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

NucPred

Fetching Q5ARK3 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MQNGTTIGIPPENERVTERAEPVPSDLLPNNSPVNSPTIDPTLSEIKDVA    50
  51  ADHNEEPPSKRRKVAGSTPSRRSHSRAASPPWKKAGADGPTSKIVDGKRR   100
 101  STRVSNVGPVEQPPSDAKPTRSSQKQYVSKAVSSQRNAAVSSPLPMSPSR   150
 151  SGINRRSLAGVAVNGSPSTTAKGSIGRRRRESPSPVSKRASTRTRPDNMD   200
 201  AYHPSNGVTPRSNSTKTRSTRSFQLASSDFREETADDIGNDGQDEHGQRI   250
 251  QRLRIKVKKPALSIQHPSHVLPTRKYGSFKEWLENEGTGPGRMLTMTDAL   300
 301  EEAQKRRQVTEAMEPGGLLSSEVCSAFLPEPQEELPQQFSHQDHLVAHAL   350
 351  YFKKLLDKEHRAHRQAAKSLAAACAEVWRKRNKDPEDILREQQEEMRGKR   400
 401  KQLAKDLKKMFELARAEIDRVRLARWEEEQKAKDQRALDRAIKQSTMLFE   450
 451  KRRLEILGETGSDAPETTTDDEEVETDNGSENDDEEGESNMSTETEEEDG   500
 501  DDRDDDVGLTAEELRLKYANLPDTNPHPDQSPYSDEDSEDSDDIAADNTP   550
 551  GDTSGGVNRSPPPDSSGQVELDEVDPVLIDDSDESTDMDDDMGDSDDDGY   600
 601  SEAESDDEDGGEPGLLGFFSAKDLSLSNLHQTNSGEGDTHQTGADGDRNE   650
 651  DSSFDESEFGSEDPDEVTLVPTGPTNKDLSTPATVTASAELEPAAMTPSI   700
 701  DQTSTEEPIAIGTETPIETVAEDAAALADTEPVDVDVLDTSTNDSVPPVM   750
 751  SPATNLLKQIERQQHEPYHSRAASSEASPGTVATKPSEPESVSSIEAPAE   800
 801  KHAQPSESPGPGLKTPIPHLLRGTLREYQHFGLDWLAGLYSNHINGILAD   850
 851  EMGLGKTIQTIALLAHLAVEHGVWGPHLVVVPTSVILNWEMEFKKWCPGF   900
 901  KIMTYYGNQEERRQKRRGWMDDNSWNVLITSYQLVLQDQQVLKRRSWHYM   950
 951  ILDEAHNIKNFRSQRWQALLTFRTRARLLLTGTPLQNNLTELWSLLFFLM  1000
1001  PTDGDEAGIEGFADLRNFSEWFRRPVEQILEHGRETMDDEAKQVVTKLHT  1050
1051  VLRPYILRRLKADVEKQMPGKYEHVVYCRLSKRQRYLYDGFMSRAQTKET  1100
1101  LASGNYLSIINCLMQLRKVCNHPDLFETRPISTSFAMPRSVATEFETSEA  1150
1151  LVRRRLLYQHPLEKLDLDFLNLVPISREDISRRLADDSARIMAYAPFNTL  1200
1201  RERQYHRTNWEMKFNGSTVQSTLEALENDCRKRRMAELERSLYFESKRHG  1250
1251  RRPVYGSSLIEFLTADSKQRPTAHGPLRKRSYADWLSSQSSVLASMMMSL  1300
1301  EERSQAMDGYIQRFACVTPAAVAAGVTEAALTPISTRHLTNKERFPPHDP  1350
1351  FHEAQMRLSIAFPDKRLLQYDCGKLQRLDKLLRDLKAGGHRALIFTQMTK  1400
1401  MLDVLEQFLNIHGHRYLRLDGTTKVEQRQILTDRFNNDNRILAFILSSRS  1450
1451  GGLGINLTGADTVIFYDLDWNPAMDKQCQDRCHRIGQTRDVHIYRFVSEY  1500
1501  TIESNILRKANQKRMLDDVVIQEGEFTTDYFTKLDVRDMIGNDEALKDEA  1550
1551  SAAMDRVLENRVTNTSRVFEQAEDKEDIDAAKNAQKELEHADDGDFDDRA  1600
1601  NANASGVTAASASASGAGQTPTQAGTPLPDEAQQSLNANNAEVAEDTADS  1650
1651  DPSVGHIDDYLLRFMEWNMKDEPLVLPVDKSMKKSKKGKEHRLRKRRR    1698

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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