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

NucPred

Fetching Q61982 from www.uniprot.org...

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

   1  MGLGARGRRRRRRLMALPPPPPPMRALPLLLLLAGLGAAAPPCLDGSPCA    50
  51  NGGRCTHQQPSLEAACLCLPGWVGERCQLEDPCHSGPCAGRGVCQSSVVA   100
 101  GTARFSCRCLRGFQGPDCSQPDPCVSRPCVHGAPCSVGPDGRFACACPPG   150
 151  YQGQSCQSDIDECRSGTTCRHGGTCLNTPGSFRCQCPLGYTGLLCENPVV   200
 201  PCAPSPCRNGGTCRQSSDVTYDCACLPGFEGQNCEVNVDDCPGHRCLNGG   250
 251  TCVDGVNTYNCQCPPEWTGQFCTEDVDECQLQPNACHNGGTCFNLLGGHS   300
 301  CVCVNGWTGESCSQNIDDCATAVCFHGATCHDRVASFYCACPMGKTGLLC   350
 351  HLDDACVSNPCHEDAICDTNPVSGRAICTCPPGFTGGACDQDVDECSIGA   400
 401  NPCEHLGRCVNTQGSFLCQCGRGYTGPRCETDVNECLSGPCRNQATCLDR   450
 451  IGQFTCICMAGFTGTYCEVDIDECQSSPCVNGGVCKDRVNGFSCTCPSGF   500
 501  SGSMCQLDVDECASTPCRNGAKCVDQPDGYECRCAEGFEGTLCERNVDDC   550
 551  SPDPCHHGRCVDGIASFSCACAPGYTGIRCESQVDECRSQPCRYGGKCLD   600
 601  LVDKYLCRCPPGTTGVNCEVNIDDCASNPCTFGVCRDGINRYDCVCQPGF   650
 651  TGPLCNVEINECASSPCGEGGSCVDGENGFHCLCPPGSLPPLCLPANHPC   700
 701  AHKPCSHGVCHDAPGGFRCVCEPGWSGPRCSQSLAPDACESQPCQAGGTC   750
 751  TSDGIGFRCTCAPGFQGHQCEVLSPCTPSLCEHGGHCESDPDRLTVCSCP   800
 801  PGWQGPRCQQDVDECAGASPCGPHGTCTNLPGNFRCICHRGYTGPFCDQD   850
 851  IDDCDPNPCLHGGSCQDGVGSFSCSCLDGFAGPRCARDVDECLSSPCGPG   900
 901  TCTDHVASFTCACPPGYGGFHCEIDLPDCSPSSCFNGGTCVDGVSSFSCL   950
 951  CRPGYTGTHCQYEADPCFSRPCLHGGICNPTHPGFECTCREGFTGSQCQN  1000
1001  PVDWCSQAPCQNGGRCVQTGAYCICPPGWSGRLCDIQSLPCTEAAAQMGV  1050
1051  RLEQLCQEGGKCIDKGRSHYCVCPEGRTGSHCEHEVDPCTAQPCQHGGTC  1100
1101  RGYMGGYVCECPAGYAGDSCEDNIDECASQPCQNGGSCIDLVARYLCSCP  1150
1151  PGTLGVLCEINEDDCDLGPSLDSGVQCLHNGTCVDLVGGFRCNCPPGYTG  1200
1201  LHCEADINECRPGACHAAHTRDCLQDPGGHFRCVCHPGFTGPRCQIALSP  1250
1251  CESQPCQHGGQCRHSLGRGGGLTFTCHCVPPFWGLRCERVARSCRELQCP  1300
1301  VGIPCQQTARGPRCACPPGLSGPSCRVSRASPSGATNASCASAPCLHGGS  1350
1351  CLPVQSVPFFRCVCAPGWGGPRCETPSAAPEVPEEPRCPRAACQAKRGDQ  1400
1401  NCDRECNTPGCGWDGGDCSLNVDDPWRQCEALQCWRLFNNSRCDPACSSP  1450
1451  ACLYDNFDCYSGGRDRTCNPVYEKYCADHFADGRCDQGCNTEECGWDGLD  1500
1501  CASEVPALLARGVLVLTVLLPPEELLRSSADFLQRLSAILRTSLRFRLDA  1550
1551  RGQAMVFPYHRPSPGSESRVRRELGPEVIGSVVMLEIDNRLCLQSAENDH  1600
1601  CFPDAQSAADYLGALSAVERLDFPYPLRDVRGEPLEAPEQSVPLLPLLVA  1650
1651  GAVFLLIIFILGVMVARRKREHSTLWFPEGFALHKDIAAGHKGRREPVGQ  1700
1701  DALGMKNMAKGESLMGEVVTDLNDSECPEAKRLKVEEPGMGAEEPEDCRQ  1750
1751  WTQHHLVAADIRVAPATALTPPQGDADADGVDVNVRGPDGFTPLMLASFC  1800
1801  GGALEPMPAEEDEADDTSASIISDLICQGAQLGARTDRTGETALHLAARY  1850
1851  ARADAAKRLLDAGADTNAQDHSGRTPLHTAVTADAQGVFQILIRNRSTDL  1900
1901  DARMADGSTALILAARLAVEGMVEELIASHADVNAVDELGKSALHWAAAV  1950
1951  NNVEATLALLKNGANKDMQDSKEETPLFLAAREGSYEAAKLLLDHLANRE  2000
2001  ITDHLDRLPRDVAQERLHQDIVRLLDQPSGPRSPSGPHGLGPLLCPPGAF  2050
2051  LPGLKAVQSGTKKSRRPPGKTGLGPQGTRGRGKKLTLACPGPLADSSVTL  2100
2101  SPVDSLDSPRPFSGPPASPGGFPLEGPYATTATAVSLAQLGASRAGPLGR  2150
2151  QPPGGCVLSFGLLNPVAVPLDWARLPPPAPPGPSFLLPLAPGPQLLNPGA  2200
2201  PVSPQERPPPYLAAPGHGEEYPAAGTRSSPTKARFLRVPSEHPYLTPSPE  2250
2251  SPEHWASPSPPSLSDWSDSTPSPATATNATASGALPAQPHPISVPSLPQS  2300
2301  QTQLGPQPEVTPKRQVMA                                  2318

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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