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

NucPred

Fetching Q8AV58 from www.uniprot.org...

The NucPred score for your sequence is 0.40 (see score help below)

   1  MVGRKVDREIIARRNSRRDGMMMKLNFCFFFCRRWWAFLLLQLHMLQALA    50
  51  QDDVAPYFKTEPGLPQIHLEGNRLVLTCLAEGSWPLEFKWLHNDSEITTY   100
 101  SSEYKYIIPALQRSDAGFYQCIVRNRMGALLQRRSEVQVAYMGNFMDANQ   150
 151  KKTVTEGEAAVLNFMHIFSYPRPQVTWFRDGHKIIPSSRIAITLENQLVI   200
 201  LATSVADAGGYYAQAVNEKNGENKTSPLIHLSIASATDPSDPTAPIIVIP   250
 251  PQNKSVVVGTSEVTLECVASARPVERLSIMWKRNGIKITSGISSFGRRLT   300
 301  ITNPTSADVGMYFCEAKLRDSTEEPARAKAFISLMVPPYFTAEPEGVILA   350
 351  EVEKDVDILCQAMGVPIPSLVWYKDSVPLSKLQNPRYKVLLSGGLRIHAL   400
 401  RPQDAGIFQCFASNKAGEIQTYTYLDVTNIKPAFIQPPEDTTVTEGMTAM   450
 451  LTCEVSGAPKPAISWKKGNQILASGSVQIPRFVLLESGGLQITPVFLQDA   500
 501  GNYTCHAVNSEGALNAFVMLTVWNRTFIVHPPENSTVIKGTTATLRCEAT   550
 551  HDPRISIRYVWKKDSVVINPSSSSRITVEKDGTLLISQTWSGDIGDYTCE   600
 601  VISFGGNDSRMARLEVIELPHSPQNLLATLNSSYSRSVVLSWVRPFDGNS   650
 651  PVLYYMVELSENNSPWKVHLSNLDPKMTSVTVSGLTPARTYQFRVCAVNQ   700
 701  VGKGQYSSETSRLMLPEEPPSAPPKNIVASGRTNQSIMVQWQPPPESEHN   750
 751  GVLHGYILRYRLAGLPGEYQYKNITSAEINYCLVTDLIIWTQYEIQVASY   800
 801  NGAGLGAFSRPVTEYTLQGVPTAPPQNVQVEAVNSTTIQFLWSPPPQQFI   850
 851  NGINQGYKLLAWPVDAPGSVTVVTIAPDFHGVHSGCITNLKKYTTYYTSV   900
 901  LCFTTPGDGPRSAPQLLRTLEDKPGAVGHLSFTEILDTSLKVSWQEPVEK   950
 951  NGIITGYQLSWEVYGRNESRLTRTLTNTTLEYKITGLSSLTTYTIEVAAV  1000
1001  TAKGSGWVTSSTISSGVPPELPGAPSNLVISNISPRSATLQFRPGYDGKT  1050
1051  SICKWIVEGQVGVLGEEEEWVSLHEVDNEPDAQMLEVPNLTPYTHYRFRM  1100
1101  RQVNVVGASPLSQPSRVIQTLQAPPDVAPGSVSVRTASESSLRMRWVPLP  1150
1151  DTQYNGNPESVGYRIKFWRVDLQPSALLKVISDRLERECTIQDLEEWTEY  1200
1201  ELQIQAFNAIGAGPWNEVVGVRTRESVPSAPPENVSAEAVSSTQILLTWS  1250
1251  AVPESEQNGLILGYKILYKAKDLDSEPRSQTVRGNHTQSCLLSGLRKYVL  1300
1301  YEIRVLAFTRIGDGVPSSPVLTERTKDDAPGPPIRLVFPEVRLTSVRIVW  1350
1351  QPPEEPNGIILGYQIAYRLASSSPNKFTTVEVGSTVRQFTATDLTPESAY  1400
1401  IFRTSAKTRQGWGEPLEATVITTEKRERPAPPQQLTTPQSDVSSRSLQLH  1450
1451  WVPGSDGSSPIRYFTVQVRELPNGDWQTYSSSISHEATSCIIESLNPFTS  1500
1501  YKLRVKATNDIGDSDYSAETEAVTTLQDVPDEPPSSVLVTPHTTSSVLVQ  1550
1551  WQPPKAESLNGLLLGYRIYYRELDYDAGSATESKAVKNPSALRAELTPQS  1600
1601  SFKTVNSSSALTTYELTQLKKYKRYEVLMTAYNVIGESPTSTPVEVFVGE  1650
1651  AAPAMAPQNIQVNSLSASQLELTWDPPPADSQNGNIQGYKIYYWEGDVQN  1700
1701  DTEKVKVFSSLRQLSASKNLTSHTRYLVCISAFNAAGDGPRSRPSAGRTH  1750
1751  QAAPSAPSFLVFSEITSTTLNVSWGEPTAANGVLQGYRVVYEPLAPVQGV  1800
1801  SKVVTVDIKGNWQRWLKVRDLTKGMTYLFRVQARTIAYGPELQANVTAGP  1850
1851  AEGSPGSPHEILVTKSASGLTVQWTEGDSGEKPTTGYIIEARPSDEGLWD  1900
1901  MFVKDIPRSATSYTVSLDKLKQGVTYEFRVVAVNEFGYGEPSVPSVAVSA  1950
1951  QTEAPFYEEWWFLLVMALSSLILILLVVFALVLHGQSKKYKNCSTGKTIS  2000
2001  NVEESVTLDNGGFTALELNSRHLNIKSTFSKKNGTRSPPRPSPGGLHYSD  2050
2051  EDICNKYNGAVLTEGLGLNEKPLEMSESEATDSDYEDELPKHSFVNHYMS  2100
2101  DPTYYNSWKRQQKGVKHPTSYRYEECSASETEPYFQTVITTQSSGGVYTP  2150
2151  TGQPAPGSRTPVTGFSSFV                                 2169

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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