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

NucPred

Fetching Q921C3 from www.uniprot.org...

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

   1  MAEPSPARRPVPLIESELYFLIARYLSAGPCRRAAQVLVQELEQYQLLPK    50
  51  RLDWEGNEHNRSYEELVLSNKHVAPDHLLQICQRIGPMLDKEVPPSISRV   100
 101  TSLLGAGRQSLLRTAKDCRHTVWKGSAFAALHRGRPPEMPVNYGPPPSLV   150
 151  EIHRGRQLTGCSTFSTAFPGTMYQHIKMHRRILGHLSAVYCVAFDRTGHR   200
 201  IFTGSDDCLVKIWSTHNGRLLSTLRGHSAEISDMAVNYENTLIAAGSCDK   250
 251  IIRVWCLRTCAPVAVLQGHTGSITSLQFSPMAKGPQRYMVSTGADGTVCF   300
 301  WQWDLESLKFSPRPLKFTEKPRPGVQMLCSSFSVGGMFLATGSTDHVIRM   350
 351  YFLGFDAPEKIAELESHTDKVDSIQFCNNGDRFLSGSRDGTARIWRFEQL   400
 401  EWRSILLDMSARISGDTSSEEERFMKPKVTMIAWNQDDSTVVTAVNDHVL   450
 451  KVWSSYTGQLLHNLLGHADEVFVLETHPFDSRIMLSAGHDGSIFIWDITK   500
 501  GIKMKHYFNMIEGQGHGAVFDCKFSQDGQHFACTDSHGHLLIFGFGCSKP   550
 551  YEKIPDQMFFHTDYRPLIRDSNNYVLDEQTQQAPHLMPPPFLVDVDGNPH   600
 601  PTKFQRLVPGRENSADEHLVPQLGYVATSDGEVIEQIISLHTNDSGDASP   650
 651  ESSVLDGMIRQLQQQQDQRLGVDQDGTANGLPSGEGTPRRGSFRRLSLDI   700
 701  QSPPNIGLRRSGQVEGVRQMHQNAPRSQIATERDLQAWKRRVVVPEAPPG   750
 751  MFRRLEDIRIERGEEERNLYVIGRKKKTFQVPQKSNSMVLVSQSRQRTCR   800
 801  RKYANYSRRNADQCELSSGNESSGSVRHETSYDQSEGSCSSEDDEWRNDR   850
 851  RSGSDSDSSSDSSSQYSDWTADTGINLQPPLRMSCRRRVTRFCSTSEDEM   900
 901  SMENISPPKRRRKRRKESKPKRESLRRMTPAELANMEHLYEFHPPVWITD   950
 951  TTLRKSPFVPQMGDEVMYFRQGHEAYIEAVRRNNIYELNPHKEPWRKMDL  1000
1001  RDQELVKIVGLRYEVGPPTLCCLKLAFIDPATGRLTDKSFSIRYHDMPDV  1050
1051  IDFLVLRQFYDEARQRNWQPCDRFRSIIDDAWWFGTVLSQEPYQPQYPDS  1100
1101  HFQCYIVRWDNTETEKLSPWDMEPIPDNVDPPEELGASISVTSDELEKLL  1150
1151  YKPQEGEWGQRSRDEECDRIISGIDQLLNLDIAAAFAGPVDLCTYPKYCT  1200
1201  VVAYPTDLYTIRMRLVNRFYRRLSALIWEVRYIEHNARTFNEPESVIARS  1250
1251  AKKITDQLLKFIKNQDCTNISELCNTSDNDEDDSADDLDDSDLPKTSSGR  1300
1301  RKVHNWKRRSRASGCIESDWRRQCKALLILIFQCEDSEPFRQPVDLDEYP  1350
1351  DYRDIIDTPMDFGTVRETLEAGNYDSPVEFCKDIRLIFSNAKAYTPNKRS  1400
1401  KIYSMTLRLSALFEEKMKKISFDFKIGQKFKEKLRRSQRFKQRQNCNGAV  1450
1451  PGDRRRRNVKQKQFKSQTKVIPQLMCPPSQSTSSKVPLSATRKTSAGVSS  1500
1501  GFTSGDSSDSAGSLERVRRQRPEVLRSGSVLFGSEMEDFLATSSSSSASN  1550
1551  SSEESKASPGARESSLRSGVLRGSNLGVTRTRAARRKAGSVSLENGCGRK  1600
1601  ATRKRVYLSDSDNNSVETDENLKNRKCGSSRKVLRKCAAVAASKIKLMSD  1650
1651  AEDSSSESPCSGRKLPHRNASAVARKKLLHNSDDQSLKSETEELKDQNQS  1700
1701  LLISGPHSVHNSISDSESDSDLRATRKTWNANGCTSHTAATCKTKSRPIE  1750
1751  SSEEDSRCHGSDHGPSSTGDPSTSGQKLRADSISEEADSEPESSVLCKNT  1800
1801  HLCKKAKILSDSEDCEEKCGERRGPEVEGSPVSEALREAILAPQCLSHRG  1850
1851  SETDVDSDGGAVREKSYSNENGSVSLENGQRRKVSRKSSSDKESNLQVTQ  1900
1901  KSPKDRSSPSRITQRASVATDKMKLTSDAEDLSLESVCTRSKRRRKKPAR  1950
1951  FACTPAKTALSSEEKHAHCEVPEAQPACRNKLPEPEHQDSAENPSQAASA  2000
2001  DLNSGGGSSFEQRKSIQSRQMGAVCVRPPPKTQSSSAGLSQENARSQTLD  2050
2051  SETSLPSESVLTQKATVESNFEEELNYGLRRWNGRRLRTYGKAPLSRTAQ  2100
2101  VTPSLQASAEVGVKRRRMHPEVDGEDVPGQMGSSGCGPDTSPKASDLGSV  2150
2151  TDSDVDCTDNTQTQRKKKRKGKARVLSKESVRKDREPHTKMRPCMLNEKD  2200
2201  AVQMHSDTLKAKTVPEKVPRRCATVAANKIKMMCNLKEVVSGPENVGIRT  2250
2251  ISRKLPYRQASAAAKKKLLSVYKEDDAPIHSENEKELYLRRFRSRKEKAQ  2300
2301  PTPR                                                2304

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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