SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q6KCD5 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MNGDMPHVPITTLAGIASLTDLLNQLPLPSPLPATTTKSLLFNSRIAEEV    50
  51  NCLLACRDDNLVSQLVHSLNQVSTDHIELKDNLGSDDPEGDIPVLLQAVL   100
 101  ARSPNVFREKSMQNRYVQSGMMMSQYKLSQNSMHSSPASSNYQQTTISHS   150
 151  PSSRFVPPQTSSGNRFMPQQNSPVPSPYAPQSPAGYMPYSHPSSYTTHPQ   200
 201  MQQASVSSPIVAGGLRNIHDNKVSGPLSGNSANHHADNPRHGSSDDYLHM   250
 251  VHRLSSDDGDSSTMRNAASFPLRSPQPVCSPAGSDGTPKGSRPPLILQSQ   300
 301  SLPCSSPRDVPPDILLDSPERKQKKQKKIKLGKDEKDQNEKAAMYDIISS   350
 351  PTKDSTKLTLRLSRVRSSDMDQQDDMLSGMENSNVSENDIPFNVQYPGQT   400
 401  SKTPITPQDVNRPLNAAQCLSQQEQTAFLPANQVPVLQQNTSVATKQPQT   450
 451  SVVQNQQQVSQQGPIYDEVELDALAEIERIERESAIERERFSKEVQDKDK   500
 501  PLKKRKQDSYPQEAGGATGGNRPASQETGSTGNGSRPALMVSIDLHQAGR   550
 551  VDSQASITQDSDSIKKPEETKQCNDAPISVLQEDIVGSLKSIPENHPETP   600
 601  KKKSDPELSKSEMKQNESRLSESKPNENQLGESKSNESKLETKTETPTEE   650
 651  LKQNENKTTESKQSESAVVEPKQNENRPCDTKPNDNKQNNTRSENTKARP   700
 701  ETPKQKAESRPETPKQKSEGRPETPKQKGDGRPETPKQKSEGRPETPKQK   750
 751  GEGRPETPKHRHENRRDSGKPSTEKKPDVSKHKQDIKSDSPRLKSERAEA   800
 801  LKQRPDGRWESLRRDHDSKQKSDDRGESERHRGDQSRVRRPETLRSSSRN   850
 851  DHSTKSDGSKTEKLERKHRHESGDSRDRPSGEQKSRPDSPRVKQGDTNKS   900
 901  RPGFKSPNSKDDKRTEGNRSKVDSNKAHTDNKAEFPSYLLGGRSGALKNF   950
 951  VIPKIKRDKDGNITQETKKMDMKGEQKDKVEKMGLVEDLNKGAKPVVVLQ  1000
1001  KLSLDDVQKLIKDREEKSRSSLKSIKNKPSKSNKGSIDQSVLKELPPELL  1050
1051  AEIESTMPLCERVKMNKRKRSTVNEKPKYAEISSDEDNDSDEAFESSRKR  1100
1101  HKKDDDKAWEYEERDRRSSGDHRRSGHSHDGRRSSGGGRYRNRSPSDSDM  1150
1151  EDYSPPPSLSEVARKMKKKEKQKKRKAYEPKLTPEEMMDSSTFKRFTASI  1200
1201  ENILDNLEDMDFTAFGDDDEIPQELLLGKHQLNELGSESAKIKAMGIMDK  1250
1251  LSTDKTVKVLNILEKNIQDGSKLSTLLNHNNDTEEEERLWRDLIMERVTK  1300
1301  SADACLTTINIMTSPNMPKAVYIEDVIERVIQYTKFHLQNTLYPQYDPVY  1350
1351  RVDPHGGGLLSSKAKRAKCSTHKQRVIVMLYNKVCDIVSSLSELLEIQLL  1400
1401  TDTTILQVSSMGITPFFVENVSELQLCAIKLVTAVFSRYEKHRQLILEEI  1450
1451  FTSLARLPTSKRSLRNFRLNSSDVDGEPMYIQMVTALVLQLIQCVVHLPS  1500
1501  SEKDPNSEEDSNKKVDQDVVITNSYETAMRTAQNFLSIFLKKCGSKQGEE  1550
1551  DYRPLFENFVQDLLSTVNKPEWPAAELLLSLLGRLLVHQFSNKSTEMALR  1600
1601  VASLDYLGTVAARLRKDAVTSKMDQGSIERILKQVSGGEDEIQQLQKALL  1650
1651  DYLDENTETDPSLVFSRKFYIAQWFRDTTLETEKAMKSQKDEESSDATHH  1700
1701  AKELETTGQIMHRAENRKKFLRSIIKTTPSQFSTLKMNSDTVDYDDACLI  1750
1751  VRYLASMRPFAQSFDIYLTQILRVLGENAIAVRTKAMKCLSEVVAVDPSI  1800
1801  LARLDMQRGVHGRLMDNSTSVREAAVELLGRFVLCRPQLAEQYYDMLIER  1850
1851  ILDTGISVRKRVIKILRDICIEQPTFPKITEMCVKMIRRVNDEEGIKKLV  1900
1901  NETFQKLWFTPTPHNDKEAMTRKILNITDVVAACRDTGYDWFEQLLQNLL  1950
1951  KSEEDSSYKPVKKACTQLVDNLVEHILKYEESLADSDNKGVNSGRLVACI  2000
2001  TTLFLFSKIRPQLMVKHAMTMQPYLTTKCSTQNDFMVICNVAKILELVVP  2050
2051  LMEHPSETFLATIEEDLMKLIIKYGMTVVQHCVSCLGAVVNKVTQNFKFV  2100
2101  WACFNRYYGAISKLKSQHQEDPNNTSLLTNKPALLRSLFTVGALCRHFDF  2150
2151  DLEDFKGNSKVNIKDKVLELLMYFTKHSDEEVQTKAIIGLGFAFIQHPSL  2200
2201  MFEQEVKNLYNSILSDKNSSVNLKIQVLKNLQTYLQEEDTRMQQADRDWK  2250
2251  KVAKQEDLKEMGDVSSGMSSSIMQLYLKQVLEAFFHTQSSVRHFALNVIA  2300
2301  LTLNQGLIHPVQCVPYLIAMGTDPEPAMRNKADQQLVEIDKKYAGFIHMK  2350
2351  AVAGMKMSYQVQQAINTCLKDPVRGFRQDESSSALCSHLYSMIRGNRQHR  2400
2401  RAFLISLLNLFDDTAKTEVTMLLYIADNLACFPYQTQEEPLFIMHHIDIT  2450
2451  LSVSGSNLLQSFKESMVKDKRKERKTSPAKENESSESEEEVSRPRKSRKR  2500
2501  VDSESDSDSEDDINSVMKCLPENSAPLIEFANVSQGILLLLMLKQHLKNL  2550
2551  CGFSDSKIQKYSPSESAKVYDKAINRKTGVHFHPKQTLDFLRSDMANSKL  2600
2601  TEDVKRSIVRQYLDFKLLMEHLDPDEEEEEGEVSASTNARNKAITSLLGG  2650
2651  GSPKNNTAADTEDEESDGEDRGGGTSGSLRRSKRNSDSTELAAQMNESVD  2700
2701  VMDVIAICCPKYKDRPQIARVVQRTSSGVSVQWMAGSYSGSWTEAKRRDG  2750
2751  RKLVPWVDTIKESDIIYKKIALTSANKLTNKVVQTLRSLYAAKDGTSS    2798

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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