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

NucPred

Fetching O23372 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MSDGGVACMPLLNIMEKLPIVEKTTLCGGNESKTAATTENGHTSIATKVP    50
  51  ESQPANKPSASSQPVKKKRIVKVIRKVVKRRPKQPQKQADEQLKDQPPSQ   100
 101  VVQLPAESQLQIKEQDKKSEFKGGTSGVKEVENGGDSGFKDEVEEGELGT   150
 151  LKLHEDLENGEISPVKSLQKSEIEKGEIVGESWKKDEPTKGEFSHLKYHK   200
 201  GYVERRDFSADKNWKGGKEEREFRSWRDPSDEIEKGEFIPDRWQKMDTGK   250
 251  DDHSYIRSRRNGVDREKTWKYEYEYERTPPGGRFVNEDIYHQREFRSGLD   300
 301  RTTRISSKIVIEENLHKNEYNNSSNFVKEYSSTGNRLKRHGAEPDSIERK   350
 351  HSYADYGDYGSSKCRKLSDDCSRSLHSDHYSQHSAERLYRDSYPSKNSSL   400
 401  EKYPRKHQDASFPAKAFSDKHGHSPSRSDWSPHDRSRYHENRDRSPYARE   450
 451  RSPYIFEKSSHARKRSPRDRRHHDYRRSPSYSEWSPHDRSRPSDRRDYIP   500
 501  NFMEDTQSDRNRRNGHREISRKSGVRERRDCQTGTELEIKHKYKESNGKE   550
 551  STSSSKELQGKNILYNNSLLVEKNSVCDSSKIPVPCATGKEPVQVGEAPT   600
 601  EELPSMEVDMDICDTPPHEPMASDSSLGKWFYLDYYGTEHGPARLSDLKA   650
 651  LMEQGILFSDHMIKHSDNNRWLVNPPEAPGNLLEDIADTTEAVCIEQGAG   700
 701  DSLPELVSVRTLPDGKEIFVENREDFQIDMRVENLLDGRTITPGREFETL   750
 751  GEALKVNVEFEETRRCVTSEGVVGMFRPMKRAIEEFKSDDAYGSESDEIG   800
 801  SWFSGRWSCKGGDWIRQDEASQDRYYKKKIVLNDGFPLCLMQKSGHEDPR   850
 851  WHHKDDLYYPLSSSRLELPLWAFSVVDERNQTRGVKASLLSVVRLNSLVV   900
 901  NDQVPPIPDPRAKVRSKERCPSRPARPSPASSDSKRESVESHSQSTASTG   950
 951  QDSQGLWKTDTSVNTPRDRLCTVDDLQLHIGDWFYTDGAGQEQGPLSFSE  1000
1001  LQKLVEKGFIKSHSSVFRKSDKIWVPVTSITKSPETIAMLRGKTPALPSA  1050
1051  CQGLVVSETQDFKYSEMDTSLNSFHGVHPQFLGYFRGKLHQLVMKTFKSR  1100
1101  DFSAAINDVVDSWIHARQPKKESEKYMYQSSELNSCYTKRARLMAGESGE  1150
1151  DSEMEDTQMFQKDELTFEDLCGDLTFNIEGNRSAGTVGIYWGLLDGHALA  1200
1201  RVFHMLRYDVKSLAFASMTCRHWKATINSYKDISRQVDLSSLGPSCTDSR  1250
1251  LRSIMNTYNKEKIDSIILVGCTNVTASMLEEILRLHPRISSVDITGCSQF  1300
1301  GDLTVNYKNVSWLRCQNTRSGELHSRIRSLKQTTDVAKSKGLGGDTDDFG  1350
1351  NLKDYFDRVEKRDSANQLFRRSLYKRSKLYDARRSSAILSRDARIRRWAI  1400
1401  KKSEHGYKRVEEFLASSLRGIMKQNTFDFFALKVSQIEEKMKNGYYVSHG  1450
1451  LRSVKEDISRMCREAIKDELMKSWQDGSGLSSATKYNKKLSKTVAEKKYM  1500
1501  SRTSDTFGVNGASDYGEYASDREIKRRLSKLNRKSFSSESDTSSELSDNG  1550
1551  KSDNYSSASASESESDIRSEGRSQDLRIEKYFTADDSFDSVTEEREWGAR  1600
1601  MTKASLVPPVTRKYEVIEKYAIVADEEEVQRKMRVSLPEDYGEKLNAQRN  1650
1651  GIEELDMELPEVKEYKPRKLLGDEVLEQEVYGIDPYTHNLLLDSMPGELD  1700
1701  WSLQDKHSFIEDVVLRTLNRQVRLFTGSGSTPMVFPLRPVIEELKESARE  1750
1751  ECDIRTMKMCQGVLKEIESRSDDKYVSYRKGLGVVCNKEGGFGEEDFVVE  1800
1801  FLGEVYPVWKWFEKQDGIRSLQENKTDPAPEFYNIYLERPKGDADGYDLV  1850
1851  VVDAMHMANYASRICHSCRPNCEAKVTAVDGHYQIGIYSVRAIEYGEEIT  1900
1901  FDYNSVTESKEEYEASVCLCGSQVCRGSYLNLTGEGAFQKVLKDWHGLLE  1950
1951  RHRLMLEACVLNSVSEEDYLELGRAGLGSCLLGGLPDWMIAYSARLVRFI  2000
2001  NFERTKLPEEILKHNLEEKRKYFSDIHLDVEKSDAEVQAEGVYNQRLQNL  2050
2051  AVTLDKVRYVMRHVFGDPKNAPPPLERLTPEETVSFVWNGDGSLVDELLQ  2100
2101  SLSPHLEEGPLNELRSKIHGHDPSGSADVLKELQRSLLWLRDEIRDLPCT  2150
2151  YKCRNDAAADLIHIYAYTKCFFKVREYQSFISSPVHISPLDLGAKYADKL  2200
2201  GESIKEYRKTYGENYCLGQLIYWYNQTNTDPDLTLVKATRGCLSLPDVAS  2250
2251  FYAKAQKPSKHRVYGPKTVKTMVSQMSKQPQRPWPKDKIWTFKSTPRVFG  2300
2301  SPMFDAVLNNSSSLDRELLQWLRNRRHVFQATWDS                 2335

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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