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

NucPred

Fetching Q8TDX9 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MAEEAAQNISDDQERCLQAACCLSFGGELSVSTDKSWGLHLCSCSPPGGG    50
  51  LWVEVYANHVLLMSDGKCGCPWCALNGKAEDRESQSPSSSASRQKNIWKT   100
 101  TSEAALSVVNEKTQAVVNEKTQAPLDCDNSADRIPHKPFIIIARAWSSGG   150
 151  PRFHHRRLCATGTADSTFSALLQLQGTTSAAAPCSLKMEASCCVLRLLCC   200
 201  AEDVATGLLPGTVTMETPTKVARPTQTSSQRVPLWPISHFPTSPRSSHGL   250
 251  PPGIPRTPSFTASQSGSEILYPPTQHPPVAILARNSDNFMNPVLNCSLEV   300
 301  EARAPPNLGFRVHMASGEALCLMMDFGDSSGVEMRLHNMSEAMAVTAYHQ   350
 351  YSKGIFFHLLHFQLDMSTYKEAETQNTTLNVYLCQSENSCLEDSDPSNLG   400
 401  YELISAFVTKGVYMLKAVIYNEFHGTEVELGPYYVEIGHEAVSAFMNSSS   450
 451  VHEDEVLVFADSQVNQKSTVVIHHFPSIPSYNVSFISQTQVGDSQAWHSM   500
 501  TVWYKMQSVSVYTNGTVFATDTDITFTAVTKETIPLEFEWYFGEDPPVRT   550
 551  TSRSIKKRLSIPQWYRVMVKASNRMSSVVSEPHVIRVQKKIVANRLTSPS   600
 601  SALVNASVAFECWINFGTDVAYLWDFGDGTVSLGSSSSSHVYSREGEFTV   650
 651  EVLAFNNVSASTLRQQLFIVCEPCQPPLVKNMGPGKVQIWRSQPVRLGVT   700
 701  FEAAVFCDISQGLSYTWNLMDSEGLPVSLPAAVDTHRQTLILPSHTLEYG   750
 751  NYTALAKVQIEGSVVYSNYCVGLEVRAQAPVSVISEGTHLFFSRTTSSPI   800
 801  VLRGTQSFDPDDPGATLRYHWECATAGSPAHPCFDSSTAHQLDAAAPTVS   850
 851  FEAQWLSDSYDQFLVMLRVSSGGRNSSETRVFLSPYPDSAFRFVHISWVS   900
 901  FKDTFVNWNDELSLQAMCEDCSEIPNLSYSWDLFLVNATEKNRIEVPFCR   950
 951  VVGLLGSLGLGAISESSQLNLLPTEPGTADPDATTTPFSREPSPVTLGQP  1000
1001  ATSAPRGTPTEPMTGVYWIPPAGDSAVLGEAPEEGSLDLEPGPQSKGSLM  1050
1051  TGRSERSQPTHSPDPHLSDFEAYYSDIQEAIPSGGRQPAKDTSFPGSGPS  1100
1101  LSAEESPGDGDNLVDPSLSAGRAEPVLMIDWPKALLGRAVFQGYSSSGIT  1150
1151  EQTVTIKPYSLSSGETYVLQVSVASKHGLLGKAQLYLTVNPAPRDMACQV  1200
1201  QPHHGLEAHTVFSVFCMSGKPDFHYEFSYQIGNTSKHTLYHGRDTQYYFV  1250
1251  LPAGEHLDNYKVMVSTEITDGKGSKVQPCTVVVTVLPRYHGNDCLGEDLY  1300
1301  NSSLKNLSTLQLMGSYTEIRNYITVITRILSRLSKEDKTASCNQWSRIQD  1350
1351  ALISSVCRLAFVDQEEMIGSVLMLRDLVSFSNKLGFMSAVLILKYTRALL  1400
