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

NucPred

Fetching Q6DHV5 from www.uniprot.org...

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

   1  MKKSQREDIFKKMSEEMDNITAEEIIDKHLQKDLDAEENQNVAKTLRGKV    50
  51  REKLKISKINKGEKSSTEQLIDSEIHQRSKLSPQTEVSLDESLSFFILSG   100
 101  EEGSALGKSSEQRPVNRSYPKCFSLGVNLQNVAESEEEEFMKEFILTDIL   150
 151  KVKAADYEDDQEQIKKQKANIFVPSSSPVVNQRKLPKDMMPRILEDEGFY   200
 201  IQRKPEIYKKTCNKMENRLLKLEEGKCWFGESGEIMSLPTPIKQSWNFRL   250
 251  NVRKEPLNPLLKTIYRKAVKYDLGSSFMNKMEGSREIYQLDLNIVGLQFS   300
 301  HHHLFNQEQVLCARLLQLYECFQDRQQQNVSQLLYEKLKALTDATKLSNE   350
 351  NSEINQLTRKSLQDYYWQISNTKQMYDLERGKDLSLLHSILRTWKQIKSL   400
 401  RHGQGFTSTPIKLQVQRIKMNKCDEQEQISEMSETEKKNEGKELKNGKKL   450
 451  ESLSYLASDETEIERIKPITLRPQLSFTAELTSLSKCSLHEQKRRAKIQK   500
 501  LKYFIKIFYNNKQVSCTSVSPLQFDFKVMFQQIFNIQLMYWPEVICLEVY   550
 551  EKSKRTSLLAKLYIPLPNYTELKGKTALQYVEFSSDKLVMPADGEVGSNV   600
 601  PFLLEGNGTEELCLLTSGKLSYSLSWSLDENGLPLIPMPQSLRSSYCSML   650
 651  RNVDARSVPGIPWLMNEQKLFEWANEVRIDPNNPEYSDLMESVTYMRLKG   700
 701  QDIPKYFRLEQLQDEFNFVSEEEMAKSKRFQLLQLRNAGQLDNFLLQQMP   750
 751  LHDTEIPDLVFQEYESQKEKEVSVSDVNSITAQRINSANFLKKVRRLIMK   800
 801  RIVKISKCNLSDIVNDYEEIVSTSQLTDAVCKFVEPRRKLKPQRKERKKV   850
 851  TAQAISDGDIKILVRIVRAYNIPTRKTTINGSLDMPTCLKSSISCLRHRE   900
 901  TIKSVASDETLHEDTVHPFVEVSFQHTVYKTNTASGSHPCWNEEIKVDFV   950
 951  SPGHDYSFSSLSKIKDNIYINIFDEMMTEKHEDHCLKSCSGHSYIRKNWL  1000
1001  GCIVFPFSALLQQSEISGTFQVTIPPVLLGYTWSNTYVFPKEDSNEQNLK  1050
1051  ECTFLNIFATIEPQISYVTCNPTLDKFLDQTEVLQRAQIFKKNCKAMFPN  1100
1101  RRIVTTVFNDEGIQFLVTRYIKALNPPQQLLDIFLHNSNATFDLIARFVS  1150
1151  LIPFVPNTPDENDGSDIWMTSEHCISLAIGNKEEHAILLCNFFLYFGKKA  1200
1201  LVLLGTSVLEGHVAYVVTQETNEYLLWNPSTGQCYKQFDPFCPLKSVDCL  1250
1251  FDDRNVWFNIQQNNTPMAVFFDYSKESFWKQLLPKNVQGTKIQSIQPEEI  1300
1301  IYFETDKSMVEDLRNRIERTLKSKVMEWRPKHPTHWNRQCTFILRQILPK  1350
1351  LEFGIGSFVSSEGDNEFERILQFYWVTGFPIQMPYIDVQSIIDAVYQTGI  1400
1401  HSAEFPQTEFALAVYIHPYPNNILSVWVYLASLVQHQ               1437

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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