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

NucPred

Fetching Q09725 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MLFEMTPETFKKVNSSNRIIKGLQYTPLASSIPLENGLQNVLYPSSKFQN    50
  51  EPLQLNSEESSIMQRYVDMLNPGATFVNDSETFNFYKNALSAMITEPAMP   100
 101  AMRVNASPVLDQKVCNSDSLSELNDFTKSLIQPSMLMCEPKEKPDASSIN   150
 151  TNRSSSDNGFLTPSSSPRSPSCSRVFNAVQLCSPKKSKDDITTPKKRLME   200
 201  DTYSPRESPSKIQRLQDVLLKQLQDTRLLISQVIEAENSEDFSSNSLFIK   250
 251  REDDDGKHISSHAIEKLYMALTKLSRLGACDKLLEEGSIILVKQILEKEL   300
 301  KELPVACYSIINLHDSLTQFPNLDFILKTTALVLFIIFLVPSFKKLQNEE   350
 351  SILHLLNILHSIFEYTVPEAIDNIVQSKTSDARTSEIQHLSVLLQKVANV   400
 401  LNILSKVAHEIPLSEAVVIRIVYLFPKVSTLDNSFKTKLPNCNSSSFDFL   450
 451  KAPLFQTLQYLFRLYPYQRDFIIEESLTNFSHLPTARSVSRTYRLSNGKS   500
 501  IQYYSTLFVRLIQSCSIQNLFDSEIVQSESKSTEALHSGNLTEHLKTVES   550
 551  ILSKSRHEEYRIANHIVAYLLSRSLKQNKTESDNSFAILTKILLEDLLNM   600
 601  LSLPEWCGTETIIRQFAMNLVMTVTNDKQAVSSKNAALDLISLIVNKVLA   650
 651  LFDLSLFEKHNIPAPTNFNDIISFIPSITRLNELSQVSFNHFYFLCKGDI   700
 701  SLENILPYNYNKWFSFLLQLRKVCNDSEALKIIDNCIDKNMQKSQEGFQG   750
 751  PSPFKADENDEDIFIISLYHSSLFLNLKFFVSLIIGFLDSPQASLRTKCL   800
 801  RIINQMKTIPSILRTHPEVLAQIISKSNDQSAIVRDTVLDLLGTYIMAYR   850
 851  ETIPQIYGCIISGISDPSTIVRKRAIKQLCEVYEATEDLNIRVDIASKLL   900
 901  TRSNDEEETISELSLEVLEKLWFSPASNELDCQKGYEQLTFLEKQKLRVQ   950
 951  YFPILKLCAEPSTERHVLLVTSLKTMLTSKEEINLSTLHTQIRLLLSCLF  1000
1001  NQLIEVVTEDQVDESTKGILYEIMSTLFVFSRAFPFLFDLSYLHLLKPYL  1050
1051  RSASTIEEQRFLYYVVAIFRQVLPFQKEISESFLRSLESVLLQRLTKAGT  1100
1101  ATLMEIVPCLCSLFTRLNDYERLKKIVVSCLKSLEEARHSENNFQKMVRL  1150
1151  IDLIGLFSRYGDLNRINDDWKHSLDFISPECDDAYVILLGYFQKLLKDAK  1200
1201  GQLRIHIIDNMSRICLRETSLFISPLMLSTLDMIIAENNVNEVSVLFKSF  1250
1251  LELLAADEDLIFEADQKLSLKGKQNVQSNKSVDRDMLKGTKDKQWIEGVS  1300
1301  ASLMQHFLPCILDSCFSKNLRYSMLGIEILKCIIHQGLVNPRMCFSTIIA  1350
1351  LESNAIKETREVAILLHTELHRRHESLIDGLYAQSADLIFSLQKTEEYQT  1400
1401  FKLGEFSPFQSAYTIVSADKSSKSRKKLIMQILKPLKLDGIDLPSFTEEK  1450
1451  VSFVSFCCVCLAGIPYVSIEEPLMIISTVDSVLATIGPTITGWMKKLDHE  1500
1501  RFKILAGINLCNLIYLKRYIKYAFSISDSSRPIREKKPLTLLNRGYVDLI  1550
1551  TSDAKPDIVSKLVIKLFEEENILSGEDQVEGEQLTVV               1587

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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