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

NucPred

Fetching Q69ZK6 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MAVETRPELVGKRFLCVAAGEDARPERGQSGCGRGWRAGVIRAVSHRDRG    50
  51  HPDLAVYVEFDDLEWDKREWVRVYEDFSTFLVEYHLIWAKRKDPSQTQGS   100
 101  KSRQIQWPALTFKPLVENSIPSSITAVEFLIDKQLDFLTEDSAFQPYQDD   150
 151  IDSLKPVLRDNPQLHAEVKVWVKEQKVQEIFMQGPYSLNGYRVRVYRQDS   200
 201  ATQWFTGIITHHDLFTRTMIVMNDQVLEPQNVDPSMVQMTFLDDVVHSLL   250
 251  KGENIGITSRRRSRASQNISTVHGHYTRAQANSPRPAMNSQAAVPKQNTH   300
 301  QQQQQRSIRPNKRKGSDSSIPDEEKMKEDKYDCVSRGENPKGKNKHVVTK   350
 351  RRKPEEAEKRLSMKRLRTDNASDASESSDAESSSKRVTETSSSEPMPEYE   400
 401  PKNKVTSKVNGEEGQSQAAEEAGEETLIDTRPPWDQMQEDKNHNEGEKPK   450
 451  STDSHLQDKMTLRSSEQATVADHNSNDSVLQECNVENQRTVELLPKDRLV   500
 501  SRTPTPKCVTDIKNDTHSERAAQENLNTFGLQTPENMDPNVSDSKHSNAK   550
 551  YLETAKQDCDQSWVSDVVKVDLTQSSVTNAPSGSDKRDTEKERNHYVSYM   600
 601  SSLSAVSVTEDQLHKRSPPPETIKAKLTTSVDTQKAKSSSSPEVVKPKIT   650
 651  HSPDSVKSKAAYGNSQAVGERRLANKIEHELSRGSFHPVPTRGSALETTK   700
 701  SPLIIDKNEHFTVYRDPALIGSETGANHISPFLSQHPFSLHSSSHRTCLN   750
 751  PGTHHPALTPGPHLLAGSTSQTPLPTINTHPLTSGPHHPVHHPHLLPTVL   800
 801  PGVPTASLLGGHPRLESAHASSLSHLALAHQQQQQLLQHQSPHLLGQAHP   850
 851  SASYNQLGLYPIIWQYPNGTHAYSGLGLPSSKWVHPENAVNAEASLRRNS   900
 901  PSPWLHQPTPVTSADGIGLLSHIPVRPSSAEPHRPHKITVHSSPPLTKTL   950
 951  ADHHKEELERKAFMEPLRSNASTSVKGDLDLNRSQAGKDCHLHRHFVGPR  1000
1001  PPQETGERLNKYKEEHRRILQESIDVAPFTTKIKGHEVERENYSRVVPSS  1050
1051  SSPKSHAIKQDKDVDRSVSEIYKMKHSVPQSLPQSNYFTTLSNSVVNEPP  1100
1101  RSYPSKEVSNIYTEKQNNNLSATANPQTHSFISSLSKPPPLIKHQPESES  1150
1151  LVGKIPDHLPHQSASHSVTTFRSDCRSPTHLTVSSTNALRSMPALHRAPV  1200
1201  FHPPIHHSLERKESSYSSLSPPTLTPVMPVNAGGKVQESQKPPTLIPEPK  1250
1251  DSQSNFKNSSDQSLTEMWRSNNNLNREKAEWPVEKSSGKSQAAVASVIVR  1300
1301  PPSSTKVDSVPSVPLASKDRVCERSSSGANKTDYLKPEAGETGRIILPNV  1350
1351  NLESAHVKSEKNFEAVSQGNVPVSVMSAVNVVSTTKADVFTSAATTTSVS  1400
1401  SLSSAETSYSLSNTISASTPFECTSSKSVVSQAVAQAKDCTVSTAVPGTL  1450
1451  ACSKTGSAVQPGSGFSGTTDFIHLKKHKAALAAAQFKNSSVSEAELNTVR  1500
1501  NQTVAASLPLDSTMTCTASNKAISVGNGPAAQSSQPNYHTKLKKAWLTRH  1550
1551  SEEDKNTNKMENSGNSVSEIIKPCSVNLIASTSNDIENRADGRVAVDKYG  1600
1601  RDEKVSRRKAKRTYESGSESGDSDESESKSEQRTKRQPKPTYKKKQNDLQ  1650
1651  KRKGEVEEDSKPNGVLSRSAKDKSKLKLQNSNSAGVPRSVLKDWRKVKKL  1700
1701  KQTGESFLQDDSCCEIGPNLQKCRECRLIRSKKGEESTHSPVFCRFYYFR  1750
1751  RLSFSKNGVVRIDGFSSPDQYDDEAMSLWTHENYEDDEVDVETSKYILDI  1800
1801  IGDKFCQLVTSEKTALSWVKKDAKIAWKRAVRGVREMCDACEATLFNVHW  1850
1851  VCRKCGFVACLDCYKAKERKSSRDKELYAWMKCVKGQPHDHKHLMLTQII  1900
1901  PGSVLTDLLDAMHILREKYGIKSHCHCTNRQNLQGGNVPTMNGVSQVLQN  1950
1951  VLHHSNKTSVSLPESQQQNSPQKSQTNGNSSPGSASTDSRLTPPESQSPL  2000
2001  HWLADLAEQKSREEKQENKEFTLEREIKEDGDQDASDSPNGSTSPPASQS  2050
2051  NEQGSTLRDLLTTTAGKLRVGSTDAGIAFAPVYSMGTSSGKGGRTMPNIL  2100
2101  DDIIASVVENKIPPNKTSKINIKSEPNEEPKESSLPATDESNKSYRDIPH  2150
2151  SWICDQHILWLKDYKNSNNWKLFKECWKQGQPAVVSGVHKKMNISLWKAE  2200
2201  SISLDFGDHQADLLNCKDSIVSNANVKEFWDGFEEVSKRQKNKGGETVVL  2250
2251  KLKDCPSGEDFKAMMPTRYEDFLRCLPLPEYCNPEGKFNLASHLPGFFVR  2300
2301  PDLGPRLCSAYGVAAAKDHDIGTTNLHIEASDVVNVLVYVGIAKGNGVLS  2350
2351  KAGILKKFEEEELDDVLRKRLKDSSEIPGALWHIYAGKDVDKIREFLQKI  2400
2401  SKEQGLEVLPEHDPIRDQSWYVNRKLRQRLLEEYGVRACTLIQFLGDAIV  2450
2451  LPAGTLHQVQNFHSCVQVTEDFVSPEHLVQSFHLTQELRLLKEEINYDDK  2500
2501  LQVKNILYHAVKEMVRALKMHEDEVEDMEDT                     2531

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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