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

NucPred

Fetching Q99246 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MMMMMMMKKMQHQRQHQEDHANEANYARGTRLPISGEGPTSQPNSSKQTV    50
  51  LSWQAAIDAARQAKAAQTMSTSAPPPVGSLSQRKRQQYAKSKKQGNSSNS   100
 101  RPARALFCLSLNNPIRRACISIVEWKPFDIFILLAIFANCVALAIYIPFP   150
 151  EDDSNSTNHNLEKVEYAFLIIFTVETFLKIIAYGLLLHPNAYVRNGWNLL   200
 201  DFVIVIVGLFSVILEQLTKETEGGNHSSGKSGGFDVKALRAFRVLRPLRL   250
 251  VSGVPSLQVVLNSIIKAMVPLLHIALLVLFVIIIYAIIGLELFIGKMHKT   300
 301  CFFADSDIVAEEDPAPCAFSGNGRQCTANGTECRSGWVGPNGGITNFDNF   350
 351  AFAMLTVFQCITMEGWTDVLYWVNDAIGWEWPWVYFVSLIILGSFFVLNL   400
 401  VLGVLSGEFSKEREKAKARGDFQKLREKQQLEEDLKGYLDWITQAEDIDP   450
 451  ENEEEGGEEGKRNTSMPTSETESVNTENVSGEGETQGCCGTLWCWWKRRG   500
 501  AAKTGPSGCRRWGQAISKSKLSRRWRRWNRFNRRRCRAAVKSVTFYWLVI   550
 551  VLVFLNTLTISSEHYNQPDWLTQIQDIANKVLLALFTCEMLVKMYSLGLQ   600
 601  AYFVSLFNRFDCFVVCGGITETILVELELMSPLGVSVFRCVRLLRIFKVT   650
 651  RHWTSLSNLVASLLNSMKSIASLLLLLFLFIIIFSLLGMQLFGGKFNFDE   700
 701  TQTKRSTFDNFPQALLTVFQILTGEDWNAVMYDGIMAYGGPSSSGMIVCI   750
 751  YFIILFICGNYILLNVFLAIAVDNLADAESLNTAQKEEAEEKERKKIARK   800
 801  ESLENKKNNKPEVNQIANSDNKVTIDDYQEDAEDKDPYPPCDVPVGEEEE   850
 851  EEEEDEPEVPAGPRPRRISELNMKEKIAPIPEGSAFFILSKTNPIRVGCH   900
 901  KLINHHIFTNLILVFIMLSSAALAAEDPIRSHSFRNTILGYFDYAFTAIF   950
 951  TVEILLKMTTFGAFLHKGAFCRNYFNLLDMLVVGVSLVSFGIQSSAISVV  1000
1001  KILRVLRVLRPLRAINRAKGLKHVVQCVFVAIRTIGNIMIVTTLLQFMFA  1050
1051  CIGVQLFKGKFYRCTDEAKSNPEECRGLFILYKDGDVDSPVVRERIWQNS  1100
1101  DFNFDNVLSAMMALFTVSTFEGWPALLYKAIDSNGENVGPVYNYRVEISI  1150
1151  FFIIYIIIVAFFMMNIFVGFVIVTFQEQGEKEYKNCELDKNQRQCVEYAL  1200
1201  KARPLRRYIPKNPYQYKFWYVVNSSPFEYMMFVLIMLNTLCLAMQHYEQS  1250
1251  KMFNDAMDILNMVFTGVFTVEMVLKVIAFKPKGYFSDAWNTFDSLIVIGS  1300
1301  IIDVALSEADPSESETIPLPTATPGNSEESNRISITFFRLFRVMRLVKLL  1350
1351  SRGEGIRTLLWTFIKSFQALPYVALLIAMLFFIYAVIGMQMFGKVAMRDN  1400
1401  NQINRNNNFQTFPQAVLLLFRCATGEAWQEIMLACLPGKLCDPDSDYNPG  1450
1451  EEYTCGSNFAIVYFISFYMLCAFLIINLFVAVIMDNFDYLTRDWSILGPH  1500
1501  HLDEFKRIWSEYDPEAKGRIKHLDVVTLLRRIQPPLGFGKLCPHRVACKR  1550
1551  LVAMNMPLNSDGTVMFNATLFALVRTALKIKTEGNLEQANEELRAVIKKI  1600
1601  WKKTSMKLLDQVVPPAGDDEVTVGKFYATFLIQDYFRKFKKRKEQGLVGK  1650
1651  YPAKNTTIALQAGLRTLHDIGPEIRRAISCDLQDDEPEDSKPEEEDVFKR  1700
1701  NGALLGNHVNHVNSDRRDSLQQTNTTHRPLHVQRPSMPPASDTEKPLFPP  1750
1751  AGNSGCHNHHNHNSIGKQAPTSTNANLNNANMSKAAHGKPPSIGNLEHVS  1800
1801  ENGHYSCKHDRELQRRSSIKRTRYYETYIRSESGDEQFPTICREDPEIHG  1850
1851  YFRDPRCLGEQEYFSSEECCEDDSSPTWSRQNYNYYNRYPGSSMDFERPR  1900
1901  GYHHPQGFLEDDDSPTGYDSRRSPRRRLLPPTPPSHRRSSFNFECLRRQS  1950
1951  SQDDVLPSPALPHRAALPLHLMQQQIMAVAGLDSSKAQKYSPSHSTRSWA  2000
2001  TPPATPPYRDWSPCYTPLIQVDRSESMDQVNGSLPSLHRSSWYTDEPDIS  2050
2051  YRTFTPASLTVPSSFRNKNSDKQRSADSLVEAVLISEGLGRYARDPKFVS  2100
2101  ATKHEIADACDLTIDEMESAASTLLNGSVCPRANGDMGPISHRQDYELQD  2150
2151  FGPGYSDEEPDPGREEEDLADEMICITTL                       2179

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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