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

NucPred

Fetching Q9V727 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MKTITPDTTTTTSSQHQQLLIPQADQHHQPMLQQQSLLAAPPPTMIMEHV    50
  51  NLVDDDEKDPLALEQLEVSPSTKHTHSLRRHLPRIIVKPIPPEKKPMAPS   100
 101  EEAAVSTAPAPPTRLICSRRIQQQQQVKAAAAAAAAAAAAAAAAAAAAQA   150
 151  QATSSYPSAISPGSKAGTSQASTMREVLASIPGFSVKPRRRSNKKLTTAA   200
 201  QIEQTKDGKIDLETPDSILASTNLRALLNKQTFSLLPPLYQYNLIQLLPS   250
 251  VDREASELEQPSSSASGGSPSEAIRLSASCLNNEFFARACLEWRERLSEG   300
 301  EFTPENQLKLKTEAEREKNKLDPWKLKHFEPFWGEKNSRGKDKDKLESDC   350
 351  KNQKLSASIKSEPKPPATSQQKPLQQATCDNETELKFDLSTKCETTSAKT   400
 401  TVAVAVADKSSTFPPTGSQNNVLNEQQRRVLKRPSSSPSQRKQAPTTIAT   450
 451  INLDDDLDELPSTSKDSKQPKMDEIVPNASGNVVAAPMVDVVDHSAVEMK   500
 501  IKDEQQHQRQHQPLINSTCDKIEPSECSKEMIVAMKQVDSKEDVDSIASA   550
 551  AAMPAIAAVTPHTPKPEALAPNPDVANQFVSYLQNVELAAETKAPLDNSN   600
 601  EADITTGTNSHDFVFSDTIDHAYFQEHQSTINHNFFTSSSSSNTATTAAN   650
 651  KLEEHSDKPEDSPLPIASSISGSTPASSITSTSCTSSSSSSASMSSSCSS   700
 701  SNSGSTTTAPTTSSSAGAPTAPLTLAAAAETTLANVQAMLSTVAKLQQQQ   750
 751  QELPVELNSNEMYQHVQHDWNFGDIKLSSSQSSGDQQRNLSHEAIDLMDV   800
 801  VQDADVIDDIMHNDVCHDVLGDEDEGDQEEDEDDEVVECMTEEQQLIDED   850
 851  SEAVREIVDKLQQHQQQQNQQQHHQQLHIQDVVQLAQHSFMPQAHSEFGN   900
 901  DIGQEMLCDAVPMSAAEMEVSSTVITNSSNSNDSSNNISLCSSTNSLTIN   950
 951  QMPHQASQQPQQNAQSNAQQQRQILVDSNGQIIGNFLLQQQRQQQQQQLL  1000
1001  QQFTLQAAAAQQQQQQQQQHQQQQQQQQQATSSNSLGKTLPVALRNGTQQ  1050
1051  FLSPNLIAQQHQQQQQQQLEQHQQQATAQQKHQQIQQFALQQAQLHQRQL  1100
1101  LAQAANNNLLQQQQQQQQNVALPTTQAKFIAKPLNIISMTRPANASPTTA  1150
1151  ATTANTASIPSAYANVVAVTGAQQQQSPPVPAPQQQTVQQQQLANHNSNM  1200
1201  QQLPNVLTMKTLPPSGVPTTIAQQRLQPKMPTGKGRKATSNRLPPGAVNL  1250
1251  ERSYQICQAVIQNSPNRENLKAQLRPPAAILNQHQPTTTTAPAPINPVTL  1300
1301  NVSTVAATPMSNITTATGSMAAAVAAAPPQNVLKQEELLVSGAVGAGALP  1350
1351  AGLPPNVMGVGRPGVYKVIGPRMSGFPRKKYVQRKPSPTTLIRHVFSPGP  1400
1401  GGATATAQQLQMLQQHHQSTTSPVPVQNPQQPAPEQLIHQNGNGQYVLVH  1450
1451  RANVGAADNQAPRASSAPPMHQNQFVTVQNPLHSINGIPMGGRGRPASVD  1500
1501  TTAGSGNVIAPPISATDALHHHHHEMQQQQQHQQPQPLGNVGAAANIVRR  1550
1551  NIAAGPNIAYIDGSNTNSSAVALMEAGNNYIVTTNASPTAAPSPINQQPQ  1600
1601  SQPTGTQHQHPLLQLHQTGENTPPGNEATATANNCACSLNAMVICQQCGA  1650
1651  FCHDDCIGAAKLCVACVIR                                 1669

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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