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

NucPred

Fetching Q95XZ5 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MDPNNLQNSLNGTGNPNFQPVQTNAGGFGHQMAQTGAAAAAAATGQYNPM    50
  51  LLQQQYLNFGFGMNYNNQLFDFQAQQQQQQQYLMQQQQQQQQLHHQQQQQ   100
 101  HQNIAQPQAQHHQMNMFTQHQMLQLMQQQQQQQQQQPVQQIQRQQPIAQP   150
 151  IPQHTIPPSTSNQFQQQIQSAASSIFDSSVISSHQKLYEEQCRQIEKERK   200
 201  EQEERKRKQELEEQRKRNEELKRLRIAEEKRLLEEQQRLREQMERERLAE   250
 251  IKRLEEAARLEDERRIAADIEAQKQAMLQKMQAEQNKHIAEVERQRSELE   300
 301  ERFARVSQPMTLVGTHFLPNFLDMIPFPYESMVDSTLPQVFDMERDSAIL   350
 351  ESCDPQMVATISNILNATNIDDIITRMDKLRPDDKETNDLFLDKLPPIIQ   400
 401  AVVNYNTSALDVDSHNDMELLENEDVMMTEDITRTTAPSTSSSSYNNHHQ   450
 451  NSIVMMTSSSVSMSEATQSSSVTMNHHDVDEEGPAPISIEKRRQMMSVGK   500
 501  APKAGGGGGQNQRKKRDMVENLYDSLTDNFVPTDTGRRGRRRGRGSDDDE   550
 551  DELLQRDLKLIEEMEKGVKLPASVTGFTTTEEDVQHFFGSQKKRRKEDRI   600
 601  RKDRSPTPEDVIESRDAEWQERLRLKMEREKSRKADEESQNAWSLQALAD   650
 651  NETFTRFCQTVDGVLEQGDSLDTELKMPKNKKRRSGGDHHHKGDENSDES   700
 701  DEEEEMDEIDPDLRIELYILEELRRGSARLRENHALQAVGADKLLKLVAM   750
 751  LDRNIRDAISADNQRLLVPCDDDVDVGDVLEKEICEERVKRASDAAVVAL   800
 801  NIMSSHRMHKQVIIEDVIDRCVGLTRLLLIHLIYPASDSIYKSVNSKKKD   850
 851  RAPEEARRRKKAGVCTRDKFSEYIYERITEAIGLLAVLVKSESMTDTSVH   900
 901  NVASVALTPFFVANVGSLQITAMLLASNIFSRAEDSLRFSMITDLLSSLH   950
 951  RAPQFTQKNSNNGYSLPDGSWISTTTALFIQLVQSTIKIPKFKKHADEDE  1000
1001  LAKRSKKEEAMVKEGFLKASKVTNAFLNGFLAKCSQKGNKMDGEEDYRIL  1050
1051  FSNFLQELLSALYSPEWPAAEMILTALGSLLVKNFRSKSSDMTIRQASLD  1100
1101  YLGNITAKLRKDQKEAIAGERRLDAVVKKSFLLLSDKGVEDYESVDISNL  1150
1151  KQNDKLKVLETSLIDYLVITNSSDIIVYACNFYVGEWYKEVAEDLESARS  1200
1201  KLKQTVDTNESEKDVKKAERKYEKIQYRGAEMKVFLSKILDKKEIKRRLE  1250
1251  KSNKVKMLDSDAFWAVKFLAQSREFTHSFDTYLKHIVFGAGSETIVALRS  1300
1301  KALKCLSSIIEADSSVLILEDVQQAVHTRMVDSHAQVRESAVELIGRFVL  1350
1351  YDEEYVRKYYSQIAERILDTGVAVRKRVIRIMREICEKFPTFEMIPDMLA  1400
1401  RMIRRVTDEEGVKKLVFETFTTLWFQPVDTRIYTNAVATKVTTMCSVAQH  1450
1451  CIKDAMSDYLEQLILHIVKNGQEGSGMSVAVKQIIDSLVDHILNLEQHKS  1500
1501  SENVSEVELMRRKEQEEKYMAYLSTLAVFSKIRPLLLTSHVEVLLPYLTF  1550
1551  SGAKTNAENQVTKEMIGMLERVIPLVPFPSNIVLDSIDENLCKVIMFNGM  1600
1601  ALVVSAVSCVASIYKKFKRGATKTIDVFSTYLKHLEVIKRNFDSNPRYDL  1650
1651  DPKLFPILSRSIFTLGVLSRYFQFEEFVKEDPTEEKVEALKEKVFITLEF  1700
1701  FSRYHKGGLRQKALTAMGHFCAQHSTYLTKRQLTNTYLEILNAANSPQQQ  1750
1751  QQRILVLQNLEMFLQCEEQKLAASHDKWDENKEAQNLKEMELSGSGLGSS  1800
1801  VIQKYWKAVLESYVDADIQLRRAAVQVVWLTLNQGLVTPGASIPTLIAMT  1850
1851  TDPVDVIRNRIDILLKEIDSKYSGMVQSKAMQGVRLSYKLHLKLRMLQQE  1900
1901  KFVRGFRFCDFHLNTLPNALPEKTHDGMAVLSGLYQSLRTNRQQRRSFLQ  1950
1951  SMVKLFSEEFSHDKPQLMEYIFIADNLAMFPYQMIDEPLYVMRQIDQNIA  2000
2001  QTGQSLLVQYKLQLRMQESEDEDIVFLDENMMSRLSQLGQIETFHQLFLD  2050
2051  SQVPSLLLYVRTFLMQLYGFNETKVAEYQPSEAAKVYEKAVTRRNIHMFK  2100
2101  PITALEALNFPFEWGSFQHTAFLAEKICSFRKMLLSLDQVEEVEVSNTIT  2150
2151  AANDDYDEEEDGGEDSRGPIMEQMEH                          2176

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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