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

NucPred

Fetching Q8N787 from www.uniprot.org...

The NucPred score for your sequence is 0.75 (see score help below)

   1  MASEVVCGLIFRLLLPICLAVACAFRYNGLSFVYLIYLLLIPLFSEPTKT    50
  51  TMQGHTGRLLKSLCFISLSFLLLHIIFHITLVSLEAQHRIAPGYNCSTWE   100
 101  KTFRQIGFESLKGADAGNGIRVFVPDIGMFIASLTIWLLCRNIVQKPVTD   150
 151  EAAQSNPEFENEELAEGEKIDSEEALIYEEDFNGGDGVEGELEESTKLKM   200
 201  FRRLASVASKLKEFIGNMITTAGKVVVTILLGSSGMMLPSLTSSVYFFVF   250
 251  LGLCTWWSWCRTFDPLLFSCLCVLLAIFTAGHLIGLYLYQFQFFQEAVPP   300
 301  NDYYARLFGIKSVIQTDCSSTWKIIVNPDLSWYHHANPILLLVMYYTLAT   350
 351  LIRIWLQEPLVQDEGTKEEDKALACSPIQITAGRRRSLWYATHYPTDERK   400
 401  LLSMTQDDYKPSDGLLVTVNGNPVDYHTIHPSLPMENGPGKADLYSTPQY   450
 451  RWEPSDESSEKREEEEEEKEEFEEERSREEKRSIKVHAMVSVFQFIMKQS   500
 501  YICALIAMMAWSITYHSWLTFVLLIWSCTLWMIRNRRKYAMISSPFMVVY   550
 551  GNLLLILQYIWSFELPEIKKVPGFLEKKEPGELASKILFTITFWLLLRQH   600
 601  LTEQKALQEKEALLSEVKIGSQENEEKDEELQDIQVEGEPKEEEEEEAKE   650
 651  EKQERKKVEQEEAEEEDEQDIMKVLGNLVVAMFIKYWIYVCGGMFFFVSF   700
 701  EGKIVMYKIIYMVLFLFCVALYQVHYEWWRKILKYFWMSVVIYTMLVLIF   750
 751  IYTYQFENFPGLWQNMTGLKKEKLEDLGLKQFTVAELFTRIFIPTSFLLV   800
 801  CILHLHYFHDRFLELTDLKSIPSKEDNTIYRLAHPEGSLPDLTMMHLTAS   850
 851  LEKPEVRKLAEPGEEKLEGYSEKAQKGDLGKDSEESEEDGEEEEESEEEE   900
 901  ETSDLRNKWHLVIDRLTVLFLKFLEYFHKLQVFMWWILELHIIKIVSSYI   950
 951  IWVSVKEVSLFNYVFLISWAFALPYAKLRRLASSVCTVWTCVIIVCKMLY  1000
1001  QLQTIKPENFSVNCSLPNENQTNIPFNELNKSLLYSAPIDPTEWVGLRKS  1050
1051  SPLLVYLRNNLLMLAILAFEVTIYRHQEYYRGRNNLTAPVSRTIFHDITR  1100
1101  LHLDDGLINCAKYFINYFFYKFGLETCFLMSVNVIGQRMDFYAMIHACWL  1150
1151  IAVLYRRRRKAIAEIWPKYCCFLACIITFQYFICIGIPPAPCRDYPWRFK  1200
1201  GASFNDNIIKWLYFPDFIVRPNPVFLVYDFMLLLCASLQRQIFEDENKAA  1250
1251  VRIMAGDNVEICMNLDAASFSQHNPVPDFIHCRSYLDMSKVIIFSYLFWF  1300
1301  VLTIIFITGTTRISIFCMGYLVACFYFLLFGGDLLLKPIKSILRYWDWLI  1350
1351  AYNVFVITMKNILSIGACGYIGTLVHNSCWLIQAFSLACTVKGYQMPAAN  1400
1401  SPCTLPSGEAGIIWDSICFAFLLLQRRVFMSYYFLHVVADIKASQILASR  1450
1451  GAELFQATIVKAVKARIEEEKKSMDQLKRQMDRIKARQQKYKKGKERMLS  1500
1501  LTQEPGEGQDMQKLSEEDDEREADKQKAKGKKKQWWRPWVDHASMVRSGD  1550
1551  YYLFETDSEEEEEEELKKEDEEPPRRSAFQFVYQAWITDPKTALRQRHKE  1600
1601  KKRSAREERKRRRKGSKEGPVEWEDREDEPIKKKSDGPDNIIKRIFNILK  1650
1651  FTWVLFLATVDSFTTWLNSISREHIDISTVLRIERCMLTREIKKGNVPTR  1700
1701  ESIHMYYQNHIMNLSRESGLDTIDEHPGAASGAQTAHRMDSLDSHDSISS  1750
1751  EPTQCTMLYSRQGTTETIEEVEAEQEEEAGSTAPEPREAKEYEATGYDVG  1800
1801  AMGAEEASLTPEEELTQFSTLDGDVEAPPSYSKAVSFEHLSFGSQDDSAG  1850
1851  KNRMAVSPDDSRTDKLGSSILPPLTHELTASELLLKKMFHDDELEESEKF  1900
1901  YVGQPRFLLLFYAMYNTLVARSEMVCYFVIILNHMVSASMITLLLPILIF  1950
1951  LWAMLSVPRPSRRFWMMAIVYTEVAIVVKYFFQFGFFPWNKNVEVNKDKP  2000
2001  YHPPNIIGVEKKEGYVLYDLIQLLALFFHRSILKCHGLWDEDDMTESGMA  2050
2051  REESDDELSLGHGRRDSSDSLKSINLAASVESVHVTFPEQQTAVRRKRSG  2100
2101  SSSEPSQRSSFSSNRSQRGSTSTRNSSQKGSSVLSIKQKGKRELYMEKLQ  2150
2151  EHLIKAKAFTIKKTLEIYVPIKQFFYNLIHPEYSAVTDVYVLMFLADTVD  2200
2201  FIIIVFGFWAFGKHSAAADITSSLSEDQVPGPFLVMVLIQFGTMVVDRAL  2250
2251  YLRKTVLGKVIFQVILVFGIHFWMFFILPGVTERKFSQNLVAQLWYFVKC  2300
2301  VYFGLSAYQIRCGYPTRVLGNFLTKSYNYVNLFLFQGFRLVPFLTELRAV  2350
2351  MDWVWTDTTLSLSSWICVEDIYAHIFILKCWRESEKRYPQPRGQKKKKVV  2400
2401  KYGMGGMIIVLLICIVWFPLLFMSLIKSVAGVINQPLDVSVTITLGGYQP  2450
2451  IFTMSAQQSQLKVMDQQSFNKFIQAFSRDTGAMQFLENYEKEDITVAELE  2500
2501  GNSNSLWTISPPSKQKMIHELLDPNSSFSVVFSWSIQRNLSLGAKSEIAT  2550
2551  DKLSFPLKNITRKNIAKMIAGNSTESSKTPVTIEKIYPYYVKAPSDSNSK  2600
2601  PIKQLLSENNFMDITIILSRDNTTKYNSEWWVLNLTGNRIYNPNSQALEL  2650
2651  VVFNDKVSPPSLGFLAGYGIMGLYASVVLVIGKFVREFFSGISHSIMFEE  2700
2701  LPNVDRILKLCTDIFLVRETGELELEEDLYAKLIFLYRSPETMIKWTREK  2750
2751  TN                                                  2752

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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