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

NucPred

Fetching Q93148 from www.uniprot.org...

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

   1  MDFIDNQAEESDASTGRSDDDEPQSKKMKMAKDKLKKKKKVVASSDEDED    50
  51  DEDDEEEGRKEMQGFIADEDDEEEDARSEKSDRSRRSEINDELDDEDLDL   100
 101  IDENLDRQGERKKNRVRLGDSSDEDEPIRRSNQDDDDLQSERGSDDGDKR   150
 151  RGHGGRGGGGYDSDSDRSEDDFIEDDGDAPRRHRKRHRGDEHIPEGAEDD   200
 201  ARDVFGVEDFNFDEFYDDDDGEEGLEDEEEEIIEDDGEGGEIKIRRKRDT   250
 251  TKKTTLLESIEPSELERGFLSAADKKIMIEDAPERFQLRRTPVTEADDDE   300
 301  LEREAQWIMKFAFEETTVTNQAAVDADGKLECLMNIDSSEIEDKRRAVVN   350
 351  AIKAVLHFIRVRSNSFEVPFIGFYRKESIDNLLTMNNLWIVYDYDEKYCH   400
 401  LSEKKRRLYDLMRRMREYQELSDDITAKRRPINEMDLIDINFAETLEQLT   450
 451  DIHANFQLLYGSLLEDMTKWEKERRAADGEETEYRAKFKSSIRNDKYQMC   500
 501  VENGIGELAGRFGLTAKQFAENLDWRKHDIDQDSAFPLEAAEEYICPAFI   550
 551  DRETVLNGAKFMLAKEISRQPLVRSRVRQEFRDNAHFWVKPTKKGRDTID   600
 601  ETHPLFNKRYIKNKPIRNLTDEEFLYYHKAKQDGLIDMVLMYESDEDQAA   650
 651  NQFLVKKFLSDSIFRKDEYTDNVEQWNAVRDQCVNMAITEMLVPYMKEEV   700
 701  YNTILEEAKMAVAKKCKKEFASRIARSGYVPEKEKLDEEDEEHSARRRMM   750
 751  AICYSPVRDEASFGVMVDENGAIVDYLRMVHFTKRGHGGGNTGALKEESM   800
 801  ELFKKFVQRRRPHAIALNIEDMECTRLKRDLEEAVAELYSQSKIFSQINV   850
 851  YLMDNELAKVYMRSNISIAENPDHPPTLRQAVSLARQLLDPIPEYAHLWN   900
 901  SDEDIFCLSLHPLQRDIDQEILAQLLNHELVNRVNEEGVDINKCAEFPHY   950
 951  TNMLQFTCGLGPRKATSLLKSIKANDNLIESRSKLVVGCKLGPKVFMNCA  1000
1001  GFIRIDTRRVSDKTDAYVEVLDGSRVHPETYEWARKMAVDALEVDDSADP  1050
1051  TAALQEIMETPERLRDLDLDAFADELNRQGFGEKKATLYDISSELSERYK  1100
1101  DLRAPFVEPSGEALYDLLTRSGKEVKVGCKMLGTVQSVQYRKVERDTIDS  1150
1151  MIPEHTEEDQYICPSCKIFTAADPQSVREHLLNAGRPGGCVGSACGIRVR  1200
1201  LDNGMTAFCPNKFISSSHVDNPLTRVKLNQPYWFKVMAINKEKFSILLSC  1250
1251  KSSDLKEDAPAERDDFWDQQQYDDDVAAMKKETTKKKDADTRVKRVIAHP  1300
1301  NFHNVSYEAATKMLDEMDWSDCIIRPSANKESGLSVTWKICDRIYHNFFV  1350
1351  KESAKDQVFSIGRTLSVGGEDFEDLDELIARFVLPMIQISHEITTHKYFF  1400
1401  TQGTSEDTDQVETFVHEKRRELGRSPYVFSASYRQPCQFCISYMFDNSNR  1450
1451  IRHEHFKISPRGIRFRQQNFDSLDRMMAWFKRHFNEPPPGIRSSLSYRPT  1500
1501  GRTGPPPSAPYQQPPQQQYYR                               1521

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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