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

NucPred

Fetching P35749 from www.uniprot.org...

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

   1  MAQKGQLSDDEKFLFVDKNFINSPVAQADWAAKRLVWVPSEKQGFEAASI    50
  51  KEEKGDEVVVELVENGKKVTVGKDDIQKMNPPKFSKVEDMAELTCLNEAS   100
 101  VLHNLRERYFSGLIYTYSGLFCVVVNPYKHLPIYSEKIVDMYKGKKRHEM   150
 151  PPHIYAIADTAYRSMLQDREDQSILCTGESGAGKTENTKKVIQYLAVVAS   200
 201  SHKGKKDTSITGELEKQLLQANPILEAFGNAKTVKNDNSSRFGKFIRINF   250
 251  DVTGYIVGANIETYLLEKSRAIRQARDERTFHIFYYMIAGAKEKMRSDLL   300
 301  LEGFNNYTFLSNGFVPIPAAQDDEMFQETVEAMAIMGFSEEEQLSILKVV   350
 351  SSVLQLGNIVFKKERNTDQASMPDNTAAQKVCHLMGINVTDFTRSILTPR   400
 401  IKVGRDVVQKAQTKEQADFAVEALAKATYERLFRWILTRVNKALDKTHRQ   450
 451  GASFLGILDIAGFEIFEVNSFEQLCINYTNEKLQQLFNHTMFILEQEEYQ   500
 501  REGIEWNFIDFGLDLQPCIELIERPNNPPGVLALLDEECWFPKATDKSFV   550
 551  EKLCTEQGSHPKFQKPKQLKDKTEFSIIHYAGKVDYNASAWLTKNMDPLN   600
 601  DNVTSLLNASSDKFVADLWKDVDRIVGLDQMAKMTESSLPSASKTKKGMF   650
 651  RTVGQLYKEQLGKLMTTLRNTTPNFVRCIIPNHEKRSGKLDAFLVLEQLR   700
 701  CNGVLEGIRICRQGFPNRIVFQEFRQRYEILAANAIPKGFMDGKQACILM   750
 751  IKALELDPNLYRIGQSKIFFRTGVLAHLEEERDLKITDVIMAFQAMCRGY   800
 801  LARKAFAKRQQQLTAMKVIQRNCAAYLKLRNWQWWRLFTKVKPLLQVTRQ   850
 851  EEEMQAKEDELQKTKERQQKAENELKELEQKHSQLTEEKNLLQEQLQAET   900
 901  ELYAEAEEMRVRLAAKKQELEEILHEMEARLEEEEDRGQQLQAERKKMAQ   950
 951  QMLDLEEQLEEEEAARQKLQLEKVTAEAKIKKLEDEILVMDDQNNKLSKE  1000
1001  RKLLEERISDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSR  1050
1051  QELEKLKRKLEGDASDFHEQIADLQAQIAELKMQLAKKEEELQAALARLD  1100
1101  DEIAQKNNALKKIRELEGHISDLQEDLDSERAARNKAEKQKRDLGEELEA  1150
1151  LKTELEDTLDSTATQQELRAKREQEVTVLKKALDEETRSHEAQVQEMRQK  1200
1201  HAQAVEELTEQLEQFKRAKANLDKNKQTLEKENADLAGELRVLGQAKQEV  1250
1251  EHKKKKLEAQVQELQSKCSDGERARAELNDKVHKLQNEVESVTGMLNEAE  1300
1301  GKAIKLAKDVASLSSQLQDTQELLQEETRQKLNVSTKLRQLEEERNSLQD  1350
1351  QLDEEMEAKQNLERHISTLNIQLSDSKKKLQDFASTVEALEEGKKRFQKE  1400
1401  IENLTQQYEEKAAAYDKLEKTKNRLQQELDDLVVDLDNQRQLVSNLEKKQ  1450
1451  RKFDQLLAEEKNISSKYADERDRAEAEAREKETKALSLARALEEALEAKE  1500
1501  ELERTNKMLKAEMEDLVSSKDDVGKNVHELEKSKRALETQMEEMKTQLEE  1550
1551  LEDELQATEDAKLRLEVNMQALKGQFERDLQARDEQNEEKRRQLQRQLHE  1600
1601  YETELEDERKQRALAAAAKKKLEGDLKDLELQADSAIKGREEAIKQLRKL  1650
1651  QAQMKDFQRELEDARASRDEIFATAKENEKKAKSLEADLMQLQEDLAAAE  1700
1701  RARKQADLEKEELAEELASSLSGRNALQDEKRRLEARIAQLEEELEEEQG  1750
1751  NMEAMSDRVRKATQQAEQLSNELATERSTAQKNESARQQLERQNKELRSK  1800
1801  LHEMEGAVKSKFKSTIAALEAKIAQLEEQVEQEAREKQAATKSLKQKDKK  1850
1851  LKEILLQVEDERKMAEQYKEQAEKGNARVKQLKRQLEEAEEESQRINANR  1900
1901  RKLQRELDEATESNEAMGREVNALKSKLRRGNETSFVPSRRSGGRRVIEN  1950
1951  ADGSEEETDTRDADFNGTKASE                              1972

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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