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

NucPred

Fetching Q6KC79 from www.uniprot.org...

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

   1  MNGDMPHVPITTLAGIASLTDLLNQLPLPSPLPATTTKSLLFNARIAEEV    50
  51  NCLLACRDDNLVSQLVHSLNQVSTDHIELKDNLGSDDPEGDIPVLLQAVL   100
 101  ARSPNVFREKSMQNRYVQSGMMMSQYKLSQNSMHSSPASSNYQQTTISHS   150
 151  PSSRFVPPQTSSGNRFMPQQNSPVPSPYAPQSPAGYMPYSHPSSYTTHPQ   200
 201  MQQASVSSPIVAGGLRNIHDNKVSGPLSGNSANHHADNPRHGSSEDYLHM   250
 251  VHRLSSDDGDSSTMRNAASFPLRSPQPVCSPAGSEGTPKGSRPPLILQSQ   300
 301  SLPCSSPRDVPPDILLDSPERKQKKQKKMKLGKDEKEQSEKAAMYDIISS   350
 351  PSKDSTKLTLRLSRVRSSDMDQQEDMISGVENSNVSENDIPFNVQYPGQT   400
 401  SKTPITPQDINRPLNAAQCLSQQEQTAFLPANQVPVLQQNTSVAAKQPQT   450
 451  SVVQNQQQISQQGPIYDEVELDALAEIERIERESAIERERFSKEVQDKDK   500
 501  PLKKRKQDSYPQEAGGATGGNRPASQETGSTGNGSRPALMVSIDLHQAGR   550
 551  VDSQASITQDSDSIKKPEEIKQCNDAPVSVLQEDIVGSLKSTPENHPETP   600
 601  KKKSDPELSKSEMKQSESRLAESKPNENRLVETKSSENKLETKVETQTEE   650
 651  LKQNESRTTECKQNESTIVEPKQNENRLSDTKPNDNKQNNGRSETTKSRP   700
 701  ETPKQKGESRPETPKQKSDGHPETPKQKGDGRPETPKQKGESRPETPKQK   750
 751  NEGRPETPKHRHDNRRDSGKPSTEKKPEVSKHKQDTKSDSPRLKSERAEA   800
 801  LKQRPDGRSVSESLRRDHDNKQKSDDRGESERHRGDQSRVRRPETLRSSS   850
 851  RNEHGIKSDSSKTDKLERKHRHESGDSRERPSSGEQKSRPDSPRVKQGDS   900
 901  NKSRSDKLGFKSPTSKDDKRTEGNKSKVDTNKAHPDNKAEFPSYLLGGRS   950
 951  GALKNFVIPKIKRDKDGNVTQETKKMEMKGEPKDKVEKIGLVEDLNKGAK  1000
1001  PVVVLQKLSLDDVQKLIKDREDKSRSSLKPIKNKPSKSNKGSIDQSVLKE  1050
1051  LPPELLAEIESTMPLCERVKMNKRKRSTVNEKPKYAEISSDEDNDSDEAF  1100
1101  ESSRKRHKKDDDKAWEYEERDRRSSGDHRRSGHSHEGRRSSGGGRYRNRS  1150
1151  PSDSDMEDYSPPPSLSEVARKMKKKEKQKKRKAYEPKLTPEEMMDSSTFK  1200
1201  RFTASIENILDNLEDMDFTAFGDDDEIPQELLLGKHQLNELGSESAKIKA  1250
1251  MGIMDKLSTDKTVKVLNILEKNIQDGSKLSTLLNHNNDTEEEERLWRDLI  1300
1301  MERVTKSADACLTTINIMTSPNMPKAVYIEDVIERVIQYTKFHLQNTLYP  1350
1351  QYDPVYRLDPHGGGLLSSKAKRAKCSTHKQRVIVMLYNKVCDIVSSLSEL  1400
1401  LEIQLLTDTTILQVSSMGITPFFVENVSELQLCAIKLVTAVFSRYEKHRQ  1450
1451  LILEEIFTSLARLPTSKRSLRNFRLNSSDMDGEPMYIQMVTALVLQLIQC  1500
1501  VVHLPSSEKDSNAEEDSNKKIDQDVVITNSYETAMRTAQNFLSIFLKKCG  1550
1551  SKQGEEDYRPLFENFVQDLLSTVNKPEWPAAELLLSLLGRLLVHQFSNKS  1600
1601  TEMALRVASLDYLGTVAARLRKDAVTSKMDQGSIERILKQVSGGEDEIQQ  1650
1651  LQKALLDYLDENTETDPSLVFSRKFYIAQWFRDTTLETEKAMKSQKDEES  1700
1701  SEGTHHAKEIETTGQIMHRAENRKKFLRSIIKTTPSQFSTLKMNSDTVDY  1750
1751  DDACLIVRYLASMRPFAQSFDIYLTQILRVLGENAIAVRTKAMKCLSEVV  1800
1801  AVDPSILARLDMQRGVHGRLMDNSTSVREAAVELLGRFVLCRPQLAEQYY  1850
1851  DMLIERILDTGISVRKRVIKILRDICIEQPTFPKITEMCVKMIRRVNDEE  1900
1901  GIKKLVNETFQKLWFTPTPHNDKEAMTRKILNITDVVAACRDTGYDWFEQ  1950
1951  LLQNLLKSEEDSSYKPVKKACTQLVDNLVEHILKYEESLADSDNKGVNSG  2000
2001  RLVACITTLFLFSKIRPQLMVKHAMTMQPYLTTKCSTQNDFMVICNVAKI  2050
2051  LELVVPLMEHPSETFLATIEEDLMKLIIKYGMTVVQHCVSCLGAVVNKVT  2100
2101  QNFKFVWACFNRYYGAISKLKSQHQEDPNNTSLLTNKPALLRSLFTVGAL  2150
2151  CRHFDFDLEDFKGNSKVNIKDKVLELLMYFTKHSDEEVQTKAIIGLGFAF  2200
2201  IQHPSLMFEQEVKNLYNNILSDKNSSVNLKIQVLKNLQTYLQEEDTRMQQ  2250
2251  ADRDWKKVAKQEDLKEMGDVSSGMSSSIMQLYLKQVLEAFFHTQSSVRHF  2300
2301  ALNVIALTLNQGLIHPVQCVPYLIAMGTDPEPAMRNKADQQLVEIDKKYA  2350
2351  GFIHMKAVAGMKMSYQVQQAINTCLKDPVRGFRQDESSSALCSHLYSMIR  2400
2401  GNRQHRRAFLISLLNLFDDTAKTDVTMLLYIADNLACFPYQTQEEPLFIM  2450
2451  HHIDITLSVSGSNLLQSFKESMVKDKRKERKSSPSKENESSDSEEEVSRP  2500
2501  RKSRKRVDSDSDSDSEDDINSVMKCLPENSAPLIEFANVSQGILLLLMLK  2550
2551  QHLKNLCGFSDSKIQKYSPSESAKVYDKAINRKTGVHFHPKQTLDFLRSD  2600
2601  MANSKITEEVKRSIVKQYLDFKLLMEHLDPDEEEEEGEVSASTNARNKAI  2650
2651  TSLLGGGSPKNNTAAETEDDESDGEDRGGGTSGSLRRSKRNSDSTELAAQ  2700
2701  MNESVDVMDVIAICCPKYKDRPQIARVVQKTSSGFSVQWMAGSYSGSWTE  2750
2751  AKRRDGRKLVPWVDTIKESDIIYKKIALTSANKLTNKVVQTLRSLYAAKD  2800
2801  GTSS                                                2804

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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