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

NucPred

Fetching Q9Z1N9 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MSLLCVRVKRAKFQGSPDKFNTYVTLKVQNVKSTTVAVRGDQPSWEQDFM    50
  51  FEISRLDLGLSVEVWNKGLIWDTMVGTVWIALKTIRQSDEEGPGEWSTLE   100
 101  AETLMKDDEICGTKNPTPHKILLDTRFELPFDIPEEEARYWTYKLEQINA   150
 151  LADDNEYSSQEESQRKPLPTAAAQCCHWTYLGWGEHQTFEDPDSAVDDRD   200
 201  SDYRSETSNSAPPPYHTTTQPNASVHQFPVPVRLPQQLFLQGSSHDSCND   250
 251  SMQSYDLDYPERRALSPTSSSRYGSSCNVSQGSSLLSELDQYHEQDDDGR   300
 301  ERDSIHSSHSYGSLSKDGQAGLGEQEKALEVTCESEKEKTGESKEMRDDA   350
 351  TIHPPSDLVLHKDHVLGPQESLPEETASSPFTQARAHWFRAVTKVRLQLQ   400
 401  EISDDGDPSLPQWLPEGPAGGLYGIDSMPDLRRKKPLPLVSDLSLVQSRK   450
 451  AGITSAMATRTSLKDEELKSHVYKKTLQALIYPISCTTPHNFEVWSATTP   500
 501  TYCYECEGLLWGLARQGMRCSECGVKCHEKCQDLLNADCLQRAAEKSSKH   550
 551  GAEDRTQNIIMAMKDRMKIRERNKPEIFEVIRDVFTVSKVAHVQQMKTVK   600
 601  QSVLDGTSKWSAKITITVVCAQGLQAKDKTGSSDPYVTVQVGKTKKRTKT   650
 651  IFGNLNPVWEEKFHFECHNSSDRIKVRVWDEDDDIKSRVKQRLKRESDDF   700
 701  LGQTIIEVRTLSGEMDVWYNLEKRTDKSAVSGAIRLQISVEIKGEEKVAP   750
 751  YHVQYTCLHENLFHYLTDIQGSGGVWIPEARGDDAWKVYFDETAQEIVDE   800
 801  FAMRYGIESIYQAMTHFACLSSKYMCPGVPAVMSTLLANINAYYAHTTAS   850
 851  TNVSASDRFAASNFGKERFVKLLDQLHNSLRIDLSTYRNNFPAGSPERLQ   900
 901  DLKSTVDLLTSITFFRMKVQELQSPPRASQVVKDCVKACLNSTYEYIFNN   950
 951  CHDLYSHQYQLQEQPLEEPGPSIRNLDFWPKLITLIVSIIEEDKNSYTPV  1000
1001  LSQFPQELNVGKVSAEVMWHLFAQDMKYALEEHEKDRLCKSADYMNLHFK  1050
1051  VKWLHNEYVRDLPALQGQVPEYPAWFEQFVLQWLDENEDVSLEFLRGALE  1100
1101  RDKKDGFQQTSEHALFSCSVVDVFTQLNQSFEIIRKLECPDPNILAHYMR  1150
1151  RFAKTIGKVLMQYADILSKNFPAYCTKERLPCILMNNMQQLRVQLEKMFE  1200
1201  AMGGKELDSEAADSLKELQVKLNTVLDELSMVFGNSFQVRIDECVRQMAD  1250
1251  ILGQVRGTGNASPNARASVAQDADSVLRPLMDFLDGNLTLFATVCEKTVL  1300
1301  KRVLKELWRVVMNTMERVIVLPPLTDQTGTQLILTAAKELSQLSKLKDHM  1350
1351  VREETRNLTPKQCAVLDLALDTIKQYFHAGGNGLKKTFLEKSPDLQSLRY  1400
1401  ALSLYTQTTDTLIKTFVRSQTAQGAGVDDPVGEVSIQVDLFTHPGTGEHK  1450
1451  VTVKVVAANDLKWQTAGMFRPFVEVTMVGPHQSDKKRKFTTKSKSNNWTP  1500
1501  KYNETFHFLLGNEEGPEAYELQICVKDYCFAREDRVIGLAVMPLRDVAAK  1550
1551  GSCACWCPLGRKIHMDETGMTILRILSQRSNDEVAREFVKLKSESRSTEE  1600
1601  GS                                                  1602

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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