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

NucPred

Fetching Q3UHF7 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MDTGDTALGQKATSRSGETDSVSGRWRQEQSAVLKMSTFSSQEGPRQPQI    50
  51  DPEQIGNAASAQLFGSGKLASPGEGLHQVTEKQYPPHRPSPYPCQHSLSF   100
 101  PQHSLSQGMTHSHKPHQSLEGPPWLFPGPLPSVASEDLFPFPMHGHSGGY   150
 151  PRKKISNLNPAYSQYSQKSIEQAEDAHKKEHKPKKPGKYICPYCSRACAK   200
 201  PSVLKKHIRSHTGERPYPCIPCGFSFKTKSNLYKHRKSHAHAIKAGLVPF   250
 251  TESSVSKLDLEAGFIDVEAEIHSDGEQSTDTDEESSLFAEASDKVSPGPP   300
 301  VPLDIASRGGYHGSLEESLGGPMKVPILIIPKSGIPLASEGSQYLSSEML   350
 351  PNPSLNAKADDSHTVKQKLALRLSEKKGQDSEPSLNLLSPHSKGSTDSGY   400
 401  FSRSESAEQQISPPNTNAKSYEEIIFGKYCRLSPRNTLSVTPTGQERTAM   450
 451  GRRGIMEPLPHLNTRLEVKMFEDPISQLNPSKGEMDPGQINMLKTTKFNS   500
 501  ECRQPQAIPSSVRNEGKPYPGNFLGSNPMLLEAPVDSSPLIRSNSMPTSS   550
 551  ATNLSVPPSLRGSHSFDERMTGSDDVFYPGTVGIPPQRMLRRQAAFELPS   600
 601  VQEGHMESEHPARVSKGLASPSLKEKKLLPGDRPGYDYDVCRKPYKKWED   650
 651  SETLKQSYLGSFKQGGEYFMDPSVPVQGVPTMFGTTCENRKRRKEKSVGD   700
 701  EEDVPMICGGMGNAPVGMMSSEYDPKLQDGGRSGFAMTAHESLAHGHSDR   750
 751  LDPARPQLPSRSPSLGSEDLPLAADPDKMTDLGKKPPGNVISVIQHTNSL   800
 801  SRPNSFERSESTEMVACPQDKTPSPAETCDSEVLEAPVSPEWAPPGDGGE   850
 851  SGSKPTPSQQVPQHSYHAQPRLVRQHNIQVPEIRVTEEPDKPEKEKEAPT   900
 901  KEPEKPVEEFQWPQRSETLSQLPAEKLPPKKKRLRLADLEHSSGESSFES   950
 951  TGTGLSRSPSQESNLSHSSSFSMSFDREETVKLTAPPKQDESGKHSEFLT  1000
1001  VPAGSYSLSVPGHHHQKEMRRCSSEQMPCPHPTEVPEIRSKSFDYGNLSH  1050
1051  APVAGTSPSTLSPSRERKKCFLVRQASFSGSPEIAQGEAGVDPSVKQEHM  1100
1101  EHLHAGLRAAWSSVLPPLPGDDPGKQVGTCGPLSSGPPLHLTQQQIMHMD  1150
1151  SQESLRNPLIQPTSYMTSKHLPEQPHLFPHQDAVPFSPIQNALFQFQYPT  1200
1201  VCMVHLPAQQPPWWQTHFPHPFAPHPQNSYSKPPFQADLHSSYPLEHVAE  1250
1251  HTGKKSADYPHAKEQTYPCYSGTSGLHSKNLPLKFPSDPGSKSTETPTEQ  1300
1301  LLREDFASENAGPLQSLPGTVVPVRIQTHVPSYGSVMYTSISQILGQNSP  1350
1351  AIVICKVDENMTQRTLVTNAAMQGIGLNIAQVLGQHTGLEKYPLWKVPQT  1400
1401  LPLGLESSIPLCLPSTSDNAASLGGSKRMLSPASSLELFMETKQQKRVKE  1450
1451  EKMYGQIVEELSAVELTNSDIKKGLSRPQKPQLVRQGCASEPKDGCFQSR  1500
1501  SSSFSSLSPSSSQDHPSASGPFPPNREILPGSRAPPRRKFSGPSESRESS  1550
1551  DELDMDETSSDMSMSPQSSALPTGGGQQEEEGKARKLPVSMLVHMASGPG  1600
1601  GNVANSTLLFTDVADFQQILQFPSLRTTTTVSWCFLNYTKPSFVQQATFK  1650
1651  SSVYASWCISSCNPNPSGLNTKTTLALLRSKQKITAEIYTLAAMHRPGAG  1700
1701  KLTSSSVWKQFAQMKPDAPFLFGNKLERKLAGNVLKERGKGEIHGDKDLG  1750
1751  SKQTEPIRIKIFEGGYKSNEDYVYVRGRGRGKYICEECGIRCKKPSMLKK  1800
1801  HIRTHTDVRPYVCKLCNFAFKTKGNLTKHMKSKAHMKKCLELGVSMTSVD  1850
1851  DTETEEAENMEELHKTSEKHSMSGISTDHQFSDAEESDGEDGDDNDDDDE  1900
1901  DDDDFDDQGDLTPKTRSRSTSPQPPRFSSLPVNVGAVAHGVPSDSSLGHS  1950
1951  SLISYLVTLPSIQVTQLMTPSDSCDDTQMTEYQRLFQSKSTDSEPDKDRL  2000
2001  DIPSSMDEEAMLSSEPSSSPRDFSPSSYRSSPGYDSSPCRDNSPKRYLIP  2050
2051  KGDLSPRRHLSPRRDLSPMRHLSPRKEAALRREMSQGDASPRRHLSPRRP  2100
2101  LSPGKDITARRDLSPRRERRYMTTIRAPSPRRALYPNPPLSMGQYLQTEP  2150
2151  IVLGPPNLRRGIPQVPYFSLYGDQEGAYEHHGSSLFPEGPTDYVFSHLPL  2200
2201  HSQQQVRAPIPMVPVGGIQMVHSLPPALSGLHPPPTLPLPTEGSEEKKGA  2250
2251  PGEAFAKDPYILSRRHEKQAPQVLQSSGLPSSPSSPRLLMKQSTSEDSLN  2300
2301  STEREQEENIQTCTKAIASLRIATEEAALLGADPPTWVQESPQKPLESAH  2350
2351  VSIRHFGGPEPGQPCTSAAHPDLHDGEKDTFGTSQTAVAHPTFYSKSSVD  2400
2401  EKRVDFQSSKELSLSTEEGNEPSPEKNQLH                      2430

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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