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

NucPred

Fetching O74805 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MSHARLSVGSECWVSNNNGHWDAARLIEIKDNGGGKVVATVAKSSGVLET    50
  51  VNYQQLQNRNIGQSESPSDLTNLPYLNEPSVLHALHNRYNNKQIYTYSGI   100
 101  VLVSINPYQNLPEFYNDNLIKHFHKDPEAAKVPHLYSIASSCYHALTTDS   150
 151  KNQTIIVSGESGAGKTVAAKYIMRYLTSVQGVDHNGVVKRSVENQVLATN   200
 201  PIMEAFGNAKTIRNDNSSRFGKYVTISFDENLLITGANVNTYLLERSRVV   250
 251  SLLKGERNYHIFYQLITGCTEEQRDKWFLESASSFNYLSQGNCDEISGVD   300
 301  DSNDFTITCRALSTIGISESRQEDVFCLLAALLHLGNIEVCATRNEAQIQ   350
 351  PGDGYLQKAALLLGVDSSTLAKWIVKRQLKTRSETIITSSTLEHAISIRD   400
 401  SVAKYLYSALFLWIVHMINASLDHNKVKRAAYKYIGVVDIYGFEHFEKNS   450
 451  MEQFCINYANEKLQQEFNKHVFKLEQEEYVKEGLDWRLIEYSDNQGCISL   500
 501  IEDKLGILSLLDEECRLPSGNHQSFLQKLNNQLPTKHSQFYKKSRFNDGS   550
 551  FMVKHYALDVSYQVHDFLAKNSDAIPDEFISLLQNSKNEFITYLLDFYMQ   600
 601  LVSSQNKNPRKTAISRKPTLSSMFKSSLSQLMTTVSSTNVHYIRCIKPNE   650
 651  EKLPWTFSPPMVLSQLRACGVFETIRISSLGFPARFSYEEFAHRFRILLS   700
 701  SKEWEEDNKKLTLNIVNSVIPHDNLNFQVGRSKIFFRSNVIGNFEEAHRA   750
 751  TCSKSTVLLQSAIRGFFTRKEYQRTVKFIIKLQSVIMGWLTRQRFEREKI   800
 801  ERAAILIQAHWRSYIQRKRYLSLIKCAIVIQSIVRKNIAYSRYINELRES   850
 851  SATLLAKFWRAYNARKTFRGLKKSVIALQCVSRSVLTRRYLRRLQDSAGR   900
 901  TSILYEKQKNLQASITEVSKQLKSNSKKVTVLRNKLNILNNSLSKWKCLI   950
 951  KKPSDFSEPVSMDFTSNDEQLVQLLQAESKLRQASQQLYMAAKKSELGFV  1000
1001  QSQTARENLSNYYQALQMTVSEKFEYDTEQLPSRVLFYAMDRYFSIHKKL  1050
1051  KQLLELVGVENASLLPNEVVNKQTKDLLYEKRVVFLKQIKQALTVSSLFN  1100
1101  AVGYKDGVMRLLETDQNSLLFAGVVNFLIFAGISLDLKTQISEFLSQLCS  1150
1151  YFTKIVDGTVIENDKTLDFYEKPLQAVLYWFATLHKIRSFLVHLLSINSH  1200
1201  GKQSVVEDLWNPLILKFSKHFSNLENSFHSLVQKLLSCCTEGSINALLNS  1250
1251  KCLPEFIDAADENTTPTGMNIYELIDRMNLIHKLLISSALQPNLLELTIS  1300
1301  HMLQHIGQRAFQTLIHGRSPYTWKSASQVSYNASLLINWCHQKGISYVNS  1350
1351  SLLPLMQSPLVFCLRKNDANDLDVILSVCNLLSPFEVVCLLNRYQPCAGE  1400
1401  NPLPKSFSKAVEALSCKYKQSGFTNGKITNTNGHAIPIAASKNPLLSLEN  1450
1451  NHIYEELRLSELINLLAKATL                               1471

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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