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

NucPred

Fetching Q01082 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MTTTVATDYDNIEIQQQYSDVNNRWDVDDWDNENSSARLFERSRIKALAD    50
51 EREAVQKKTFTKWVNSHLARVSCRITDLYTDLRDGRMLIKLLEVLSGERL 100
101 PKPTKGRMRIHCLENVDKALQFLKEQRVHLENMGSHDIVDGNHRLTLGLI 150
151 WTIILRFQIQDISVETEDNKEKKSAKDALLLWCQMKTAGYPNVNIHNFTT 200
201 SWRDGMAFNALIHKHRPDLIDFDKLKKSNAHYNLQNAFNLAEQHLGLTKL 250
251 LDPEDISVDHPDEKSIITYVVTYYHYFSKMKALAVEGKRIGKVLDNAIET 300
301 EKMIEKYESLASDLLEWIEQTIIILNNRKFANSLVGVQQQLQAFNTYRTV 350
351 EKPPKFTEKGNLEVLLFTIQSKMRANNQKVYMPREGKLISDINKAWERLE 400
401 KAEHERELALRNELIRQEKLEQLARRFDRKAAMRETWLSENQRLVSQDNF 450
451 GFDLPAVEAATKKHEAIETDIAAYEERVQAVVAVARELEAENYHDIKRIT 500
501 ARKDNVIRLWEYLLELLRARRQRLEMNLGLQKIFQEMLYIMDWMDEMKVL 550
551 VLSQDYGKHLLGVEDLLQKHTLVEADIGIQAERVRGVNASAQKFATDGEG 600
601 YKPCDPQVIRDRVAHMEFCYQELCQLAAERRARLEESRRLWKFFWEMAEE 650
651 EGWIREKEKILSSDDYGKDLTSVMRLLSKHRAFEDEMSGRSGHFEQAIKE 700
701 GEDMIAEEHFGSEKIRERIIYIREQWANLEQLSAIRKKRLEEASLLHQFQ 750
751 ADADDIDAWMLDILKIVSSSDVGHDEYSTQSLVKKHKDVAEEIANYRPTL 800
801 DTLHEQASALPQEHAESPDVRGRLSGIEERYKEVAELTRLRKQALQDTLA 850
851 LYKMFSEADACELWIDEKEQWLNNMQIPEKLEDLEVIQHRFESLEPEMNN 900
901 QASRVAVVNQIARQLMHSGHPSEKEIKAQQDKLNTRWSQFRELVDRKKDA 950
951 LLSALSIQNYHLECNETKSWIREKTKVIESTQDLGNDLAGVMALQRKLTG 1000
1001 MERDLVAIEAKLSDLQKEAEKLESEHPDQAQAILSRLAEISDVWEEMKTT 1050
1051 LKNREASLGEASKLQQFLRDLDDFQSWLSRTQTAIASEDMPNTLTEAEKL 1100
1101 LTQHENIKNEIDNYEEDYQKMRDMGEMVTQGQTDAQYMFLRQRLQALDTG 1150
1151 WNELHKMWENRQNLLSQSHAYQQFLRDTKQAEAFLNNQEYVLAHTEMPTT 1200
1201 LEGAEAAIKKQEDFMTTMDANEEKINAVVETGRRLVSDGNINSDRIQEKV 1250
1251 DSIDDRHRKNRETASELLMRLKDNRDLQKFLQDCQELSLWINEKMLTAQD 1300
1301 MSYDEARNLHSKWLKHQAFMAELASNKEWLDKIEKEGMQLISEKPETEAV 1350
1351 VKEKLTGLHKMWEVLESTTQTKAQRLFDANKAELFTQSCADLDKWLHGLE 1400
1401 SQIQSDDYGKDLTSVNILLKKQQMLENQMEVRKKEIEELQSQAQALSQEG 1450
1451 KSTDEVDSKRLTVQTKFMELLEPLNERKHNLLASKEIHQFNRDVEDEILW 1500
1501 VGERMPLATSTDHGHNLQTVQLLIKKNQTLQKEIQGHQPRIDDIFERSQN 1550
1551 IVTDSSSLSAEAIRQRLADLKQLWGLLIEETEKRHRRLEEAHRAQQYYFD 1600
1601 AAEAEAWMSEQELYMMSEEKAKDEQSAVSMLKKHQILEQAVEDYAETVHQ 1650
1651 LSKTSRALVADSHPESERISMRQSKVDKLYAGLKDLAEERRGKLDERHRL 1700
1701 FQLNREVDDLEQWIAEREVVAGSHELGQDYEHVTMLQERFREFARDTGNI 1750
1751 GQERVDTVNHLADELINSGHSDAATIAEWKDGLNEAWADLLELIDTRTQI 1800
1801 LAASYELHKFYHDAKEIFGRIQDKHKKLPEELGRDQNTVETLQRMHTTFE 1850
1851 HDIQALGTQVRQLQEDAARLQAAYAGDKADDIQKRENEVLEAWKSLLDAC 1900
1901 ESRRVRLVDTGDKFRFFSMVRDLMLWMEDVIRQIEAQEKPRDVSSVELLM 1950
1951 NNHQGIKAEIDARNDSFTTCIELGKSLLARKHYASEEIKEKLLQLTEKRK 2000
2001 EMIDKWEDRWEWLRLILEVHQFSRDASVAEAWLLGQEPYLSSREIGQSVD 2050
2051 EVEKLIKRHEAFEKSAATWDERFSALERLTTLELLEVRRQQEEEERKRRP 2100
2101 PSPEPSTKVSEEAESQQQWDTSKGEQVSQNGLPAEQGSPRMAETVDTSEM 2150
2151 VNGATEQRTSSKESSPIPSPTSDRKAKTALPAQSAATLPARTQETPSAQM 2200
2201 EGFLNRKHEWEAHNKKASSRSWHNVYCVINNQEMGFYKDAKTAASGIPYH 2250
2251 SEVPVSLKEAVCEVALDYKKKKHVFKLRLNDGNEYLFQAKDDEEMNTWIQ 2300
2301 AISSAISSDKHEVSASTQSTPASSRAQTLPTSVVTITSESSPGKREKDKE 2350
2351 KDKEKRFSLFGKKK 2364

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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