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

NucPred

Fetching Q9R172 from www.uniprot.org...

The NucPred score for your sequence is 0.62 (see score help below)

   1  MGPGARGRRRRRRLMALPPPPPPMRALPLLLLLLAGLGAAAPPCLDGSPC    50
  51  ANGGRCTHQQPSREAACLCLPGWVGERCQLEDPCHSGPCAGRGVCQSSVV   100
 101  AGVARFSCRCLRGFRGPDCSLPDPCFSSPCAHGAPCSVGSDGRYACACPP   150
 151  GYQGRNCRSDIDECRAGASCRHGGTCINTPGSFHCLCPLGYTGLLCENPI   200
 201  VPCAPSPCRNGGTCRQSSDVTYDCACLPGFEGQNCEVNVDDCPGHRCLNG   250
 251  GTCVDGVNTYNCQCPPEWTGQFCTEDVDECQLQPNACHNGGTCFNLLGGH   300
 301  SCVCVNGWTGESCSQNIDDCATAVCFHGATCHDRVASFYCACPMGKTGLL   350
 351  CHLDDACVSNPCHEDAICDTNPVSGRAICTCPPGFTGGACDQDVDECSIG   400
 401  ANPCEHLGRCVNTQGSFLCQCGRGYTGPRCETDVNECLSGPCRNQATCLD   450
 451  RIGQFTCICMAGFTGTFCEVDIDECQSSPCVNGGVCKDRVNGFSCTCPSG   500
 501  FSGSTCQLDVDECASTPCRNGAKCVDQPDGYECRCAEGFEGTLCERNVDD   550
 551  CSPDPCHHGRCVDGIASFSCACAPGYTGIRCESQVDECRSQPCRYGGKCL   600
 601  DLVDKYLCRCPPGTTGVNCEVNIDDCASNPCTFGVCRDGINRYDCVCQPG   650
 651  FTGPLCNVEINECASSPCGEGGSCVDGENGFHCLCPPGSLPPLCLPANHP   700
 701  CAHKPCSHGVCHDAPGGFQCVCDPGWSGPRCSQSLAPDACESQPCQAGGT   750
 751  CTSDGIGFHCTCAPGFQGHQCEVLSPCTPSLCEHGGHCESDPDQLTVCSC   800
 801  PPGWQGPRCQQDVDECAGASPCGPHGTCTNLPGSFRCICHGGYTGPFCDQ   850
 851  DIDDCDPNPCLNGGSCQDGVGSFSCSCLSGFAGPRCARDVDECLSSPCGP   900
 901  GTCTDHVASFTCTCPPGYGGFHCETDLLDCSPSSCFNGGTCVDGVNSFSC   950
 951  LCRPGYTGTHCQYKVDPCFSRPCLHGGICNPTHSGFECTCREGFTGNQCQ  1000
1001  NPVDWCSQAPCQNGGRCVQTGAYCICPPEWSGPLCDIPSLPCTEAAAHMG  1050
1051  VRLEQLCQAGGQCIDKDHSHYCVCPEGRMGSHCEQEVDPCTAQPCQHGGT  1100
1101  CRGYMGGYVCECPTGYSGDSCEDDVDECASQPCQNGGSCIDLVAHYLCSC  1150
1151  PPGTLGVLCEINEDDCGPGPSLDSGLRCLHNGTCVDLVGGFRCNCPPGYT  1200
1201  GLHCEADINECRPGTCHAAHTRDCLQDPGGHFRCICLPGFTGPRCQTALF  1250
1251  PCESQPCQHGGQCRPSLGRGGGLTFTCHCVQPFWGLRCERVARSCRELQC  1300
1301  PVGIPCQQTARGPRCACPPGLSGPSCRVSRASPSGATNTSCAATPCLHGG  1350
1351  SCLPVQSVPFFRCVCAPGWGGPRCETPSAAPEVPEEPRCPRAACQAKRGD  1400
1401  QNCDRECNSPGCGWDGGDCSLNVDDPWRQCEALQCWRLFNNSRCDPACSS  1450
1451  PACLYDNFDCYSGGRDRTCNPVYKKYCADHFADGRCDQGCNTEECGWDGL  1500
1501  DCASEVPALLARGVLVLTVLLPPEELLRSSADFLQRLSAILRTSLRFRLD  1550
1551  ARGQAMVFPYHRPSPGSESRVRRELGPEVIGSVVMLEIDNRLCLKSAEND  1600
1601  HCFPDAQSAADYLGALSAVERLDFPYPLRDVRGEPLEPPEQSVPLLPLLV  1650
1651  AGAVFLLVIFVLGVMVARRKREHSTLWFPEGFALHKDIAAGHKGRREPVG  1700
1701  QDALGMKNMTKGESLMGEVATDWNDSECPEAKRLKVEEPGMGAEEPVDCR  1750
1751  QWTQHHLVAADIRVAPAMALTPPQGDADADGMDVNVRGPDGFTPLMLASF  1800
1801  CGGALEPMPAEEDEADDTSASIISDLICQGAQLGARTDRTGETALHLAAR  1850
1851  YARADAAKRLLDAGADTNAQDHSGRTPLHTAVTADAQGVFQILIRNRSTD  1900
1901  LDARMADGSTALILAARLAVEGMVEELIASHADVNAVDELGKSALHWAAA  1950
1951  VNNVEATLALLKNGANKDMQDSKEETPLFLAAREGSYEAAKLLLDHFANR  2000
2001  EITDHLDRLPRDVAQERLHQDIVRLLDQPSGPRSPSGPHGLGPLLCPPGA  2050
2051  FLPGLKAVQSGTKKSRRPPGKTGLGPQGTRGRGKKLTLACPGPLADSSVT  2100
2101  LSPVDSLDSPRPFGGPPASPGGFPLEGPYATTATTVSLAQLGASRAGPLG  2150
2151  RQPPGGCVLSLGLLNPVAVPLDWARLPPPAPPGPSFLLPLAPGSQLLNPA  2200
2201  TPVSPHERPPPYLAAPGHGEEYPAAGTHSSPTKARFLRVPSEHPYLTPSP  2250
2251  ESPEHWASPSPPSLSDWSDSTPSPATATSATAAGALPAQPHPISVPSLPQ  2300
2301  SQTQLGPQPEVTPKRQVMA                                 2319

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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