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

NucPred

Fetching O08638 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MAQKGQLSDDEKFLFVDKNFMNSPMAQADWVAKKLVWVPSEKQGFEAASI    50
  51  KEEKGDEVVVELVENGKKVTVGKDDIQKMNPPKFSKVEDMAELTCLNEAS   100
 101  VLHNLRERYFSGLIYTYSGLFCVVVNPYKYLPIYSEKIVDMYKGKKRHEM   150
 151  PPHIYAIADTAYRSMLQDREDQSILCTGESGAGKTENTQKVIQYLAVVAS   200
 201  SHKGKKDSSITGELEKQLLQANPILEAFGNAKTVKNDNSSRFGKFIRINF   250
 251  DVTGYIVGANIETYLLEKSRAIRQARDERTFHIFYYLLAGAKEKMKSDLL   300
 301  LESFNSYTFLSNGFVPIPAAQDDEMFQETLEAMSIMGFNEEEQLAILKVV   350
 351  SSVLQLGNIVFKKERNTDQASMPDNTAAQKVCHLVGINVTDFTRAILTPR   400
 401  IKVGRDVVQKAQTKEQADFAIEALAKATYERLFRWILSRVNKALDKTHRQ   450
 451  GASFLGILDIAGFEIFEVNSFEQLCINYTNEKLQQLFNHTMFILEQEEYQ   500
 501  REGIEWNFIDFGLDLQPSIELIERPNNPPGVLALLDEECWFPKATDKSFV   550
 551  EKLCSEQGNHPKFQKPKQLKDKTEFSIIHYAGKVDYNASAWLTKNMDPLN   600
 601  DNVTSLLNASSDKFVADLWKDVDRIVGLDQMAKMTESSLPSASKTKKGMF   650
 651  RTVGQLYKEQLGKLMATLRNTTANFVRCIIPNHEKRSGKLDAFLVLEQLR   700
 701  CNGVLEGIRICRQGFPNRIVFQEFRQRYEILAANAIPKGFMDGKQACILM   750
 751  IKALELDPNLYRIGQSKIFFRTGVLAHLEEERDLKITDVIMAFQAMCRGY   800
 801  LARKAFTKRQQQLTAMKVIQRNCAAYLKLRNWQWWRLFTKVKPLLQVTRQ   850
 851  EEEMQAKEEEMQKITERQQKAETELKELEQKHTQLAEEKTLLQEQLQAET   900
 901  ELYAESEEMRVRLAAKKQELEEILHEMEARLEEEEDRRQQLQAERKKMAQ   950
 951  QMLDLEEQLEEEEAARQKLQLEKVTAEAKIKKLEDDILVMDDQNSKLSKE  1000
1001  RKLLEERVSDLTTNLAEEEEKAKNLTKLKSKHESMISELEVRLKKEEKSR  1050
1051  QELEKLKRKLEGDASDFHEQIADLQAQIAELKMQLAKKEEELQAALARLD  1100
1101  EEIAQKNNALKKIRELEGHISDLQEDLDSERAARNKAEKQKRDLGEELEA  1150
1151  LKTELEDTLDSTATQQELRAKREQEVTVLKKALDEETRSHEAQVQEMRQK  1200
1201  HTQAVEELTEQLEQFKRAKANLDKSKQTLEKENADLAGELRVLGQAKQEV  1250
1251  EHKKKKLEVQLQDLQSKCSDGERARAELSDKVHKLQNEVESVTGMLNEAE  1300
1301  GKAIKLAKDVASLGSQLQDTQELLQEETRQKLNVSTKLRQLEDERNSLQD  1350
1351  QLDEEMEAKQNLERHVSTLNIQLSDSKKKLQDFASTIEVMEEGKKRLQKE  1400
1401  MEGLSQQYEEKAAAYDKLEKTKNRLQQELDDLVVDLDNQRQLVSNLEKKQ  1450
1451  KKFDQLLAEEKNISSKYADERDRAEAEAREKETKALSLARALEEALEAKE  1500
1501  ELERTNKMLKAEMEDLVSSKDDVGKNVHELEKSKRALETQMEEMKTQLEE  1550
1551  SEDDVQATEDAKLRLEVNMQALKGQFERDLQARDEQNEEKRRQLQRQLHE  1600
1601  YETELEDERKQRALAAAAKKKLEGDLKDLELQADSAIKGREEAIKQLRKL  1650
1651  QAQMKDFQRELDDARASRDEIFATSKENEKKAKSLEADLMQLQEDLAAAE  1700
1701  RARKQADLEKEELAEELASSLSGRNTLQDEKRRLEARIAQLEEELEEEQG  1750
1751  NMEAMSDRVRKATLQAEQLSNELATERSTAQKNESARQQLERQNKELRSK  1800
1801  LQEVEGAVKAKLKSTVAALEAKIAQLEEQVEQEAREKQAATKSLKQKDKK  1850
1851  LKEVLLQVEDERKMAEQYKEQAEKGNTKVKQLKRQLEEAEEESQCINANR  1900
1901  RKLQRELDEATESNEAMGREVNALKSKLRRGNEASFVPSRRAGGRRVIEN  1950
1951  TDGSEEEMDARDSDFNGTKASE                              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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