1401  AQGQFSGPFVIDKGVRLELIGLISRVWEVSEQENSKEEVYRHEEGITVIS  1450
1451  DLLLGCLSLNHVSTGQMEFRTLLHYNLQSSVQSLGSVQVHLPGDLAGHSP  1500
1501  AGAETQSPCYISQLILFKKNPYPGSQAPGQIGGVVGLNLYTCSSRRPINR  1550
1551  QWLRKPVMVEFGEEDGLDNRRNKTTFVLLRDKVNLHQFTELSENPQESLQ  1600
1601  IEIEFSKPVTRAFPVMLLVRFSEKPTPSDFLVKQIYFWDESIVQIYIPAA  1650
1651  SQKDASVGYLSLLDADYDRKPPNRYLAKAVNYTVHFQWIRCLFWDKREWK  1700
1701  SERFSPQPGTSPEKVNCSYHRLAAFALLRRKLKASFEVSDISKLQSHPEN  1750
1751  LLPSIFIMGSVILYGFLVAKSRQVDHHEKKKAGYIFLQEASLPGHQLYAV  1800
1801  VIDTGFRAPARLTSKVYIVLCGDNGLSETKELSCPEKPLFERNSRHTFIL  1850
1851  SAPAQLGLLRKIRLWHDSRGPSPGWFISHVMVKELHTGQGWFFPAQCWLS  1900
1901  AGRHDGRVERELTCLQGGLGFRKLFYCKFTEYLEDFHVWLSVYSRPSSSR  1950
1951  YLHTPRLTVSFSLLCVYACLTALVAAGGQEQPHLDVSPTLGSFRVGLLCT  2000
2001  LLASPGAQLLSLLFRLSKEAPGSARVEPHSPLRGGAQTEAPHGPNSWGRI  2050
2051  PDAQEPRKQPASAILSGSGRAQRKAASDNGTACPAPKLQVHGADHSRTSL  2100
2101  MGKSHCCPPHTQAPSSGLEGLMPQWSRALQPWWSSAVWAICGTASLACSL  2150
2151  GTGFLAYRFGQEQCVQWLHLLSLSVVCCIFITQPLMVCLMALGFAWKRRA  2200
2201  DNHFFTESLCEATRDLDSELAERSWTRLPFSSSCSIPDCAGEVEKVLAAR  2250
2251  QQARHLRWAHPPSKAQLRGTRQRMRRESRTRAALRDISMDILMLLLLLCV  2300
2301  IYGRFSQDEYSLNQAIRKEFTRNARNCLGGLRNIADWWDWSLTTLLDGLY  2350
2351  PGGTPSARVPGAQPGALGGKCYLIGSSVIRQLKVFPRHLCKPPRPFSALI  2400
2401  EDSIPTCSPEVGGPENPYLIDPENQNVTLNGPGGCGTREDCVLSLGRTRT  2450
2451  EAHTALSRLRASMWIDRSTRAVSVHFTLYNPPTQLFTSVSLRVEILPTGS  2500
2501  LVPSSLVESFSIFRSDSALQYHLMLPQLVFLALSLIHLCVQLYRMMDKGV  2550
2551  LSYWRKPRNWLELSVVGVSLTYYAVSGHLVTLAGDVTNQFHRGLCRAFMD  2600
2601  LTLMASWNQRARWLRGILLFLFTLKCVYLPGIQNTMASCSSMMRHSLPSI  2650
2651  FVAGLVGALMLAALSHLHRFLLSMWVLPPGTFTDAFPGLLFHFPRRSQKD  2700
2701  CLLGLSKSDQRAMACYFGILLIVSATLCFGMLRGFLMTLPQKRKSFQSKS  2750
2751  FVRLKDVTAYMWEKVLTFLRLETPKLEEAEMVENHNYYLDEFANLLDELL  2800
2801  MKINGLSDSLQLPLLEKTSNNTGEARTEESPLVDISSYQAAEPADIKDF   2849

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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