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

NucPred

Fetching P10587 from www.uniprot.org...

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

   1  MSQKPLSDDEKFLFVDKNFVNNPLAQADWSAKKLVWVPSEKHGFEAASIK    50
  51  EEKGDEVTVELQENGKKVTLSKDDIQKMNPPKFSKVEDMAELTCLNEASV   100
 101  LHNLRERYFSGLIYTYSGLFCVVINPYKQLPIYSEKIIDMYKGKKRHEMP   150
 151  PHIYAIADTAYRSMLQDREDQSILCTGESGAGKTENTKKVIQYLAVVASS   200
 201  HKGKKDTSITQGPSFSYGELEKQLLQANPILEAFGNAKTVKNDNSSRFGK   250
 251  FIRINFDVTGYIVGANIETYLLEKSRAIRQAKDERTFHIFYYLIAGASEQ   300
 301  MRNDLLLEGFNNYTFLSNGHVPIPAQQDDEMFQETLEAMTIMGFTEEEQT   350
 351  SILRVVSSVLQLGNIVFKKERNTDQASMPDNTAAQKVCHLMGINVTDFTR   400
 401  SILTPRIKVGRDVVQKAQTKEQADFAIEALAKAKFERLFRWILTRVNKAL   450
 451  DKTKRQGASFLGILDIAGFEIFEINSFEQLCINYTNEKLQQLFNHTMFIL   500
 501  EQEEYQREGIEWNFIDFGLDLQPCIELIERPTNPPGVLALLDEECWFPKA   550
 551  TDTSFVEKLIQEQGNHAKFQKSKQLKDKTEFCILHYAGKVTYNASAWLTK   600
 601  NMDPLNDNVTSLLNQSSDKFVADLWKDVDRIVGLDQMAKMTESSLPSASK   650
 651  TKKGMFRTVGQLYKEQLTKLMTTLRNTNPNFVRCIIPNHEKRAGKLDAHL   700
 701  VLEQLRCNGVLEGIRICRQGFPNRIVFQEFRQRYEILAANAIPKGFMDGK   750
 751  QACILMIKALELDPNLYRIGQSKIFFRTGVLAHLEEERDLKITDVIIAFQ   800
 801  AQCRGYLARKAFAKRQQQLTAMKVIQRNCAAYLKLRNWQWWRLFTKVKPL   850
 851  LQVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQE   900
 901  KLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAE   950
 951  KKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQN  1000
1001  NKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLK  1050
1051  KEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQA  1100
1101  ALARLEDETSQKNNALKKIRELESHISDLQEDLESEKAARNKAEKQKRDL  1150
1151  SEELEALKTELEDTLDTTATQQELRAKREQEVTVLKRALEEETRTHEAQV  1200
1201  QEMRQKHTQAVEELTEQLEQFKRAKANLDKTKQTLEKDNADLANEIRSLS  1250
1251  QAKQDVEHKKKKLEVQLQDLQSKYSDGERVRTELNEKVHKLQIEVENVTS  1300
1301  LLNEAESKNIKLTKDVATLGSQLQDTQELLQEETRQKLNVTTKLRQLEDD  1350
1351  KNSLQEQLDEEVEAKQNLERHISTLTIQLSDSKKKLQEFTATVETMEEGK  1400
1401  KKLQREIESLTQQFEEKAASYDKLEKTKNRLQQELDDLVVDLDNQRQLVS  1450
1451  NLEKKQKKFDQMLAEEKNISSKYADERDRAEAEAREKETKALSLARALEE  1500
1501  ALEAKEELERTNKMLKAEMEDLVSSKDDVGKNVHELEKSKRTLEQQVEEM  1550
1551  KTQLEELEDELQAAEDAKLRLEVNMQAMKSQFERDLQARDEQNEEKRRQL  1600
1601  LKQLHEHETELEDERKQRALAAAAKKKLEVDVKDLESQVDSANKAREEAI  1650
1651  KQLRKLQAQMKDYQRDLDDARAAREEIFATARENEKKAKNLEAELIQLQE  1700
1701  DLAAAERARKQADLEKEEMAEELASANSGRTSLQDEKRRLEARIAQLEEE  1750
1751  LDEEHSNIETMSDRMRKAVQQAEQLNNELATERATAQKNENARQQLERQN  1800
1801  KELRSKLQEMEGAVKSKFKSTIAALEAKIASLEEQLEQEAREKQAAAKTL  1850
1851  RQKDKKLKDALLQVEDERKQAEQYKDQAEKGNLRLKQLKRQLEEAEEESQ  1900
1901  RINANRRKLQRELDEATESNDALGREVAALKSKLRRGNEPVSFAPPRRSG  1950
1951  GRRVIENATDGGEEEIDGRDGDFNGKASE                       1979

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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