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

NucPred

Fetching O35889 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MSAGGRDEERRKLADIIHHWNANRLDLFEISQPTEDLEFHGVMRFYFQDK    50
51 AAGNFATKCIRVSSTATTQDVIETLAEKFRPDMRMLSSPKYSLYEVHVSG 100
101 ERRLDIDEKPLVVQLNWNKDDREGRFVLKNENDAIPAKKAQSNGPEKQEK 150
151 EGVIQNFKRTLSKKEKKEKKKREKEALRQASDKEERPSQGDDSENSRLAA 200
201 EVYKDMPETSFTRTISNPEVVMKRRRQQKLEKRMQEFRSSDGRPDSGGTL 250
251 RIYADSLKPNIPYKTILLSTTDPADFAVAESLEKYGLEKENPKDYCIARV 300
301 MLPPGAQHSDERGAKEIILDDDECPLQIFREWPSDKGILVFQLKRRPPDY 350
351 IPKKMKKHVEGKPLKGKDRADGSGYGSALPPEKLPYLVELSPGRRNHFAY 400
401 YSYHTYEDGSDSRDKPKLYRLQLSVTEVGTEKFDDNSIQLFGPGIQPHHC 450
451 DLTNMDGVVTVTPRSMDAETYVDGQRISETTMLQSGMRLQFGTSHVFKFV 500
501 DPIQDHVLSKRSVDGGLMVKGPRHKPGAVQETTFELGGDIHSGTALPASR 550
551 STTRLDSDRVSSASSTAERGMVKPMIRLDQEQDYRRRESRTQDAAGPELM 600
601 LPASIEFRESSEDSFLSAIINYTNSSTVHFKLSPTYVLYMACRYVLSSQH 650
651 RPDISPTERTHKAIAVVNKMVSMMEGVIQEVDQVDQKQKNIAGALAFWMA 700
701 NASELLNFIKQDRDLSRITLDAQDVLAHLVQMAFKYLVHCLQSELNNYMP 750
751 AFLDDPEENSLQRPKIDDVLHTLTGAMSLLRRCRVNAALTIQLFSQLFHF 800
801 INMWLFNRLVTDPDSGLCSHYWGAIIRQQLGHIEAWAEKQGLELAADCHL 850
851 SRIVQATTLLTMDKYVPDDIPNINSTCFKLNSLQLQALLQNYHCAPDEPF 900
901 IPTDLIENVVAVAENTADELARSDGRDVQLEEDPDLQLPFLLPEDGYSCD 950
951 VVRNIPNGLQEFLDPLCQRGFCRLVPHTRSPGTWTIYFEGADYESHLMRE 1000
1001 NTELTQPLRKEPEVITVTLKKQNGMGLSIVAAKGAGQDKLGIYVKSVVKG 1050
1051 GAADVDGRLAAGDQLLSVDGRSLVGLSQERAAELMTRTSSVVTLEVAKQG 1100
1101 AIYHGLATLLNQPSPMMQRISDRRGSGKPRPKSEGFELYNNSAQNGSPES 1150
1151 PQMPWTEYSEPKKLPGDDRLMKNRADHRSSPNVANQPPSPGGKSPYTSGT 1200
1201 AAKITSVSTGNLCTEEQTPPPRPEAYPIPTQTYTREYFTFPASKSQDRMA 1250
1251 PVQNQWPNYEEKPHMHTESDHASIAIQRVTRSQEELREEKVYQLERHRVE 1300
1301 SGMDRKCDSDMWINQSSSVESSTSSQEHLNHSSKSVTPASTLTKSGPGRW 1350
1351 KTPAAVLPTPVAVSQPIRTDLPPPPPPPPAHYTSDFDGISMDLPLPPPPA 1400
1401 NQAAPQSAQVAAAERKKREEHQRWYEKEKARLEEERERKRREQERKLGQM 1450
1451 RTQSLNPASFSPLATQAKPEKPSTLQRPQETVIRELQPQQQPRTIERRDL 1500
1501 QYITISKEELSSGDSLSPDPWKRDAREKLEKQQQMHIVDMLSKEIHELQN 1550
1551 KGDRTAEESDRLRKLMLEWQFQKRLQESKQKDEDDDEEEDDDVDTMLIMQ 1600
1601 RLEAERRARLQDEERRRQQQLEEMRKREVEDRVRQEEDGRHQEEERVKRD 1650
1651 AEEKRRQEEGYYSRLEAERRRQHEEAARRLLEPEEPGLSRPPLPQDYEPP 1700
1701 SQSSAPSAPPPPPQRNASYLKTQVLSPDSLFTAKFVAYDDDDEEENYVPA 1750
1751 GPNSYSGSAGTTAGTYDAPRDTREKLSRSQDADLPGSSGAPENLTFRERQ 1800
1801 RLFSQGQDVSDKVKASRKLTELENELNTK 1829

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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