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

NucPred

Fetching Q8MSS1 from www.uniprot.org...

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

   1  MAEDSGALESSYDFSIVQPDDHEYGEADIRLAGSSNDLSSLQNVSASTTR    50
  51  GTKGKGRLDSLKENLYKQQERLTALKERALRKSQDERHKSSMSDSMESLK   100
 101  TLGQKLTVLKTRSGDSSTPLVSPTKDSDPGDVSLLQTSGSEKLLMLTQRT   150
 151  EQNRALLEQRKRDLAKSLLSVKSNIGHQTTAELGSSMTDLRHAASVSNPP   200
 201  VSRHRSALDLEAQGQEAVDESRVKLLRSRMKLTELKQGRQEQELNELRTE   250
 251  LAKRAKLIERLELSGAELQRTLTQRNEELEQLRVVQAEEDSLKVQENSRL   300
 301  QGEVLVLRERLAELENVNDLLETTRCELQEELTTARERQRNLELEQEQEK   350
 351  ASRSPQSEAAHTDAQVSAELAKQLQELTNQLADLQATNEELRQQVAAQAK   400
 401  LQVTDEIVSQRLEELEATIAAQLLELQEQKSAMAAQNEELAEKTTELNVL   450
 451  NVNLRLLEEKLAQSSRSKPLFLEDHSEDSAASKQMQEDLQQLKLKLDETN   500
 501  KANIKLKLKCKQAEKKLQKFQSQDGQQQLASLLADNEELQQRIAVLEDEK   550
 551  GQWQLANMQEDDRQPEQSTESNNPLQLETIRLLEEQKLELQQALEALLSS   600
 601  SSSAESIEIVERHHLECLGQRRPASEGDAQEQKQVHPPGPSHVSELTQTE   650
 651  QTEEEDSSGETLSQLRERLELFTQERGEVLDKLEQLSAENLQLQARLEES   700
 701  SSSLQLLQREREKDLISSTSTSSNLSQELSSMQRSSEVVATLDAGEGGPV   750
 751  LFEKCEKSLSKLNSELEAYRKANDRQAKFNVSKKLAKEAKNCHTQLSELL   800
 801  HKVKEASTAVETVTVVETVVAVTAPNGKALAEYEQLNAQNAELKAVISRL   850
 851  RQELDELRESYPETEAPLAIVGSDSQREDEILQLQSQLEDARSLQAEQRQ   900
 901  QIEEQVDQIKELRQTEAEQLQLVARQSAEITQLQLQSEQFDQLLNSKEMS   950
 951  HEKQLEQQTRIRRELEARAESLEGELSILQTLVAEQKQQLIESVSESEHA  1000
1001  LNLKMLELQSAQEELRELRAKEDPDQLREALRVSKSLVAQQVRELTSSQE  1050
1051  TVDALNQQIQEYQGLEHAHKEEQFKNRELREKLKKYALNLKKRTQDNADL  1100
1101  EQKVQELTSQLQEQQELVKQKEEVEREPIVDNHRVEQLQQQVSKLNEDLK  1150
1151  AKIHLNLENRDALRQLKQQIQEQEQLIQERDAELQDANLVSKELRRERQE  1200
1201  ADQEVFQLGQENSRLREEISKLQEEIHNLGQRVNEEPTAVEDLRRQLEAK  1250
1251  SKKFEKSKELIKLRNATIQSLQRELQQLQQDQDSEVEHVRNARAAHEQLR  1300
1301  LEKDAEITALRQEILKLERSRAAGEGDDTITKTSHQLLESQSQQQAESLQ  1350
1351  VAERELQQLRVQLTAAQEQHALLAQQYASDKANFEMTIARLETLHEGIQA  1400
1401  KLQEDASYIESLEAQNTELQARSAALEEQAASQANQQAASQDKVQILEQQ  1450
1451  LKEQREQEEQKRQQDQQLQERFYELGQREQAQSRQLELLTSEAEESRQQL  1500
1501  AGLRTEYESLLAKHSQLTATAQAEREQMSSHSQEELAELRQQLDVKEADL  1550
1551  HRQRQVYDAKLAAKATELDELECDLNSHVERAAAETRELCQQLERSQELV  1600
1601  AQRTEELQRLNEEFQEVERERSTLSREVTLLRLQHDSAEQDVLELQELRM  1650
1651  QAMQDKTEMDNLRTQIDALCANHSQELQALQQRIAELDTLGQNQTDDQVY  1700
1701  IETENKRLAEQLSELQAQLARQQHQQQQQQHHHPAVQSQQHPPPASLFFG  1750
1751  GDALAAPSPFDEIAQPLRVSSLAASAPPPISPPPTIEDLQRNVSDLEKHA  1800
1801  QDLETKLLARNQNLAEQEERRLQLEQRLSEVERLLSERTQQLADIQTANE  1850
1851  ERDRLAALEKLIQPAAAPTLDMFFGGQAEETVPDAVSHHLDLGLPQTEPV  1900
1901  VEPLIQPKKAYLCQPKQEIQEQTAQTIDWGVDEDPWASAANEAPQTDVEH  1950
1951  LHTRIAQLELQLSNAEQQKTELQTKAAKLMKRLKEYKTKATTTATPTVTV  2000
2001  DNDLDSTIIEELKHQLQLQESRLSKAEEISQQHALEKEKLAKRIDVLTAG  2050
2051  NDRMAEMKERQDMDVQMYQARIRELQEKLSQLDQWGEPAATVSSSLDGDE  2100
2101  AARIESLQQEIQQLRQQVSELEDERTRDQAELGALRQSSQGYDEAEDNQK  2150
2151  LELQQLRQQESELEALRTRDQSELEALRQSCQGHDETVRIATLQQDNQQL  2200
2201  ELQQLRQAIIELETLRARDQTELEALRQSSQGHDEAARIAIEQRDNQQLE  2250
2251  LQQLRQQLIELEALRARDQAELEALRQSCQGQQLSVDMASRNDEQMAQLQ  2300
2301  EKESEIVHLKQRIEELMREDQTEKLVFEILTKNQELQLLRMQVKQLEEDK  2350
2351  EDQQVSAAPPKDDGETVEKLKSLCQQLQQEKSDMEEELRVLNNHVLSSLE  2400
2401  LEDRMKQTLLQLDTKNIEITELRRSLEILQSQNLGQNSAAEQIPDLSAIN  2450
2451  QQWEQLVEQKCGEVASIWQEHLSQREAAFKAQLEEVTQQQQRELPQSQQS  2500
2501  TQGEATSDIMQKMQKALETQEMEIVTLKEQLAIRSAEYARLAAQYDPFRL  2550
2551  QNRGGASGGNPASTTVSAGGPPSLTANEPLPEYVLKADLDYALMMLHQRD  2600
2601  MRVEEMIVELVQLLEERDHLQLKLSDTLRQLETERSRVSDEPSATASSSA  2650
2651  ASSSSPSKISSAGSNSELLGTTSAAGSDLKQKLAELQTVKHSKDKVIVDE  2700
2701  REQRLQQMLQLQKDMAKQGSGSQSGAGAVAAVAAPTSAAPTAIGVDLSQS  2750
2751  GLRSPSMMLMDWILGNNNKEEEAGHQTTG                       2779

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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