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

NucPred

Fetching Q7TSC1 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MSDRSGPTAKGKDGKKYSSLNLFDTYKGKSLEIQKPAVAPRHGLQSLGKV    50
  51  AIARRMPPPANLPSLKAENKGNDPNVSLVPKDGTGWASKQEQSDPKSSDA   100
 101  STAQPPESQPLPASQTPASNQPKRPPTAPENTPSVPSGVKSWAQASVTHG   150
 151  AHGDGGRASNLLSRFSREEFPTLQAAGDQDKAAKERESAEQSSGPGPSLR   200
 201  PQNSTTWRDGGGRGPDDLEGPDSKLHHGHDPRGGLQPSGPPQFPPYRGMM   250
 251  PPFMYPPYLPFPPPYGPQGPYRYPTPDGPSRFPRVAGPRGSGPPMRLVEP   300
 301  VGRPSILKEDNLKEFDQLDQENDDGWAGAHEEVDYTEKLKFSDEEDGRDS   350
 351  DEEGAEGHKDSQSAAAEEPETDGKKGTSPGSELPPPKTAWTENARPSETE   400
 401  PAPPTPKPPPPPPHRGPVGNWGPPGDYPDRGGPPCKPPAPEDEDEAWRQR   450
 451  RKQSSSEISLAVERARRRREEEERRMQEERRAACAEKLKRLDEKFGAPDK   500
 501  RLKAEPAAPPVTPAAPALPPVVPKEIPAAPALPPTPTPTPEKEPEEPAQA   550
 551  PPVQAAPSPGVAPVPTLVSGGGCTANSNSSGSFEASPVEPQLPSKEGPEP   600
 601  PEEVPPPTTPPAPKMEPKGDGVGSTRQPPSQGLGYPKYQKSLPPRFQRQQ   650
 651  QEQLLKQQQQQQQWQQQQQGTAPPAPVPPSPPQPVTLGAVPAPQAPPPPP   700
 701  KALYPGALGRPPPMPPMNFDPRWMMIPPYVDPRLLQGRPPLDFYPPGVHP   750
 751  SGLVPRERSDSGGSSSEPFERHAPPLLRERGTPPVDPKLAWVGDVFTTTP   800
 801  TDPRPLTSPLRQAADEEEKSMRSETPPVPPPPPYLANYPGFPENGTPGPP   850
 851  ISRFPLEESAPPGPRPLPWPPGNDEAAKMQAPPPKKEPSKEEPPQLSGPE   900
 901  AGRKPARGGQGPPPPRRENRTETRWGPRPGSCRRGIPPEEPGVPPRRAGP   950
 951  IKKPPPPVKVEELPPKSLEQGDETPKVPKPDALKTAKGKVGPKETPPGGN  1000
1001  LSPAPRLRRDYSYERVGPTSCRGRGRGEYFARGRGFRGTYGGRGRGARSR  1050
1051  EFRSYREFRGDDGRGGGSGGTNHPSAPRGRTASETRSEGSEYEEIPKRRR  1100
1101  QRGSETGSETHESDLAPSDKEAPPPKEGVLGQVPLAPPQPGAPPSPAPAR  1150
1151  FSTARGGRVFTPRGVPSRRGRGGGRPPPVCSGWSPPAKSLVPKKPPTGPL  1200
1201  PPSKEPLKEKLISGPLSPMSRAGNMGVGMEDGERPRRRRHGRAQQQDKPP  1250
1251  RFRRLKQERENAARGADGKPPSLTLAASTPGPEETLTAATVPPPPRRTAA  1300
1301  KSPDLSNQNSDQANEEWETASESSDFASERRGDKETPPAALMTSKAVGTP  1350
1351  GANAGGAGPGISAMSRGDLSQRAKDLSKRSFSSQRPGMDRQNRRPGTGGK  1400
1401  TGSGGGSSGGGGAGPGGRTGPGRGDKRSWPSPKNRSRPPEERPPGLPLPP  1450
1451  PPPSSSAVFRLDQVIHSNPAGIQQALAQLSSRQGNVTAPGGHPRPKPGPP  1500
1501  QAPQGSSPRPPTRYDPPRASSAISSDPHFEEPGPMVRGVGGTPRDSAGVN  1550
1551  PFPPKRRERPPRKPELLQEETVPASHSSGFLGSKPEVPGPQEESRDSGTE  1600
1601  ALTPHIWNRLHTATSRKSYQPGSIEPWMEPLSPFEDVAGTEMSQSDSGVD  1650
1651  LSGDSQVSSGPCSQRSSPDGGLKGSAEGPPKRPGGPSPLNAVPGESASGS  1700
1701  EPSEPPRRRPPASHEGERKELPREQPLPPGPIGTERSQRTDRGPEPGPLR  1750
1751  PAHRPGSQVEFGTTNKDSDLCLVVGDTLKGEKELVASATEAVPISRDWEL  1800
1801  LPSASTSAEPQPKSLGSGQCVPEPSPSGQRPYPEVFYGSPGPPNSQQVSG  1850
1851  GAPIDSQLHPNSGGFRPGTPSLHQYRSQPLYLPPGPAPPSALLSGVALKG  1900
1901  QFLDFSALQATELGKLPAGGVLYPPPSFLYSAAFCPSPLPDPPLLQVRQD  1950
1951  LPSPSDFYSTPLQPGGQSGFLPSGAPAQQMLLPVVDSQLPVVNFGSLPPA  2000
2001  PPPAPPPLSLLPVGPALQPPNLAVRPPPAPAARVLPSPARPFAPSLGRAE  2050
2051  LHPVELKPFQDYRKLSSNLGGPGSSRTPPSGRPFSGLNSRLKAPPSTYSG  2100
2101  VFRTQRIDLYQQASPPDALRWMPKPWERAGPPSREGPPRRAEEPGSRGEK  2150
2151  EPGLPPPR                                            2158

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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