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

NucPred

Fetching Q10161 from www.uniprot.org...

The NucPred score for your sequence is 0.59 (see score help below)

   1  MAQQLPIRFSEVLQLASVGIQPSSFGFANVTLESDKYVCVRDNPNGVNQV    50
  51  VIVDLEDPSNVLRRPISADSVILHPKKKIIALKAQRQLQVFDLEAKAKIN   100
 101  SYVMNQDVVYWTWISDSVIGMVTDTSVFHWTVSGSDPVKMFDRHSSLNGT   150
 151  QIISYKSNYNEEWFTLIGISSRDNRIAGNLQLYSKKRKVSQPLESHASAF   200
 201  AVIQPEGVDHEVQVLALASRLPTGSKLSIVEVDRNPNNPAFATKTVDLFF   250
 251  PPEAVNDFPIAIEIGSTYNVAYVVTKYGFIHVYDLETAKCIYMNRVSGES   300
 301  IFVTTAHKSVNGLMAINRKGQVLSVSINPETIIPYILSNLNDPGLAVRMA   350
 351  SHANLPGADNLYMQQFQQLMAQGNYSEAAKVAASSPRGILRTSQVIDQFK   400
 401  LIQAAPGQIAPILQYFGTLLDKGPLNEHETIELARPVLAQNRIQLLEKWY   450
 451  GENKLACTEALGDLVKPYNTPFALKIYETANVPNKVVMCLSELGDFGKLA   500
 501  TYTSQQNITPDYVSLLQNLVRVNPDQAAEFATQMFNSNPSINLEKIVDIF   550
 551  MSQNLVQQATAFLLDALKDDNPEHSHLQTRLLEINLINAPQVADAILGNQ   600
 601  MFTHFDRAVIASLCERAGLVQRALELYDKPADIKRVIVHSNLLNPEWLMN   650
 651  YFSRFSPDEVYDYLREMLRSNLRQNLQIVVQIATRYSDLVGAQRIIEMFE   700
 701  KFKTFEGLYYYLGSIVNITEDPEVVYKYIQAACLMNQFTEVERICRDNNV   750
 751  YNPEKVKNLLKEAKLADQLPLILVCDRYDFVNDLVFYLFRNNMFQFIEIY   800
 801  VQRINPSKTPQVVGALLDIDCDEELVQNLLMSVVGQVPVDELVEEVERRN   850
 851  RLKLLLPYLESLLQSGSQDRAIYDALAKIYIDSNNNPEVFLKENNFYDTL   900
 901  TVGKYCEKRDPYLAFIAYEKGGNDTEIINLCNENSMFKQLARYLLKRSDS   950
 951  NLWSEVLQDSAYRRPLLDQVIATAVPESSDPEAVSIVVKALMEVDLPSQL  1000
1001  IELLEKIVLQPSSFSENANLQNLLFLTAIKADKSRVMEYIDKLDKYDVDE  1050
1051  IAEIAIENGLYEEAFRIYKIHNKHEQAMKVLVEDIVSLDRAQDYAETVEQ  1100
1101  PEVWSRLAKAQLDGIRIPDAIESYLKADDPSNYSEVIELASRAGKYEELI  1150
1151  KYLLMARSKMHEPDVDSALLIAYAKTNQLTEMETFLIGSNVADVKAVGDE  1200
1201  CFESKNYEAAKLMYSSISNWSMLATTLVYLGEYQGAVDCARKANSIKVWK  1250
1251  QVGTACIDKREFRLAQICGLNLIVHAEELPGLIRLYEERGYFEEVISLME  1300
1301  AGLGLERAHMAFYTELAILYAKYKPERMMEHLKLFWGRLNMAKVIRACDQ  1350
1351  MHLWNEAVFLYVHDQSYDNAAAVMMEQPEAFDHQSFKDIIVHVANLELYY  1400
1401  RALNFYLEQHPMLLTDLLAALTPRIDHPRVIRIFEKSENTPLILNFMVAI  1450
1451  QHLNIQAVNHAYNDLLIEMEDYQSLQDSIENYDHFDAIALARRLEKHSLL  1500
1501  EFRRIAAYIYRKNKRWTQSIELSKQDRFYKDAIITARDSDQTTIAEDLMK  1550
1551  YFVEIGNYECFAAILYTCYHLLRNDLVMEISWRKGLQDYAYPYFINFQCE  1600
1601  MFSKVLNLEKDLKDRQAVKSEEESASTIGAGILGNTLMLTQGPMANNNDQ  1650
1651  FDSFQQASPMPRLGNF                                    1666

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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