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

NucPred

Fetching Q9USK8 from www.uniprot.org...

The NucPred score for your sequence is 0.56 (see score help below)

   1  MHGLQGLCFRRAVIALALLLFHSVFAAPYSEDEEPWNLNQNKNASSVLEY    50
  51  SGEWADHDFFPSPDNWRMSFITVILDRWYDGDPSNNDIEKTPFEYDISEV   100
 101  SFRNGGDIVGLELSLDYLEGLGTQGIYIAGTPFVNMPWGADQYSPLDYTI   150
 151  LDHHLGTIDQWRSTITAMHERGMYLVVDLTVATLGDLIGMVGHLNDTSGV   200
 201  DFNLNEYNAMWKTSEYRYVDFNFTNVYNTSCEYPRFWGEDGGPVSIQFKG   250
 251  CYVSDYDHYGDTEAFGSHPDWQRQLSKFASVQDRLRDWKPDVAEKLMHLS   300
 301  CLVISMLDVDGFRIDKATQMTADFIVDWSMYVRECAAKYNKKNFLIVGEV   350
 351  TGSSSYGSIYYNRGRQPDQRPPNVTAAFNYTSDESQYSLRDSDHYGFDGS   400
 401  AFHYSIYRALLRFLGMDSKMEIDFDVSSVLTTAWNGIQINEDAVNINTGT   450
 451  VEPLHMYGVANHDVFRWGAIENGTARLILGTMITSLLFPGIPLLYYGDEQ   500
 501  GMYVLDNSANNYLYGRQAMNSARAWYIHGCYNGSATSYPTVDLSPAQRGC   550
 551  QDSWNYLDHFDIASAHRNVYRNIHSIRRHYLSLSEGWRFDHIANWTDDVY   600
 601  FPDSQPYASPMGLYSVLRGPMKEIQDFDSITNASNVSKSEVWVLYANRND   650
 651  THLWSYDCTDEDSAIIGPWKSGTTLRNLIYPYDTIELEDSWNSSWGCIPN   700
 701  IELDPYAFKLYVPEEDFIENDPIITSLTPEHDARVVASGNEIDLTIEFSR   750
 751  SMDCDSIKNALSVVSSTRPKNTTAVIDVDSSFCRNYSEDASTSLHGQTAG   800
 801  RFAWYGTLTNIDPGIHRISLKSVPTSDFSSRTLSTDNFLIRVGSTNNPIV   850
 851  HYSANYSDTLLIMQDGDLYINHSAPGAVLFRYSTDFQSHWSDWEEYNGGL   900
 901  TKVQASNWTGTRRQGWEGHHIHVQYWSDLGGSANHMQQSDYGFKYRRFLP   950
 951  HMFLEGDFNEYGYDSGVENRFLQKSDFYWEAGFISETYPAAIQLNVWGMN  1000
1001  PDGIPDKTRVYGSQGNSTVLSRSDPASLVGNNITIYHPPPHGYLSYKILL  1050
1051  RDDDMIYRLAPSGEWGVSIAIYVLCIVIPPLSAIVVSWAFKNSFYTVKFN  1100
1101  KHGNNDLGKFYPLKSLVPFRKKNDLDSPAKVTPVVSGVSARKKKCVLIAT  1150
1151  LEYDITDWKIRIKIGGLGVMAQLMAQHLKHEDLVWVVPCVGDVVYPEAEE  1200
1201  ASPIEVKIIDQTYTINVYHHYLDNIKYVLLDAPVFRRQTSKEPYPARMDD  1250
1251  LGSAIFYSAWNQCIAEVIRRNPIDIYHINDYHGALAPCYLLPDIIPCALS  1300
1301  LHNAEFQGLWPLRTPEEKEEVCAVYNISQRVCTKYVQFGNVFNLLHAAVS  1350
1351  YIRIHQKGFGAVGVSNKYGKRSWARYPIFWGLKKIGKLPNPDPTDTDEIV  1400
1401  DDKAVAITDIDPDMEKSKVEHKRLAQEWAGLEVNEKYDLLVFVGRWSSQK  1450
1451  GIDLIADIAPSLLESYKVQLICVGPIIDLYGKFAAEKLDVLQKKYPTRVF  1500
1501  SQPKFTQLPPYIFSGADFALIPSRDEPFGLVAVEFGRKGALGIGARVGGL  1550
1551  GQMPGWWYSVESSATPHLLKQFEQACQQALSSSQRTRARLRARSAKQRFP  1600
1601  VSQWKAKLEALTDGCIKCSQKYGRNSRSRSSFYSLIHESFSRSSEVLPTS  1650
1651  SDTNLDAKRAEEAEMIMIETPPTAEANTGAKLDRSLSLGSRRGPGHTTED  1700
1701  DASDGLDTIQEESMTAGDSTSGGSDISRYRAERLNPDSHSPSEYSFDSGD  1750
1751  YEFDPQRSYYYDDLFDDDTTIRNAPSFRPQMGSFDAEHAVGATFSQDDLS  1800
1801  DPARSVDSDSVSPPLPPFVAGSNPNARNNNNPYFYGNLHTESSLSLASVM  1850
1851  SGKEKRDFSLTRVEETFTDEDGQALRSFSEKLQKLNAKNSKDDLCIEQYL  1900
1901  MKSERSFFHERRAIKLGLQKPNKLHVNELSSHSGTEESESLSNGQTSYDD  1950
1951  IIAMTDESNYTQLGDDDFKTIHGLKKFMLFKIYDWPIYSIFLALGQILAA  2000
2001  TAYQLTLFTGTSNIQTYEIYSVCAFFIGASFVWWFMFARLPSYYVLSIPW  2050
2051  LFYAVALFLVGLPAFDTVAPGRVWITNVAAWIYAIASASGSIFFSLNFGE  2100
2101  EGAVQTRIWVFRACLVQGVQQVWSAALWYWGAHLNKRLTAGEANTFKMSP  2150
2151  AIPSITWPLSAVSILIFALLFKGLPEYYRQLSGSIPAFYKSLLRRKLVVW  2200
2201  FCISVFLQNFWLSSLNGRSWSYLWDIGNIHQWQIFLLIVAFYIVLWALLL  2250
2251  GVLAWISRTHSWIICVFGVGLGAPRWLQQFWATSNIGLYLPWAGYSGPYL  2300
2301  GRTLWLWLGVLDAIQSVGIGMILLQTLTRRHVASTLMTGQIVGAVATMIG  2350
2351  RGASPNREGPANVFIDFTKWNHGDGSSILASAPFWINIICQLAICVGYLA  2400
2401  FFRRENLSRP                                          2410

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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