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

NucPred

Fetching Q2U639 from www.uniprot.org...

The NucPred score for your sequence is 0.72 (see score help below)

   1  MAEITLDRTLVLLSSEKQRERSEGLAVSLFVLIVVFVIDPCISSRSSLND    50
  51  KACHKIFESLFRFISSEKSLYNRGNSKGPSASRLSTCASVLRLAVDALLH   100
 101  NLRAKSVRAVVDHITETLQDTGGSLFELLGVDYTKCLTALLNYPPHVEHL   150
 151  GASEWEKLMGFCLKIMNTQDYEDDRSHTGSDSRSTLDDFLGTGGTPTPSR   200
 201  SMPTLTAREKPKRDKGAISEAVVCIQLLTASVNAPVQEPAAKILHGLVGY   250
 251  VKSSHITGSGHQSAFNSINSVIMRVLSDQSELVQSILLDLIPVICHLWAT   300
 301  KLVGLKDELLVTIMLCIVLLTAATRQEPSELLSRYTEDLLGALYKEYIKR   350
 351  PEKDILQVDELVFHQKTSAAVDKILIWPRLESGKSEHNWTVIWAIANLVD   400
 401  LSEEITARSSSPRTSTETLNKRQRLTSMVDEIHRDCASSSGARRVCALQL   450
 451  IPLIPRHHASVDSKSSLLLRLLPNILDENGILASWTMITIASLAGSPNAD   500
 501  SPSLRAIWQQAWELTCRASTSQATSRASCILMNSILEYNLLEYSIVAEAT   550
 551  SSMLTSVNLNGPSTMSDASLTLWATTTRMTARVNPGSLPNASKQICAWLR   600
 601  EVWVIGTVTDRTQLAQLAAFARPLDLLNLLLACTNRHYIPPKPQFRGATS   650
 651  LIAKGWHFLHRSKQLLNYLFQLGGILDFDMWDTDDTIHLETFPRQDPNDN   700
 701  MVLDLLQVKSEMFLQAFQSLYEDKSHHVTVEIVQIVTSFCILVALYTECL   750
 751  PHLSASKFHNLQQNCERLWEIICTFLASHELEFIQGCLVVLSPFLNPEQF   800
 801  SYNPESTISKALLRLVIPLVSLLEAYRRSQRDNLALHNDEPMDLDDTLFN   850
 851  SKDRLAEVTSIVKSNREALPLFQEFSSFQRCITIQLSVLQKTNAFLRNHD   900
 901  QHSSRALVEYLIDLDEVDILAASNSLPYVYRAISGMDRTSLLDILEDLAE   950
 951  KCLQTYELERCEASHLLCIHMMHSFVKAWVSSEADSLSGSASDIYTWFRD  1000
1001  VLLAKDMASPSVLVVFSELLVDVINTNASYSSGESNTSPRTSLLKILEKG  1050
1051  SIPVKFDVGNLIPRLFGHYSLNDHDAIFNDVLRHLPKESDWVEGIALRLF  1100
1101  ILGQLASRWHTLLRRSIYHMFETPAHVPHSLQYAEKCICDVANKLGLKDA  1150
1151  KELFRLFSSQILYTWTEQESITAMPFSIFSYASIKDMLGDVQDELVGQII  1200
1201  MRAREDEEIEMSKYMGKPFVDLLATSFYKAEAYSIARDISTPPGQGSQPK  1250
1251  GVETRLKKILGTEQFMELIDQQFPQTIAAFFGSLDQYEQVERALSKRAKF  1300
1301  HDALDGLRCILGKSASKIVLPANQQPSFRARYLIDELEFLCKRSGYELET  1350
1351  IWTPTLASYVCRTLLESIHPALGSFHACSVIRKIRVLLCVAGSVMLRDYP  1400
1401  FEMTLHAMLPFLVDIYCSEDALGIFWYLLEAGQPYLAETPGLMAGVAVST  1450
