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

NucPred

Fetching P25439 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MASPSPANSPMPPPQAPSPMAPPSQSPAPSPHSPYPHQQPGPLQGPPPPG    50
  51  HPGAYGHPMQHGPPGQGPPGHHMPPHHQGMIFSKGPHMGMQMPPTGPNMS   100
 101  PYQTHGMPPNAPTQPCIVSPGGPPGGPPPPERSSQENLHALQRAIDSMEE   150
 151  KGLQEDPRYSQLLAMRATSKHQHLNGNQVNLLRTQITAYRLLARNKPISM   200
 201  QMQQALQAAQQQPPPGPPIGPPGAPGGPPPGSQHAGQPPVPPQQQQQPPP   250
 251  SAGTPPQCSTPPASNPYGPPVPGQKMQVAPPPPHMQQGQPLPPQPPQVGG   300
 301  PPPIQQQQPPQQQQQQSQPPPPEPHQHQLPNGGKPLSMGPSGGQPLIPSS   350
 351  PMQPQVRGTLPGMPPGSQVPQPGGGPQRQVPPAGMPMPKPNRITTVAKPV   400
 401  GLDPITLLQERENRIAARISLRMQELQRLPATMSEDLRLQAAIELRALRV   450
 451  LNFQRQLRMEFVQCTRRDTTLETALNIKLYKRTKRQGLREARATEKLEKQ   500
 501  QKLEAERKRRQKHLEFLAAVLQHGKDLREFHRNNKAQLARMNKAVMNHHA   550
 551  NAEREQKKEQERIEKERMRRLMAEDEEGYRKLIDQKKDKRLAFLLSQTDE   600
 601  YISNLTQMVKQHKDDQMKKKEEEGKRLIQFKKELLMSGEYIGIDEGSIVA   650
 651  DMRVHVVEQCTGKKLTGDDAPMLKHLHRWLNMHPGWDWIDDEEDSCGSND   700
 701  DHKPKVEEQPTATEDATDKAQATGNDEDAKDLITKAKVEDDEYRTEEQTY   750
 751  YSIAHTIHEKVVEQASIMVNGTLKEYQIKGLEWLVSLYNNNLNGILADEM   800
 801  GLGKTIQTISLVTYLMDRKKVMGPYLIIVPLSTLPNWVLEFEKWAPAVGV   850
 851  VSYKGSPQGRRLLQNQMRATKFNVLLTTYEYVIKDKAVLAKIQWKYMIID   900
 901  EGHRMKNHHCKLTQVLNTHYIAPYRLLLTGTPLQNKLPELWALLNFLLPS   950
 951  IFKSCSTFEQWFNAPFATTGEKVELNEEETILIIRRLHKVLRPFLLRRLK  1000
1001  KEVEHQLPDKVEYIIKCDMSALQRVLYKHMQSKGVLLTDGSEKGKHGKGG  1050
1051  AKALMNTIVQLRKLCNHPFMFQHIEEKYCDHTGGHGVVSGPDLYRVSGKF  1100
1101  ELLDRILPKLKATNHRVLLFCQMTQCMTIIEDYLGWRQFGYLRLDGTTKA  1150
1151  EDRGELLRKFNAKGSDVFVFLLSTRAGGLGLNLQTADTVVIFDSDWNPHQ  1200
1201  DLQAQDRAHRIGQRNEVRVLRLMTVNSVEERILAAARYKLNMDEKVIQAG  1250
1251  MFDQKSTGSERQQFLQTILHQDDNEEEEENEVPDDEMINMMIARSEEEIE  1300
1301  IFKRMDAERKKEDEEIHPGRERLIDESELPDWLTKDDDEVERFHYQYDED  1350
1351  TILGRGSRQRKEVDYTDSLTEKEWLKAIDDGAEFDEEEEEDDSKRKRRKR  1400
1401  KNRKEESDDDSLILKRRRRQNLDKRSKKQMHKIMSAVIKHNQDGRTLSEP  1450
1451  FMKLPSRQRLPDYYEIIKRPVDIKKILQRIEDCKYADLNELEKDFMQLCQ  1500
1501  NAQIYNEEASLIYLDSIALQKVFVGARQRITAAADAAAVAAGDNTGEAHG  1550
1551  NGGSDNSDNDDDDGGDDGSDDEEIATTSAAAVKMKLKLNKSLASAPATPT  1600
1601  QSSSNVSSGAATTSKKQTRRKRSQKKYTISDDDDDDMD              1638

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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