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

NucPred

Fetching Q8CIY2 from www.uniprot.org...

The NucPred score for your sequence is 0.77 (see score help below)

   1  MAVYSAVAWILLFGVLASLGAQNPVSWEVQRFDGWYNNLMEHRWGSKGSR    50
  51  LQRLVPASYADGVYQPLREPYLPNPRHLSNRVMRGPAGQPSLRNRTVLGV   100
 101  FFGYHVLSDLVSVETPGCPAEFLNIYIPRGDPVFDPDKRGNVVLPFQRSR   150
 151  WDRSTGQSPSNPRDLTNQVTGWLDGSAIYGSSHSWSDTLRSFSGGQLASG   200
 201  PDPAFPRNSQNSLLMWMAPDPATGQGGPQGLYAFGAQRGNREPFLQALGL   250
 251  LWFRYHNLCAKRLAQEHPHWGDEELFQHARKRVIATYQNIAMYEWLPSFL   300
 301  KQTPPEYPGYHPFLDPSISPEFVVASEQFLSTMVPPGVYMRNASCHFQGI   350
 351  ANRNSSVSGALRVCNSYWSRENPKLQRAEDVDALLLGMASQIAEREDHLV   400
 401  VEDVQDFWPGPLKFSRTDYLASCLQRGRDLGLPSYTKAREALGLPPVSHW   450
 451  QDINPALSRSNGTVLEATAALYNQDLSRLELLAGGLLESHGDPGPLFSAI   500
 501  VLDQFVRLRDGDRYWFENNRNGLFSKEEIAEIRNTSLRDILVAVTNVDPS   550
 551  ALQPSVFFWLAGDPCPQPSQLSTQGLPACAPLFVRDYFKGSGFGFGLTIG   600
 601  TLCCFPLVSLLSAWIVARLRMRNFKRLQRQDRQSIMCEKLVGGVEALEWQ   650
 651  GRKEPCRPVLVHLQPGQIRVVDGRLTVLRTIQLRPPQQVNLILSSNRGRR   700
 701  TLLLKIPKEYDLVLLFNMEEERQALVENIRAALKENGLSFQEWELREQEL   750
 751  MRAAVTRQQRGHLLETFFRHLFSQVLDINQADAGTLPLDSSTKVREALTC   800
 801  ELSRAEFADSLGLKPQDMFVESMFSLADKDGNGYLSFREFLDILVVFMKG   850
 851  SPEEKSRLMFRMYDFDGNGLISKDEFIRMLRSFIEISNNCLSKDQLAEVV   900
 901  ESMFRESGFQDKEELTWEDFHFMLRDHDSDLRFTQLCVKGVEVPEVIKNL   950
 951  CRRASYISQEKICPSPRMSAHCARNNTKTASSPQRLQCPVDTDPPQEIRR  1000
1001  RFGKKVTSFQPLLFTEAHREKFQRSRRHQTVQQFKRFIENYRRHIGCVAV  1050
1051  FYTITGALFLERAYYYAFAAHHSGITDTTRVGIILSRGTAASISFMFSYI  1100
1101  LLTMCRNLITFLRETFLNRYIPFDAAVDFHRFIASTAIILTVLHSAGHVV  1150
1151  NVYLFSISPLSVLSCLFPDLFHDDGSEFPQKYYWWFFQTVPGLTGVLLLL  1200
1201  ALAIMYVFASHHFRRRSFRGFWLTHHLYIFLYILLIIHGSFALIQMPRFH  1250
1251  IFFLVPAIIYVGDKLVSLSRKKVEISVVKAELLPSGVTHLRFQRPQGFEY  1300
1301  KSGQWVRIACLALGTTEYHPFTLTSAPHEDTLSLHIRAAGPWTTRLREIY  1350
1351  SPPTGDTCARYPKLYLDGPFGEGHQEWHKFEVSVLVGAGIGVTPFASILK  1400
1401  DLVFKSSVSCQVFCKKIYFIWVTRTQRQFEWLADIIREVEENDSRDLVSV  1450
1451  HIYITQLAEKFDLRTTMLYICERHFQKVLNRSLFTGLRSVTHFGRPPFEP  1500
1501  FFNSLQEVHPQVRKIGVFSCGPPGMTKNVEKACQLINKQDRTHFSHHYEN  1550
1551  F                                                   1551

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.)

Go back to the NucPred Home Page.