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

NucPred

Fetching Q8MJ05 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MSETPSTSFSMVRRISSEGQLPSPRQLGITQPVVAKRISFYKSGDPQFGG    50
  51  VRVVLNPRSFKTFDALLDNLSGKVPLPFGVRNISTPRGRHSITRLEELED   100
 101  GQSYLCSHGRKVQPVDLDKARRRPRPWLSSRALSTHVQRGPAPAAPGMLR   150
 151  APRRLVVFRNGDPKTRRAIVLNRRVTQSFEVFLQYLTQVMQRPVTKLYAT   200
 201  DGRKVPSLQAVILSSGAVVAAGREPFKPGNYDIQKYLLPARLPGISRRVY   250
 251  PKGNARSESRKMSTHVSSSPTSQIYSLSSEKMQNNDSYSDHSFASENYLA   300
 301  LEKNDSQNLLIYPSEDDVEKSIIFNQDGTMTVEMKIRFKIKEEETIKWTT   350
 351  TLCRADLSNNGEKSEINSLPGRTDDRSSGVKITACSLSADVSPLEKGGSQ   400
 401  VDSLAEEANTQVKDQDVETGSSTSWENPALDTDATQGTQDRVKHRFYRPP   450
 451  TPGPRRVRQKKSVIGSVTLVSETEVQEKMIGQFSYNEERKDWENKSEYHM   500
 501  VTHSCSKMSSVSNRPILVQVDNDEQVASSLERKKESRLLKSSAVSAGVVE   550
 551  ITSQKTLEMSHNGGLPQTTSEKSIVEEGIVDNVIADNKARVRNLRTYGNT   600
 601  DDRSSPFLGDAAHFSSNNPGTDKTISKTPASVGNSTVTTRIDQLIHEFSH   650
 651  CGLTKLPENEKQISSSVASKKKMKSQQHVINSQHQAGEMATKRIPRKNKR   700
 701  MNTRGRIAQETILRDSHSSLKGAILCEKDLHASDTVIESNYFSSKGNNPV   750
 751  NSRNFPRNKLNTIHKPKIQGLLARRKSRPLNKVNLGGPTKREIGQGEKVF   800
 801  SHNEIGCCKNTFENQNLFHLFNFLEQKPNAFCGPESQAETASWYLRGTSK   850
 851  RSLVSKVNNSHITLRSQKKQKRDKLKSDTTVSKEHVTTRANSLASLEKAV   900
 901  FPENVTHHSVQSYVQRWLQNLSPQAALQLGKSAPVYKKERGVASYNNGFL   950
 951  PGNSSHTSSGKRNDSILQSNRHTTKSASLTGDNLGKRVGMSFDKNSSEEL  1000
1001  IQDHCESQTDSLNDTYLLSVHEFCTLSQSATDDPNAKSQVSAAKSGQEMS  1050
1051  LVYKDINLAAKGPSVETAVQVDLEGDTPQHLSPVQLLHQLQALVPSSPKA  1100
1101  QNGVVQMPGPLSEVPFPSLIRNSSTNVLLAWLLVLTLKGGVSSFCPGDAL  1150
1151  KATSGSSEALALLEVLKHIAVTEEADDLKAAVASLVESTTNHSGLTEKEQ  1200
1201  DVGPIGLSANCSTPNIQIIPQCAENEKTQKISLDGSHTAGEEVSEVCVTA  1250
1251  VTRSPRKMGTVVKTYPPEETCHLSEDSFPSDDCTMDQTSMNKACFLGDIS  1300
1301  SLTEAVSSHEGCAYEQNHIYERADNLELTKELERVDEVQKDRNILADPGC  1350
1351  KHGSNMLVSHQSASSLSPCGSFQNTTESELDGEHSFLDKSESCSLKKFQD  1400
1401  KSVYTSFDKEDSKTSEEPGSTTNSMTSSERNVSEMESFEELENQNTDIFN  1450
1451  IKVNSGEQVTEELIREELEAGKSLELIEVSSRNDAEEGKDGVICETISRK  1500
1501  LVTPPSLVFCYDSKQNMEKEPSEGETETKVRKMVESLEAGSSAESPLNFK  1550
1551  SGLRRSGTSDWSDYRQNSENEPSYKASSNGPSDSDEEMTPEKECNKGFVK  1600
1601  RTIEKLYGKAEMMRPFFFRWIYTHISGLSCDSVEFQGTGKVGLYDPEGQS  1650
1651  LGSLERVSSNSTVLQKFPEQKRDKCDVNNVRASYPREDIAEHGTKQNDHK  1700
1701  TILRDREEGVLIDKGKWLLKENHLLRLSSPECSGPCGHADTTSVDTLLDN  1750
1751  SSTEVPYSHFGNLAPGPNMAELSSSELEELTQPPELRCNYFNVPHCSDSE  1800
1801  PFHDDELDTQDEACAQEREPNHPAEEKGNLRSERVCTSATHVFASAGNKV  1850
1851  HPVSDGAVRNQPLAGSNVIHGALQEGDSLDKLYNICGQHCPILTVINQPV  1900
1901  NEEHRGFAYCKDSDVENSLSLQLWMKIHPCLRHSSKTMFRDKNNKTISRR  1950
1951  ALTDNAVGNTHVWPHFNNTFDLMDRRRKLKQSNCLGLEEENNFNKFQSYL  2000
2001  KNFLHTLLLVVGQVNSNPQDPSSQTKEFFEVVDENNNLLNSRFQNSGTNL  2050
2051  NQVVREHSYHLSFEMLGQARLFCQVETFLGISNRNILEMFYIFEDENLFI  2100
2101  WEEEN                                               2105

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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