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

NucPred

Fetching O60281 from www.uniprot.org...

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

   1  MADEEAEQERLSCGEGGCVAELQRLGERLQELELQLRESRVPAVEAATDY    50
  51  CQQLCQTLLEYAEKWKTSEDPLPLLEVYTVAIQSYVKARPYLTSECENVA   100
 101  LVLERLALSCVELLLCLPVELSDKQWEQFQTLVQVAHEKLMENGSCELHF   150
 151  LATLAQETGVWKNPVLCTILSQEPLDKDKVNEFLAFEGPILLDMRIKHLI   200
 201  KTNQLSQATALAKLCSDHPEIGIKGSFKQTYLVCLCTSSPNGKLIEEISE   250
 251  VDCKDALEMICNLESEGDEKSALVLCTAFLSRQLQQGDMYCAWELTLFWS   300
 301  KLQQRVEPSIQVYLERCRQLSLLTKTVYHIFFLIKVINSETEGAGLATCI   350
 351  ELCVKALRLESTENTEVKISICKTISCLLPDDLEVKRACQLSEFLIEPTV   400
 401  DAYYAVEMLYNQPDQKYDEENLPIPNSLRCELLLVLKTQWPFDPEFWDWK   450
 451  TLKRQCLALMGEEASIVSSIDELNDSEVYEKVVDYQEESKETSMNGLSGG   500
 501  VGANSGLLKDIGDEKQKKREIKQLRERGFISARFRNWQAYMQYCVLCDKE   550
 551  FLGHRIVRHAQKHYKDGIYSCPICAKNFNSKETFVPHVTLHVKQSSKERL   600
 601  AAMKPLRRLGRPPKITTTNENQKTNTVAKQEQRPIKKNSLYSTDFIVFND   650
 651  NDGSDDENDDKDKSYEPEVIPVQKPVPVNEFNCPVTFCKKGFKYFKNLIA   700
 701  HVKGHKDNEDAKRFLEMQSKKVICQYCRRHFVSVTHLNDHLQMHCGSKPY   750
 751  ICIQMKCKAGFNSYAELLTHRKEHQVFRAKCMFPKCGRIFSEAYLLYDHE   800
 801  AQHYNTYTCKFTGCGKVYRSQGELEKHLDDHSTPPEKVLPPEAQLNSSGD   850
 851  SIQPSEVNQNTAENIEKERSMLPSENNIENSLLADRSDAWDKSKAESAVT   900
 901  KQDQISASELRQANGPLSNGLENPATTPLLQSSEVAVSIKVSLNQGIEDN   950
 951  FGKQENSTVEGSGEALVTDLHTPVEDTCNDLCHPGFQERKEQDCFNDAHV  1000
1001  TQNSLVNSETLKIGDLTPQNLERQVNNLMTFSVQNQAAFQNNLPTSKFEC  1050
1051  GDNVKTSSNLYNLPLKTLESIAFVPPQSDLSNSLGTPSVPPKAPVQKFSC  1100
1101  QVEGCTRTYNSSQSIGKHMKTAHPDQYAAFKMQRKSKKGQKANNLNTPNN  1150
1151  GKFVYFLPSPVNSSNPFFTSQTKANGNPACSAQLQHVSPPIFPAHLASVS  1200
1201  TPLLSSMESVINPNITSQDKNEQGGMLCSQMENLPSTALPAQMEDLTKTV  1250
1251  LPLNIDSGSDPFLPLPAESSSMSLFPSPADSGTNSVFSQLENNTNHYSSQ  1300
1301  IEGNTNSSFLKGGNGENAVFPSQVNVANNFSSTNAQQSAPEKVKKDRGRG  1350
1351  PNGKERKPKHNKRAKWPAIIRDGKFICSRCYRAFTNPRSLGGHLSKRSYC  1400
1401  KPLDGAEIAQELLQSNGQPSLLASMILSTNAVNLQQPQQSTFNPEACFKD  1450
1451  PSFLQLLAENRSPAFLPNTFPRSGVTNFNTSVSQEGSEIIKQALETAGIP  1500
1501  STFEGAEMLSHVSTGCVSDASQVNATVMPNPTVPPLLHTVCHPNTLLTNQ  1550
1551  NRTSNSKTSSIEECSSLPVFPTNDLLLKTVENGLCSSSFPNSGGPSQNFT  1600
1601  SNSSRVSVISGPQNTRSSHLNKKGNSASKRRKKVAPPLIAPNASQNLVTS  1650
1651  DLTTMGLIAKSVEIPTTNLHSNVIPTCEPQSLVENLTQKLNNVNNQLFMT  1700
1701  DVKENFKTSLESHTVLAPLTLKTENGDSQMMALNSCTTSINSDLQISEDN  1750
1751  VIQNFEKTLEIIKTAMNSQILEVKSGSQGAGETSQNAQINYNIQLPSVNT  1800
1801  VQNNKLPDSSPFSSFISVMPTKSNIPQSEVSHKEDQIQEILEGLQKLKLE  1850
1851  NDLSTPASQCVLINTSVTLTPTPVKSTADITVIQPVSEMINIQFNDKVNK  1900
1901  PFVCQNQGCNYSAMTKDALFKHYGKIHQYTPEMILEIKKNQLKFAPFKCV  1950
1951  VPTCTKTFTRNSNLRAHCQLVHHFTTEEMVKLKIKRPYGRKSQSENVPAS  2000
2001  RSTQVKKQLAMTEENKKESQPALELRAETQNTHSNVAVIPEKQLVEKKSP  2050
2051  DKTESSLQVITVTSEQCNTNALTNTQTKGRKIRRHKKEKEEKKRKKPVSQ  2100
2101  SLEFPTRYSPYRPYRCVHQGCFAAFTIQQNLILHYQAVHKSDLPAFSAEV  2150
2151  EEESEAGKESEETETKQTLKEFRCQVSDCSRIFQAITGLIQHYMKLHEMT  2200
2201  PEEIESMTASVDVGKFPCDQLECKSSFTTYLNYVVHLEADHGIGLRASKT  2250
2251  EEDGVYKCDCEGCDRIYATRSNLLRHIFNKHNDKHKAHLIRPRRLTPGQE  2300
2301  NMSSKANQEKSKSKHRGTKHSRCGKEGIKMPKTKRKKKNNLENKNAKIVQ  2350
2351  IEENKPYSLKRGKHVYSIKARNDALSECTSRFVTQYPCMIKGCTSVVTSE  2400
2401  SNIIRHYKCHKLSKAFTSQHRNLLIVFKRCCNSQVKETSEQEGAKNDVKD  2450
2451  SDTCVSESNDNSRTTATVSQKEVEKNEKDEMDELTELFITKLINEDSTSV  2500
2501  ETQANTSSNVSNDFQEDNLCQSERQKASNLKRVNKEKNVSQNKKRKVEKA  2550
2551  EPASAAELSSVRKEEETAVAIQTIEEHPASFDWSSFKPMGFEVSFLKFLE  2600
2601  ESAVKQKKNTDKDHPNTGNKKGSHSNSRKNIDKTAVTSGNHVCPCKESET  2650
2651  FVQFANPSQLQCSDNVKIVLDKNLKDCTELVLKQLQEMKPTVSLKKLEVH  2700
2701  SNDPDMSVMKDISIGKATGRGQY                             2723

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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