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

NucPred

Fetching Q24K09 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MPARTAPARVPALASRAFSLPDDVRRRLKDLERDSLTEKECVKEKLNLLH    50
  51  EFLRTEIKNQLCDLETKLHKEELSEEGYLAKVKSLLNKDLSLENGAHAFS   100
 101  REANGCLENGSQTSGEDCRVVMAEKGKPPKPVSRLYTPRRSKSDGETKSE   150
 151  VSSSPRITRKTTRQTTITSHFPRGPAKRKPEEEPEKVKSDDSVDEEKDQE   200
 201  EKRRRVTSRERVAGLLPAEEPGRVRPGTHMEEEGRDDKEEKRLRSQTKEP   250
 251  TPKHKAKEEPDRDVRPGGAQAEMNEGEDKDEKRHRSQPKDLASKRRPEEK   300
 301  EPERVKPQVSDEKDEDEKEEKRRRTTYRELTEKKMTRTKIAVVSKTNPPK   350
 351  CTECLQYLDDPELRYEQHPPDAVEEIQILTNERLSIFDANESGFESYEDL   400
 401  PQHKLTCFSVYCKRGHLCPIDTGLIEKDVELLFSGSAKPIYEDDPSPEGG   450
 451  INGKNFGPINEWWIAGFDGGEKALLGFSTSFAEYILMDPSPEYAPLFSVM   500
 501  QEKIYISKIVVEFLQSNPDSTYEDLINKIETTVPPCMLNLNRFTEDSLLR   550
 551  HAQFVVEQVESYDRAGDSDEQPIFLSPCMRDLIKLAGVTLGKRRAERRQT   600
 601  IRQPAKEKDKGPTKATTTKLVYQIFDTFFAEQIEKDDKEDKENAFKRRRC   650
 651  GVCEICQQPECGKCKACKDMVKFGGSGRSKQACQKRRCPNMAMKEADDDE   700
 701  EVDDNIPEMPSPKKMHQGKKKKQNKNRISWVGDAVKTDGKKSYYKKVCID   750
 751  SETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDT   800
 801  VLGATSDPLELFLVDECEDMQLSYIHSKVQVIYKAPSENWAMEGGVDPEA   850
 851  LMSEDDGKTYFYQLWYDQDYARFESPPKTQPTEDNKYKFCASCARLAEMR   900
 901  QKEIPRVVEQLQDLEGRVLYSLATKNGVQYRVGDGVYLPPEAFTFNIKLS   950
 951  SPVKRPRKEPVDEALYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCSK  1000
1001  KSNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDF  1050
1051  KAVQGRCTVEYGEDLPQCLQDFSAGGPDRFYFLEAYNAKSKSFEDPPNHA  1100
1101  RSTGNKGKGKGKGKNRTKSQTCEPSELETEIKLPKLRTLDVFSGCGGLSE  1150
1151  GFHQAGISETLWAIEMWDPAAQAFRLNNPGSTVFTEDCNVLLKLVMAGEV  1200
1201  TNSRGQKLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLS  1250
1251  YCDYYRPRYFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQ  1300
1301  YGVAQTRRRAIILAAAPGEPLPLFPEPLHVFAPRACQLSVVVDDKKFVSN  1350
1351  ITRLSSGPFRTITVRDTMSDLPEIRNGASALEISYNGEPQSWFQRQLRGS  1400
1401  QYQPILRDHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTLAR  1450
1451  KLRYNYHDKKNGCSSSGALRGVCSCVEGKPCEPAARQFNTLIPWCLPHTG  1500
1501  NRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECA  1550
1551  RSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKRCMLAKARESA  1600
1601  SAKIKEEAAKD                                         1611

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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