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

NucPred

Fetching Q5VT25 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MSGEVRLRQLEQFILDGPAQTNGQCFSVETLLDILICLYDECNNSPLRRE    50
51 KNILEYLEWAKPFTSKVKQMRLHREDFEILKVIGRGAFGEVAVVKLKNAD 100
101 KVFAMKILNKWEMLKRAETACFREERDVLVNGDNKWITTLHYAFQDDNNL 150
151 YLVMDYYVGGDLLTLLSKFEDRLPEDMARFYLAEMVIAIDSVHQLHYVHR 200
201 DIKPDNILMDMNGHIRLADFGSCLKLMEDGTVQSSVAVGTPDYISPEILQ 250
251 AMEDGKGRYGPECDWWSLGVCMYEMLYGETPFYAESLVETYGKIMNHKER 300
301 FQFPAQVTDVSENAKDLIRRLICSREHRLGQNGIEDFKKHPFFSGIDWDN 350
351 IRNCEAPYIPEVSSPTDTSNFDVDDDCLKNSETMPPPTHTAFSGHHLPFV 400
401 GFTYTSSCVLSDRSCLRVTAGPTSLDLDVNVQRTLDNNLATEAYERRIKR 450
451 LEQEKLELSRKLQESTQTVQALQYSTVDGPLTASKDLEIKNLKEEIEKLR 500
501 KQVTESSHLEQQLEEANAVRQELDDAFRQIKAYEKQIKTLQQEREDLNKE 550
551 LVQASERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQKQKLARHV 600
601 RDKEEEVDLVMQKVESLRQELRRTERAKKELEVHTEALAAEASKDRKLRE 650
651 QSEHYSKQLENELEGLKQKQISYSPGVCSIEHQQEITKLKTDLEKKSIFY 700
701 EEELSKREGIHANEIKNLKKELHDSEGQQLALNKEIMILKDKLEKTRRES 750
751 QSEREEFESEFKQQYEREKVLLTEENKKLTSELDKLTTLYENLSIHNQQL 800
801 EEEVKDLADKKESVAHWEAQITEIIQWVSDEKDARGYLQALASKMTEELE 850
851 ALRNSSLGTRATDMPWKMRRFAKLDMSARLELQSALDAEIRAKQAIQEEL 900
901 NKVKASNIITECKLKDSEKKNLELLSEIEQLIKDTEELRSEKGIEHQDSQ 950
951 HSFLAFLNTPTDALDQFERSPSCTPASKGRRTVDSTPLSVHTPTLRKKGC 1000
1001 PGSTGFPPKRKTHQFFVKSFTTPTKCHQCTSLMVGLIRQGCSCEVCGFSC 1050
1051 HITCVNKAPTTCPVPPEQTKGPLGIDPQKGIGTAYEGHVRIPKPAGVKKG 1100
1101 WQRALAIVCDFKLFLYDIAEGKASQPSVVISQVIDMRDEEFSVSSVLASD 1150
1151 VIHASRKDIPCIFRVTASQLSASNNKCSILMLADTENEKNKWVGVLSELH 1200
1201 KILKKNKFRDRSVYVPKEAYDSTLPLIKTTQAAAIIDHERIALGNEEGLF 1250
1251 VVHVTKDEIIRVGDNKKIHQIELIPNDQLVAVISGRNRHVRLFPMSALDG 1300
1301 RETDFYKLSETKGCQTVTSGKVRHGALTCLCVAMKRQVLCYELFQSKTRH 1350
1351 RKFKEIQVPYNVQWMAIFSEQLCVGFQSGFLRYPLNGEGNPYSMLHSNDH 1400
1401 TLSFIAHQPMDAICAVEISSKEYLLCFNSIGIYTDCQGRRSRQQELMWPA 1450
1451 NPSSCCYNAPYLSVYSENAVDIFDVNSMEWIQTLPLKKVRPLNNEGSLNL 1500
1501 LGLETIRLIYFKNKMAEGDELVVPETSDNSRKQMVRNINNKRRYSFRVPE 1550
1551 EERMQQRREMLRDPEMRNKLISNPTNFNHIAHMGPGDGIQILKDLPMNPR 1600
1601 PQESRTVFSGSVSIPSITKSRPEPGRSMSASSGLSARSSAQNGSALKREF 1650
1651 SGGSYSAKRQPMPSPSEGSLSSGGMDQGSDAPARDFDGEDSDSPRHSTAS 1700
1701 NSSNLSSPPSPASPRKTKSLSLESTDRGSWDP 1732

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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