1451  LLSLKKFLASPPVDTAQQGQSKIVTANIERFLQWFGEYINTYESSLDAET  1500
1501  QESFRRVVKSSQATSTVESHSDDSNERDVILEILDDRSSERSLLSKTVSD  1550
1551  HVIALLCADSEEPLGNYHKLNESDRDATANIVAIYQTLQSFNTGSGYRLW  1600
1601  AAKVIGRAFATTGKVCDALLREQDLSLFKSQLSDLRLEVHCYSKASILQE  1650
1651  LCNMLQNNSHLEVGLVERTLQLIISNLARYPDFEQCAGVVPLYLMKAFTW  1700
1701  DPYQCPPIPTLAPETERDDAKVNWQTSNSLSQWARGIALFLSKSAAEDPV  1750
1751  IGSLSHIIYVIPELAVRILPYMLHDVLLAELKGEANIRQKVSQIFKQALC  1800
1801  DVHDTTISHARLAIDCILYLRNQPKPNEATIVERDEWLEIDFAEASLAAS  1850
1851  RCRLPKTALIFLEIHASRVIFGSRRSSLAKYEAPPDMLHDIFKDIDDPDF  1900
1901  FYGIQQSPSLDSVMERLQHESSGFKNLLFQSAQYDSEIQMSADQNAYGVL  1950
1951  KALNSTNLQGIANSIFSASGGGFVDTSSSFDSMLQAATNLRQWDIPVSPL  2000
2001  NPSPPATVFRAFQSLNTSGSLAEASKSINECLLTTLESLTSASRSAMSLR  2050
2051  TAMRVLGVITEVSDVLDARSTEEIDHEWQKIAARDSWLKTTSVHEIGEIL  2100
2101  NSHEALFSSINRKSYLRSSTNISDHDAQLLEVKAIRQSLHITRTQGIQQA  2150
2151  SLKSAVYLSKLAHQCSALGINIEGAAKFDLANVLWDQGEMTASIRMLHQL  2200
2201  KDQNDLHKQAVPISRAELLVTLVSSLHIDSLRTKPCSFRTNSTSCKGHHV  2250
2251  AEARLEKPETIIQDYLLTAVKELKGRSGGEEAGRVYHGFATFCDQQLQNP  2300
2301  DGLEDFTRVEQLRNRKEKEVRALEDMMKAAEGREREALKFHRGRTKQWFD  2350
2351  LDDREYQRLRRSREAFLQQCLENYLLCLRESETYNNDVLRFCALWLDKSD  2400
2401  SDIANAAVSKHLGQVPSRKFAPLMNQLTSRLLDVPDEFQKMLFSLITRIC  2450
2451  VEHPFHGMYQIFASSKSKGGKDETALSRNRAAGRLVEGLKNDKRIGPTWV  2500
2501  AVHNTNINYVRFAIDRPDEKLKSGARVPLRKLQTGGRLEQDAATQKLPPP  2550
2551  TMNIEIRVDCDYRDVPKLVKYHPEFTIASGVSAPKIVSAFASNGLRYKQL  2600
2601  FKGGNDDLRQDAIMEQVFEQVSNLLKDHQATRQRNLGIRTYKVLPLTSNA  2650
2651  GIIEFVPHTIPLHDYLMPAHQKYYPKDMKPNVCRKHISDVQTRSFEQRVR  2700
2701  TYRQVTEHFHPVMKYFFMEKFNNPDDWFSKRLSYTRSTAAISILGHVLGL  2750
2751  GDRHGHNILLDERTGEVVHIDLGVAFEQGRVLPVPEVVPFRLTRDLVDGM  2800
2801  GVTKTEGVFRRCCEFTLETLRRESYSIMTILDVLRYDPLYSWTVSPLRMK  2850
2851  KMQDASEAGGGPPMLPGAADQRPSNEPSEADRALTVVAKKLGKTLSVTAT  2900
2901  VNELIQQATDEKNLAVLYCGWAAYA                           2925

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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