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

NucPred

Fetching Q9JIH7 from www.uniprot.org...

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

   1  MSDGTAEKQSGTPGFLSPPAPVPKNGSSSDSSVGEKLGAAVADSGIGRTE    50
  51  EYRRRRHTMDKDSRGAAATTTPTEHRFFRRSVICDSNATALELPGLPLSI   100
 101  PQPSVPAVVPQSAPPEPHREETLTATVASQVSQQPSAAASPGEQAVVGSA   150
 151  TATVPSSTSKDRPVSQPSLVGSKEEPPPSRSGSGSGGASAKEPQEERNQQ   200
 201  QDDIEELETKAVGMSNDGRFLKFDIEIGRGSFKTVYKGLDTETTVEVAWC   250
 251  ELQDRKLTKSERQRFKEEAEMLKGLQHPNIVRFYDSWESTVKGKKCIVLV   300
 301  TELMTSGTLKTYLKRFKVMKIKVLRSWCRQILKGLQFLHTRTPPIIHRDL   350
 351  KCDNIFITGPTGSVKIGDLGLATLKRASFAKSVIGTPEFMAPEMYEEKYD   400
 401  ESVDVYAFGMCMLEMATSEYPYSECQNAAQIYRRVTSGVKPASFDKVAIP   450
 451  EVKEIIEGCIRQNKDERYSIKDLLNHAFFQEETGVRVELAEEDDGEKIAI   500
 501  KLWLRIEDIKKLKGKYKDNEAIEFSFDLERDVPEDVAQEMVESGYVCEGD   550
 551  HKTMAKAIKDRVSLIKRKREQRQLVREEQEKRKQEESSFKQQNEQQASVS   600
 601  QAGIQPLSVASTGIPTAPTTSASVSTQVEPEEPEADQHQQLQYQQPSISV   650
 651  LSDGTVDSGQGSSVFTESRVSSQQTVSYGSQHEQAHSIGTAPGHTVSSIQ   700
 701  AQSQPHGVYPPSSMAQGQNQGQPSSSLAGVLSSQPVQHPQQQGIQPTVPP   750
 751  QQAVQYSLPQAASSSEGTVQPVSQPQVSAGTQSSTQGVSQAAPPEQTPIT   800
 801  QSQPTQPVPLVSSVDSAHSDVASGMSDGNENAPSSSGRHEGRTTKRHYRK   850
 851  SVRSRSRHEKTSRPKLRILNVSNKGDRVVECQLETHNRKMVTFKFDLDGD   900
 901  NPEEIATIMVNNDFILAIERESFVAQVREIIEKADEMLSEDVSVEPEGDQ   950
 951  GLESLQGKDDYGFPGSQKLEGEFKQPIAVSSMPQQIGVPTSSLTQVVHSA  1000
1001  GRRFIVSPVPESRLRESKIFTSEIPDPVAASTSQGPGMNLSHSASSLSLQ  1050
1051  QAFSELKHGQMTEGPNTAPPNFNHPGPTFSPFLTSIAGVQTVAASTPSVS  1100
1101  VPITSSPLNDISTSVMQSEGALPTDKGIGGVTTSTGVVASGGLTTLSVSE  1150
1151  TPTLSSAVSSSTAPAVVTVSTTSQPVQASTSGSIASSTGSFPSGTFSTTT  1200
1201  GTTVSSVAVPNAKPPTVLLQQVAGNTAGVAIVTSVSTTTPFPAMASQPSL  1250
1251  PLGSSTSAPTLAETVVVSAHSLDKASHSSTAGLGLSFCAPSSSSSSGTAV  1300
1301  SSSVSQPGIVHPLVISSAIASTPVLPQPAVPTSTPLLPQVPNIPPLVQPV  1350
1351  ANVPAVQQTLIHSQPQPALLPNQPHTHCPEMDADTQSKAPGIDDIKTLEE  1400
1401  KLRSLFSEHSSSGTQHASVSLETPLVVETVTPGIPTTAVAPSKLMTSTTS  1450
1451  TCLPPTNLPLGTAGMPVMPVGTPGQVSTPGTHASAPASTATGAKPGTTPP  1500
1501  KPSLTKTVVPPVGTELSAGTVPCEQLPPFPGPSLIQTQQPLEDLDAQLRR  1550
1551  TLSPETIPVTPAVGPLSTMSSTAVTEAGSQPQKDGTEVHVTASSSGAGVV  1600
1601  KMGRFQVSVTMDDAQKERKNRSEDTKSVHFESSTSESSVLSSSSPESTLV  1650
1651  KPEPNGITVSGISLDVPDSTHRTPTPEAKSETGQPTKVGRFQVTTTANKV  1700
1701  GRFSVSRTEDKVTELKKEGPVTSPFRDSEQTVIPAAIPKKEKPELAEPSH  1750
1751  LNGPSSDLEAAFLSRGGEDGSGSPHSPPHLCSKSLPIQTLSQSLSNSFNS  1800
1801  SYMSSDNESDIEDEDLRLELRRLREKHLKEIQDLQSRQKHEIESLYTKLG  1850
1851  KVPPAVIIPPAAPLSGRRRRPTKSKGSKSSRSSSLGNKSPQLSGNLSGQS  1900
1901  GTSVLNPQQTLHPPGNTPETGHNQLLQPLKPSPSSDNLYSAFTSDGAISV  1950
1951  PSLSAPGQGTSSTNTVGGTVSSQAAQAQPPAMTSSRKGTFTDDLHKLVDN  2000
2001  WARDAMNLSGRRGSKGHMNYEGPGMARKFSAPGQLCISMTSNMGGSTPIS  2050
2051  AASATSLGHFTKSMCPPQQYGFPAAPFGTQWSGTGGPAPQPLGQFQPVGT  2100
2101  TSLQNFNISNLQKSISNPPGSNLRTT                          2126

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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