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

NucPred

Fetching Q20762 from www.uniprot.org...

The NucPred score for your sequence is 0.49 (see score help below)

   1  MTSSVRLAFLATLLLLLPLEAQIQQANSANVNQNVGQQDTGTLFTGTGTN    50
  51  LYYGVNLVPFGPEVGDQEVNPGLLTAGQTIDLHMYFPFYGGLYNYSTLSV   100
 101  NGYIGFATVLDQGPTLNVGPDMTDWPRHEDPAMIAPYLCKQQIPQNLNPG   150
 151  MRSGVFYRLMMRQSLFGRQTGSNMNMGQATYQSSFFGQSASKACPGTPDS   200
 201  YVRCDSQADYFLEEMQRWLIEGVAGAAAFRADAALVVTWYNTASAISGRS   250
 251  DIDSGQLATYQAIWLTDRTARLSYVILNYDRLGFDAADFRQNSRSGRCQA   300
 301  LFNGGNHTGLVPVDPTQDFKNTPKVLAQRSGVPQMVRGRYMFRVDDVVRP   350
 351  AGCSNKTGGTYPMLIYPNIVNMLGEMTVDVNAICLDKSQTYILMIEQRQT   400
 401  ATCTVLTSAIARCNLPKIFDWGTKTVYFQPQSGGANDEKAFVGYIYFVPP   450
 451  TLDPMRLDIGNVYDWFKNPLPYTTMPLVWYPRNFTNPEMTQHMDQVRMND   500
 501  DTLYSTQLGLYVIAYREYKDDTIKKFRPEHRVICRLATYSNRNTYEYRWK   550
 551  PQEERINLYQVEQWYMNDWERQNDLYHYRFGYLKLAPLKTNQEQNPQQLL   600
 601  SGLVSSPISLHFLWTSNNPQFATTTYSQQDESARTEYVKKKSLEMCHDWY   650
 651  DEDGAQWNFIRDTETNSSCPCIERQAIADIGRFMPHPRCSQAFRDITCTT   700
 701  SIGSRNCYMSSQNVMTTYAGDGRQYNENLARFPTHYGQVCCYDDQGHLMQ   750
 751  TSYQPVIKVTPEVPYNPGFPMRAYEFGTAPYMGQYEVPGLSAFHNDYMPY   800
 801  FLCCKFADFRCQMFYWRRPSSGCQEYQPPAYGEVMGAGTFNTIDNDKFIF   850
 851  NEPGVYNGLYIPHTLSTPEVKVQIRMERYPNRRVDFSLLGRYMAQQDLVQ   900
 901  PTNATVVTGVVLEATGTDRVHVVARKDTRRFRYRTSIIVGNILRYFDTMR   950
 951  IQRFKGVMIYVNNVERGQPEIYVVLEEAQIGIRVRESYAIDIDRLSEYQE  1000
1001  SMGILNIAVSVPPQYGVRPDGDKTREQEIRQRYNLPRVSGVFRPFPDQSS  1050
1051  GSYLNTLTLNDVNSETYRQQIINMYRVQGSGEPGSDQNINNQGNNYGMPT  1100
1101  ENMFTTSRDEDKKFEVFPEAQMKSGPIFKTSPKYETGAYRFYPMTGQVLN  1150
1151  QRLQTCRDMQQNTNINMQPLQSQLTGEYGQTQCPDNPSSIIQDCGDSVPC  1200
1201  LYDYYNFNAKLLGLNVKNEWNTFTSDRFDASRQYNSCGVINIEYPEYLMK  1250
1251  TSSMSSAYLQGDVARFECFQSHWIYGVHEYKCGIVVDRNQRNIIDPRDYR  1300
1301  FEWNKGEQPWCRSREKQNFLTWLAIIGGIFGVLVFVILIFLCCWIVKQKK  1350
1351  KGEAAERRGYDMASRSSMTGSRGGKKYPIHESEPLNEKRFDADTYRDDDF  1400
1401  YPPAREEQYAARNEDLHGLKTSV                             1423

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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