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

NucPred

Fetching Q11107 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MDEFELFQQLNQTAPLVKTEEPEVPDEFQQANNNQSAPLRTGLSDLSHEI    50
  51  AAAKQREEEEAQRLADFMQKDMKEPAVKRKRGSEEYKKDPLESKAPLSTF   100
 101  GHSSRPRRSVNYASIERGDEAQAQSLVTDFGSRGNRKKPKRTRDELDENY   150
 151  MEENEGNSGRKKKPNAKGASRQFQVPGLPTYASQYSRPPKQEDVFKTIVP   200
 201  LAEDARAEGERVIGFRLDSQPAVRRASGGFRRFCAWLSDNQIFSIMQTVD   250
 251  KLCIVGANNEDHDEILLKSIRHVYNAMPPTFRRDWEYAARKDVFDSRLFV   300
 301  QNMPMPLSEISVTDPRHPPSPIARGTTVRPNCCENQPLFLNMCETIEHYL   350
 351  GHHDVVHLFGCDICYRVYPSRYELTKHDCKEFAEYLRQLTFKQQTLHLEA   400
 401  AYMYLCCSQCGLWLSVKPSGEGKKGWTYFATALMNHSCQPLVPVVAYFPK   450
 451  PLKDEGKGIRIQFQVMSELNIGLPLSCSECNIEEFHSVVEIEEHFKEKHE   500
 501  ANHTCIKCGKTFGTEFMLKHHAQSHTTQTAQFANYLQMSATYQPPPSSGR   550
 551  LPYVGFGSSIPAIGGLTSGEVQALEASENKKSEFVEPDEYTIRKKLLRWK   600
 601  HAKTKKENRNITDSNEKEFSYEPGESSGEEDFQKSLLEQDNQSSSSSDSD   650
 651  SDSDDFTSSKQKKKRNIKIRGDLGYEHINRNKFFERPESEKEARKRIEKV   700
 701  YKKHVLLSRERLLDPEEALRILEESRMVHLNSIQSTLADDIAMSCIRTIS   750
 751  LPASNCIDPLKDLLLVNKIFYFCTKCNYIFSKDPVVHCLSCEVTEDDLIE   800
 801  VYHAASGPHAGVRCIDPECKAHLCSVISLKTHLSDVHSKQATLELVSGEL   850
 851  DNFSENRFDRSLMLMAKHFTQLQFDERTYLARFTDIECFMPFSGLLEAKD   900
 901  QPRPMPIRQQPQQIKPAYSLVRPDIIAPNELMRPYTLTPAIRPGQRIKPY   950
 951  KVPRTSRWYSCSWCDREYESLNQFVDHLTRFHTHPCPSCGKAFSSQNTRR  1000
1001  THVCSRLFAEIKGRGATLCGQCPSCPEIHQVERIFVHMLNRHFSTIEYVL  1050
1051  ATGELLPPARDVGIRYNHGENGGYGRSYESLRAIEQSVVDPRSPDYRLKQ  1100
1101  VKISALPIHGVELNRLPARDPPMGSFTVCPPKDKNIDPRLMCYMCELTFD  1150
1151  SYDELTHHMDDHPEKWANCPFCAANTPTHFDLQKHLIQEHVVQISGQACC  1200
1201  AFCQEHHRFMSSHILFRCKRVSRCTICGVKSNDPLANRVHIQRSHALTLR  1250
1251  RFQCAYCIKVFVSVGEYYEHECASGGGRVYSCTCSPNKFFNSPIEFCDHF  1300
1301  DSVHILRNKCQLCSYDAPSQDGMVKHRKTHMRSGCPKEQTKKLFILMKCL  1350
1351  FPKHNSGYMRFIEGGPVPASYQDVDRSQMNYLMCNMGTVSPSCHKSYAQA  1400
1401  PRTLLEALEGVASDSRSGGLQKVVNVTTRMNEPSSSDVIMLSDDEDDDCV  1450
1451  VFEKAVPNGVAQGSSTSTPNPESSINCEVRVETSQAGYGGAQQPGYVDED  1500
1501  DTDLEVAQGGKSPYGEPVVKEVVDENGDDELAVVAEVENSTGTLPSSISA  1550
1551  GREKKFKCQKCSLAFYTNGSLESHMRDHRQDAGAQLCTETYGIPVVTKAS  1600
1601  WLCRNCCVVFENQPKYQKHMAIHGDTCLTCIHCSGIAFNHTAIQNHMKSH  1650
1651  EEKKVRYSCGTCLCTFASDLALFDHLSVAHGVSLYYFCKVCGFGSTSADS  1700
1701  VFQHISIHNGHNYSLVQRFGACPAQLLNYDPTDELEFRSQILNKTIQLVS  1750
1751  PSDCSHRSMLLQCETVVSCKTCHCTQAWFNYMAFNNHSEETGFPQFKNVD  1800
1801  LANDYRRDFPLSRHLNERNALSMSQFGNAKHGSANHSHGQAQPNKRTFRH  1850
1851  EVPYRTAAPRSSLQTNGSSMGSVTTNGGRVVRPSPPNSMNVTLRRAPPQQ  1900
1901  APPRRIVIANSAPNNTNVLRNHVAVTTKCQFKDCDKVLHSEFDRQLHSMH  1950
1951  SSNSSWFCRQCGHSPKSEIDLFLHYIQVHLKPAYDKHQSNSFKSNVFHLK  2000
2001  CPIRSCTSPEFQSPKAFEKHMRTAHAAELPFEASCCDARFASKALCVKHD  2050
2051  QEHASFLDSNGTDASCCPICGSLSMWSLPKDPHTDCLQSHIIRHGLDYRS  2100
2101  SCRQCLKQFPADVNQDQVIAHILDTHGMSMHGNTFHCNLCTTGTKTVEEF  2150
2151  AEHCRKAHVFHILVKSSHSTRGELVVTTGQEYENYVGLKSVTRASLNSIS  2200
2201  SQRASNAGETAQPSVLCAGSGNAALLTIAAAIGEPETSNNTAEVLTLD    2248

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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