLTEV-----IW-WyTPSIWIVFAIVLWEGLLGGGAYVNTFYRMSKEISP---------------ERQQFAMAMV 388 fruit fly
EMD36899      427 GMADSTGILIAALVAVPTEVGLCRA 451
XP_015781750  425 SIADALGITLSGFSSVLLHNVLCDI 449
XP_046464081  401 SLAGSVGVSTAGALAVPFHQYLCSL 425
XP_008200233  366 SFADSIGITLAGIVSIYAHNAICSL 390
EDS31304      411 SISDSVGIALAGIASIPSHNAICDL 435
12_pfamImport 383 SISDSVGIALAGIAAIPSHNAICDL 407
3_pfamImport  356 SLADAIGISLSGLLAIPLHNQICKI 380
XP_011253723  384 TMSDAIGIALAGWLSMPVHNAICKL 408
XP_011053297  383 TMADSIGIALAGWLSMPVHNAICKL 407
NP_649011     389 VQSDSYGIALAGFLAIPVHNAICGL 413 fruit fly
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