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

NucPred

Fetching Q9Y4G6 from www.uniprot.org...

The NucPred score for your sequence is 0.77 (see score help below)

   1  MVALSLKICVRHCNVVKTMQFEPSTAVYDACRVIRERVPEAQTGQASDYG    50
  51  LFLSDEDPRKGIWLEAGRTLDYYMLRNGDILEYKKKQRPQKIRMLDGSVK   100
 101  TVMVDDSKTVGELLVTICSRIGITNYEEYSLIQETIEEKKEEGTGTLKKD   150
 151  RTLLRDERKMEKLKAKLHTDDDLNWLDHSRTFREQGVDENETLLLRRKFF   200
 201  YSDQNVDSRDPVQLNLLYVQARDDILNGSHPVSFEKACEFGGFQAQIQFG   250
 251  PHVEHKHKPGFLDLKEFLPKEYIKQRGAEKRIFQEHKNCGEMSEIEAKVK   300
 301  YVKLARSLRTYGVSFFLVKEKMKGKNKLVPRLLGITKDSVMRVDEKTKEV   350
 351  LQEWPLTTVKRWAASPKSFTLDFGEYQESYYSVQTTEGEQISQLIAGYID   400
 401  IILKKKQSKDRFGLEGDEESTMLEESVSPKKSTILQQQFNRTGKAEHGSV   450
 451  ALPAVMRSGSSGPETFNVGSMPSPQQQVMVGQMHRGHMPPLTSAQQALMG   500
 501  TINTSMHAVQQAQDDLSELDSLPPLGQDMASRVWVQNKVDESKHEIHSQV   550
 551  DAITAGTASVVNLTAGDPADTDYTAVGCAITTISSNLTEMSKGVKLLAAL   600
 601  MDDEVGSGEDLLRAARTLAGAVSDLLKAVQPTSGEPRQTVLTAAGSIGQA   650
 651  SGDLLRQIGENETDERFQDVLMSLAKAVANAAAMLVLKAKNVAQVAEDTV   700
 701  LQNRVIAAATQCALSTSQLVACAKVVSPTISSPVCQEQLIEAGKLVDRSV   750
 751  ENCVRACQAATTDSELLKQVSAAASVVSQALHDLLQHVRQFASRGEPIGR   800
 801  YDQATDTIMCVTESIFSSMGDAGEMVRQARVLAQATSDLVNAMRSDAEAE   850
 851  IDMENSKKLLAAAKLLADSTARMVEAAKGAAANPENEDQQQRLREAAEGL   900
 901  RVATNAAAQNAIKKKIVNRLEVAAKQAAAAATQTIAASQNAAVSNKNPAA   950
 951  QQQLVQSCKAVADHIPQLVQGVRGSQAQAEDLSAQLALIISSQNFLQPGS  1000
1001  KMVSSAKAAVPTVSDQAAAMQLSQCAKNLATSLAELRTASQKAHEACGPM  1050
1051  EIDSALNTVQTLKNELQDAKMAAVESQLKPLPGETLEKCAQDLGSTSKAV  1100
1101  GSSMAQLLTCAAQGNEHYTGVAARETAQALKTLAQAARGVAASTTDPAAA  1150
1151  HAMLDSARDVMEGSAMLIQEAKQALIAPGDAERQQRLAQVAKAVSHSLNN  1200
1201  CVNCLPGQKDVDVALKSIGESSKKLLVDSLPPSTKPFQEAQSELNQAAAD  1250
1251  LNQSAGEVVHATRGQSGELAAASGKFSDDFDEFLDAGIEMAGQAQTKEDQ  1300
1301  IQVIGNLKNISMASSKLLLAAKSLSVDPGAPNAKNLLAAAARAVTESINQ  1350
1351  LITLCTQQAPGQKECDNALRELETVKGMLDNPNEPVSDLSYFDCIESVME  1400
1401  NSKVLGESMAGISQNAKTGDLPAFGECVGIASKALCGLTEAAAQAAYLVG  1450
1451  ISDPNSQAGHQGLVDPIQFARANQAIQMACQNLVDPGSSPSQVLSAATIV  1500
1501  AKHTSALCNACRIASSKTANPVAKRHFVQSAKEVANSTANLVKTIKALDG  1550
1551  DFSEDNRNKCRIATAPLIEAVENLTAFASNPEFVSIPAQISSEGSQAQEP  1600
1601  ILVSAKTMLESSSYLIRTARSLAINPKDPPTWSVLAGHSHTVSDSIKSLI  1650
1651  TSIRDKAPGQRECDYSIDGINRCIRDIEQASLAAVSQSLATRDDISVEAL  1700
1701  QEQLTSVVQEIGHLIDPIATAARGEAAQLGHKVTQLASYFEPLILAAVGV  1750
1751  ASKILDHQQQMTVLDQTKTLAESALQMLYAAKEGGGNPKAQHTHDAITEA  1800
1801  AQLMKEAVDDIMVTLNEAASEVGLVGGMVDAIAEAMSKLDEGTPPEPKGT  1850
1851  FVDYQTTVVKYSKAIAVTAQEMMTKSVTNPEELGGLASQMTSDYGHLAFQ  1900
1901  GQMAAATAEPEEIGFQIRTRVQDLGHGCIFLVQKAGALQVCPTDSYTKRE  1950
1951  LIECARAVTEKVSLVLSALQAGNKGTQACITAATAVSGIIADLDTTIMFA  2000
2001  TAGTLNAENSETFADHRENILKTAKALVEDTKLLVSGAASTPDKLAQAAQ  2050
2051  SSAATITQLAEVVKLGAASLGSDDPETQVVLINAIKDVAKALSDLISATK  2100
2101  GAASKPVDDPSMYQLKGAAKVMVTNVTSLLKTVKAVEDEATRGTRALEAT  2150
2151  IECIKQELTVFQSKDVPEKTSSPEESIRMTKGITMATAKAVAAGNSCRQE  2200
2201  DVIATANLSRKAVSDMLTACKQASFHPDVSDEVRTRALRFGTECTLGYLD  2250
2251  LLEHVLVILQKPTPEFKQQLAAFSKRVAGAVTELIQAAEAMKGTEWVDPE  2300
2301  DPTVIAETELLGAAASIEAAAKKLEQLKPRAKPKQADETLDFEEQILEAA  2350
2351  KSIAAATSALVKSASAAQRELVAQGKVGSIPANAADDGQWSQGLISAARM  2400
2401  VAAATSSLCEAANASVQGHASEEKLISSAKQVAASTAQLLVACKVKADQD  2450
2451  SEAMRRLQAAGNAVKRASDNLVRAAQKAAFGKADDDDVVVKTKFVGGIAQ  2500
2501  IIAAQEEMLKKERELEEARKKLAQIRQQQYKFLPTELREDEG          2542

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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