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

NucPred

Fetching Q8CIR4 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MQVKKSWIEGVFYKRECNKFIPSSKDPHRCTPGCQICHNLVRCYCGRLIE    50
  51  EHHGLDRAWNLSVTEGHGDEQWSVEKHTVKSPTDTFGTINFQDGEHIHHS   100
 101  KYIRTSWDTKSDHLLHLMLKEWNMELPKLVISVHGGLQNFKISSKLKETF   150
 151  SQGLVKAAETTGAWIITEGINSGVSKHVGDALKAHSSKSLRKIWTVGIPP   200
 201  WGVIENQRELVGKDVVCMYQTLGNPLSKLTTLNCMHSHFILCDDGTVGMY   250
 251  GNEEKLRRNLEKHLSMQKIHTCSRQGVPVVGLVMEGGPNVILWVWETVKN   300
 301  KEPVVVCEGTGRAADLLAFTYKHLEDGGILRPQVKEELFCLIQNMFNFSL   350
 351  RQSKHLFQILMECMVHKDSITIFDADSEEHQDLDLAILTALLKGTSLSIS   400
 401  EQLNLAMAWDRMDIAKKHILTYGQHWKPGALEQAMLDALVMDRVDFVKLL   450
 451  IENGVNLHRFLTIPRLEELYNTKQGPTNKFLRHLVQDVKQHTLLSSYRIT   500
 501  LIDIGLVIEYLIGGAYRSSYTRKSFRILYNNLYRKHKSVSSFAQGLSQHS   550
 551  LHQRHSLRNRKESSESTLHSQFFRTAQPYKSKEKPEDSQKSKKKSKERQS   600
 601  LSEEPEAAGFIYPYNDLLVWAVLMKRQNMAMFFWQHGEEATVKAVIASIL   650
 651  YRAMAREAKESNMVDDTSEELKNYSEQFGQLALDVLEKAFKQNEPMAMKL   700
 701  LTYELKNWSNSTCLKLAVSGGLRPFVSHSCTQMLLTDMWMGRLKMRKNSW   750
 751  LKIIISILLPPMILTLEFKSKAEMSHVPQSQDFQFTWNYSDQGLSNTKES   800
 801  ACVKDYDLERGPDEKPDEPLHLDLRNVPQSLPWTRRVYEFYSAPFVKFWF   850
 851  YTMAYLAFLMLFTYTVLVEMQPQPSVHEWLVIIYIFTNAIEKVREICISE   900
 901  PSKFKQKVKMWLSEYWNLMETVAIGLFAVGFGLRWGHPPLQTAGRLIYCI   950
 951  DIIFWFSRLMDFFAVNQHAGPYVTMIAKMAANMFYIVIIMAIVLLSFGVA  1000
1001  RKAILSPKEPPSWRLARDIVFEPYWMMYGEVYASDIDVCSNETSCPPGSF  1050
1051  LTPFLQAVYLFVQYIIMVNLLIACFNNIYLDIKSISNKLWKYNRYRYIMT  1100
1101  YHQKPWLPPPFILLNHLCLLLRGLCCRPAPQDQEEGDGGLKLYLTKDDLK  1150
1151  KLHDFEEQCVEKYFHEKTEGLNCSFEEQIRMTSERVSEMFFQLKEMNEKV  1200
1201  SFIKDSLLSLDSQVGHLQDLSAITVDTLKVLSAVDTLQEDEILLANRKHS  1250
1251  TCRKRPHSWTNVICAKVLSDMESCGKKKLQYYSMPPSLLRSLARSQLPPS  1300
1301  VQRGALVEVTHSKREASHVREEQEEREMEQRTTASGISHVRQAHSKYGQF  1350
1351  LLVPSSGKQVPLSLETPPHLFRSSEEAGIDGLVLEHIHQSDLTTHLPQQT  1400
1401  PAASHQALVAEHKDQHEAVTQMSDKPAKAEQDLLAFSGTPAPMTVTSLPS  1450
1451  RAISMQDEGGYVNWAFSENDETGVFSFKKKWKTCLASTCNSDSNPGGDYF  1500
1501  LHTGGRSGLDNSRRLAQSCECPAGPWTQARRSFWINPLCRDKALIKSHSF  1550
1551  RFHKEEKLRKTWKNNSHSKSLETRSTWLKAKLLTKTRSLSKKKRKTQGLQ  1600
1601  VPVITVNACYQSDQLNAEPGETNTTEEFSKKWLSVSNFSQIGLEPYIYQK  1650
1651  MKMKEIKRHTTQASDHLRQPQENRDKTPTWNSGSTSLSRSFLTRSPNEVH  1700
1701  KISTSLKSPQEPHHHYSAIERNNLMRLSQTIPFTPIQLFTGEEVTIYKLE  1750
1751  ESSPLTLDKSMSSWSQHGRAAMIQVLSQEEMDGGLRKAMRVISTWSEDDV  1800
1801  LKPGQVFIVKSFLPEVVQTWYKIFQESTVLHLCLREIQQQRAAQKLIYTF  1850
1851  NQVKPQTIPYTPRFLEVSLVYCHSANQWLTIEKYMTGEFRKYNNNNGDEI  1900
1901  APTNTLEELMLAFSHWTYEYTRGELLVLDLQGVGENLTDPSVIKPEDKQS  1950
1951  RGMVFGPANLGEDAIRSFIAKHRCNSCCGKLRLPDLKRNDYSLSRTHCNL  2000
2001  GFGQTIEPTEELPERDKNRSSLEDHTRL                        2028

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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