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

NucPred

Fetching Q9Y4K1 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MPLSPPAQGDPGEPSPCRPPKKHTTFHLWRSKKKQQPAPPDCGVFVPHPL    50
  51  PAPAGEARALDVVDGKYVVRDSQEFPLHCGESQFFHTTSEALGSLLLESG   100
 101  IFKKSRAQPPEDNRRKPVLGKLGTLFTAGRRRNSRNGLESPTRSNAKPLS   150
 151  PKDVVASPKLPERESERSRSQSSQLKQTDTSEEGSPRENPREAEGELPES   200
 201  GGPAAPPDAELSPRWSSSAAAVAVQQCHENDSPQLEPLEAEGEPFPDATT   250
 251  TAKQLHSSPGNSSRQENAETPARSPGEDASPGAGHEQEAFLGVRGAPGSP   300
 301  TQERPAGGLGEAPNGAPSVCAEEGSLGPRNARSQPPKGASDLPGEPPAEG   350
 351  AAHTASSAQADCTARPKGHAHPAKVLTLDIYLSKTEGAQVDEPVVITPRA   400
 401  EDCGDWDDMEKRSSGRRSGRRRGSQKSTDSPGADAELPESAARDDAVFDD   450
 451  EVAPNAASDNASAEKKVKSPRAALDGGVASAASPESKPSPGTKGQLRGES   500
 501  DRSKQPPPASSPTKRKGRSRALEAVPAPPASGPRAPAKESPPKRVPDPSP   550
 551  VTKGTAAESGEEAARAIPRELPVKSSSLLPEIKPEHKRGPLPNHFNGRAE   600
 601  GGRSRELGRAAGAPGASDADGLKPRNHFGVGRSTVTTKVTLPAKPKHVEL   650
 651  NLKTPKNLDSLGNEHNPFSQPVHKGNTATKISLFENKRTNSSPRHTDIRG   700
 701  QRNTPASSKTFVGRAKLNLAKKAKEMEQPEKKVMPNSPQNGVLVKETAIE   750
 751  TKVTVSEEEILPATRGMNGDSSENQALGPQPNQDDKADVQTDAGCLSEPV   800
 801  ASALIPVKDHKLLEKEDSEAADSKSLVLENVTDTAQDIPTTVDTKDLPPT   850
 851  AMPKPQHTFSDSQSPAESSPGPSLSLSAPAPGDVPKDTCVQSPISSFPCT   900
 901  DLKVSENHKGCVLPVSRQNNEKMPLLELGGETTPPLSTERSPEAVGSECP   950
 951  SRVLVQVRSFVLPVESTQDVSSQVIPESSEVREVQLPTCHSNEPEVVSVA  1000
1001  SCAPPQEEVLGNEHSHCTAELAAKSGPQVIPPASEKTLPIQAQSQGSRTP  1050
1051  LMAESSPTNSPSSGNHLATPQRPDQTVTNGQDSPASLLNISAGSDDSVFD  1100
1101  SSSDMEKFTEIIKQMDSAVCMPMKRKKARMPNSPAPHFAMPPIHEDHLEK  1150
1151  VFDPKVFTFGLGKKKESQPEMSPALHLMQNLDTKSKLRPKRASAEQSVLF  1200
1201  KSLHTNTNGNSEPLVMPEINDKENRDVTNGGIKRSRLEKSALFSSLLSSL  1250
1251  PQDKIFSPSVTSVNTMTTAFSTSQNGSLSQSSVSQPTTEGAPPCGLNKEQ  1300
1301  SNLLPDNSLKVFNFNSSSTSHSSLKSPSHMEKYPQKEKTKEDLDSRSNLH  1350
1351  LPETKFSELSKLKNDDMEKANHIESVIKSNLPNCANSDTDFMGLFKSSRY  1400
1401  DPSISFSGMSLSDTMTLRGSVQNKLNPRPGKVVIYSEPDVSEKCIEVFSD  1450
1451  IQDCSSWSLSPVILIKVVRGCWILYEQPNFEGHSIPLEEGELELSGLWGI  1500
1501  EDILERHEEAESDKPVVIGSIRHVVQDYRVSHIDLFTEPEGLGILSSYFD  1550
1551  DTEEMQGFGVMQKTCSMKVHWGTWLIYEEPGFQGVPFILEPGEYPDLSFW  1600
1601  DTEEAYIGSMRPLKMGGRKVEFPTDPKVVVYEKPFFEGKCVELETGMCSF  1650
1651  VMEGGETEEATGDDHLPFTSVGSMKVLRGIWVAYEKPGFTGHQYLLEEGE  1700
1701  YRDWKAWGGYNGELQSLRPILGDFSNAHMIMYSEKNFGSKGSSIDVLGIV  1750
1751  ANLKETGYGVKTQSINVLSGVWVAYENPDFTGEQYILDKGFYTSFEDWGG  1800
1801  KNCKISSVQPICLDSFTGPRRRNQIHLFSEPQFQGHSQSFEETTSQIDDS  1850
1851  FSTKSCRVSGGSWVVYDGENFTGNQYVLEEGHYPCLSAMGCPPGATFKSL  1900
1901  RFIDVEFSEPTIILFEREDFKGKKIELNAETVNLRSLGFNTQIRSVQVIG  1950
1951  GIWVTYEYGSYRGRQFLLSPAEVPNWYEFSGCRQIGSLRPFVQKRIYFRL  2000
2001  RNKATGLFMSTNGNLEDLKLLRIQVMEDVGADDQIWIYQEGCIKCRIAED  2050
2051  CCLTIVGSLVTSGSKLGLALDQNADSQFWSLKSDGRIYSKLKPNLVLDIK  2100
2101  GGTQYDQNHIILNTVSKEKFTQVWEAMVLYT                     2131

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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