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

NucPred

Fetching P15924 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MSCNGGSHPRINTLGRMIRAESGPDLRYEVTSGGGGTSRMYYSRRGVITD    50
51 QNSDGYCQTGTMSRHQNQNTIQELLQNCSDCLMRAELIVQPELKYGDGIQ 100
101 LTRSRELDECFAQANDQMEILDSLIREMRQMGQPCDAYQKRLLQLQEQMR 150
151 ALYKAISVPRVRRASSKGGGGYTCQSGSGWDEFTKHVTSECLGWMRQQRA 200
201 EMDMVAWGVDLASVEQHINSHRGIHNSIGDYRWQLDKIKADLREKSAIYQ 250
251 LEEEYENLLKASFERMDHLRQLQNIIQATSREIMWINDCEEEELLYDWSD 300
301 KNTNIAQKQEAFSIRMSQLEVKEKELNKLKQESDQLVLNQHPASDKIEAY 350
351 MDTLQTQWSWILQITKCIDVHLKENAAYFQFFEEAQSTEAYLKGLQDSIR 400
401 KKYPCDKNMPLQHLLEQIKELEKEREKILEYKRQVQNLVNKSKKIVQLKP 450
451 RNPDYRSNKPIILRALCDYKQDQKIVHKGDECILKDNNERSKWYVTGPGG 500
501 VDMLVPSVGLIIPPPNPLAVDLSCKIEQYYEAILALWNQLYINMKSLVSW 550
551 HYCMIDIEKIRAMTIAKLKTMRQEDYMKTIADLELHYQEFIRNSQGSEMF 600
601 GDDDKRKIQSQFTDAQKHYQTLVIQLPGYPQHQTVTTTEITHHGTCQDVN 650
651 HNKVIETNRENDKQETWMLMELQKIRRQIEHCEGRMTLKNLPLADQGSSH 700
701 HITVKINELKSVQNDSQAIAEVLNQLKDMLANFRGSEKYCYLQNEVFGLF 750
751 QKLENINGVTDGYLNSLCTVRALLQAILQTEDMLKVYEARLTEEETVCLD 800
801 LDKVEAYRCGLKKIKNDLNLKKSLLATMKTELQKAQQIHSQTSQQYPLYD 850
851 LDLGKFGEKVTQLTDRWQRIDKQIDFRLWDLEKQIKQLRNYRDNYQAFCK 900
901 WLYDAKRRQDSLESMKFGDSNTVMRFLNEQKNLHSEISGKRDKSEEVQKI 950
951 AELCANSIKDYELQLASYTSGLETLLNIPIKRTMIQSPSGVILQEAADVH 1000
1001 ARYIELLTRSGDYYRFLSEMLKSLEDLKLKNTKIEVLEEELRLARDANSE 1050
1051 NCNKNKFLDQNLQKYQAECSQFKAKLASLEELKRQAELDGKSAKQNLDKC 1100
1101 YGQIKELNEKITRLTYEIEDEKRRRKSVEDRFDQQKNDYDQLQKARQCEK 1150
1151 ENLGWQKLESEKAIKEKEYEIERLRVLLQEEGTRKREYENELAKVRNHYN 1200
1201 EEMSNLRNKYETEINITKTTIKEISMQKEDDSKNLRNQLDRLSRENRDLK 1250
1251 DEIVRLNDSILQATEQRRRAEENALQQKACGSEIMQKKQHLEIELKQVMQ 1300
1301 QRSEDNARHKQSLEEAAKTIQDKNKEIERLKAEFQEEAKRRWEYENELSK 1350
1351 VRNNYDEEIISLKNQFETEINITKTTIHQLTMQKEEDTSGYRAQIDNLTR 1400
1401 ENRSLSEEIKRLKNTLTQTTENLRRVEEDIQQQKATGSEVSQRKQQLEVE 1450
1451 LRQVTQMRTEESVRYKQSLDDAAKTIQDKNKEIERLKQLIDKETNDRKCL 1500
1501 EDENARLQRVQYDLQKANSSATETINKLKVQEQELTRLRIDYERVSQERT 1550
1551 VKDQDITRFQNSLKELQLQKQKVEEELNRLKRTASEDSCKRKKLEEELEG 1600
1601 MRRSLKEQAIKITNLTQQLEQASIVKKRSEDDLRQQRDVLDGHLREKQRT 1650
1651 QEELRRLSSEVEALRRQLLQEQESVKQAHLRNEHFQKAIEDKSRSLNESK 1700
1701 IEIERLQSLTENLTKEHLMLEEELRNLRLEYDDLRRGRSEADSDKNATIL 1750
1751 ELRSQLQISNNRTLELQGLINDLQRERENLRQEIEKFQKQALEASNRIQE 1800
1801 SKNQCTQVVQERESLLVKIKVLEQDKARLQRLEDELNRAKSTLEAETRVK 1850
1851 QRLECEKQQIQNDLNQWKTQYSRKEEAIRKIESEREKSEREKNSLRSEIE 1900
1901 RLQAEIKRIEERCRRKLEDSTRETQSQLETERSRYQREIDKLRQRPYGSH 1950
1951 RETQTECEWTVDTSKLVFDGLRKKVTAMQLYECQLIDKTTLDKLLKGKKS 2000
2001 VEEVASEIQPFLRGAGSIAGASASPKEKYSLVEAKRKKLISPESTVMLLE 2050
2051 AQAATGGIIDPHRNEKLTVDSAIARDLIDFDDRQQIYAAEKAITGFDDPF 2100
2101 SGKTVSVSEAIKKNLIDRETGMRLLEAQIASGGVVDPVNSVFLPKDVALA 2150
2151 RGLIDRDLYRSLNDPRDSQKNFVDPVTKKKVSYVQLKERCRIEPHTGLLL 2200
2201 LSVQKRSMSFQGIRQPVTVTELVDSGILRPSTVNELESGQISYDEVGERI 2250
2251 KDFLQGSSCIAGIYNETTKQKLGIYEAMKIGLVRPGTALELLEAQAATGF 2300
2301 IVDPVSNLRLPVEEAYKRGLVGIEFKEKLLSAERAVTGYNDPETGNIISL 2350
2351 FQAMNKELIEKGHGIRLLEAQIATGGIIDPKESHRLPVDIAYKRGYFNEE 2400
2401 LSEILSDPSDDTKGFFDPNTEENLTYLQLKERCIKDEETGLCLLPLKEKK 2450
2451 KQVQTSQKNTLRKRRVVIVDPETNKEMSVQEAYKKGLIDYETFKELCEQE 2500
2501 CEWEEITITGSDGSTRVVLVDRKTGSQYDIQDAIDKGLVDRKFFDQYRSG 2550
2551 SLSLTQFADMISLKNGVGTSSSMGSGVSDDVFSSSRHESVSKISTISSVR 2600
2601 NLTIRSSSFSDTLEESSPIAAIFDTENLEKISITEGIERGIVDSITGQRL 2650
2651 LEAQACTGGIIHPTTGQKLSLQDAVSQGVIDQDMATRLKPAQKAFIGFEG 2700
2701 VKGKKKMSAAEAVKEKWLPYEAGQRFLEFQYLTGGLVDPEVHGRISTEEA 2750
2751 IRKGFIDGRAAQRLQDTSSYAKILTCPKTKLKISYKDAINRSMVEDITGL 2800
2801 RLLEAASVSSKGLPSPYNMSSAPGSRSGSRSGSRSGSRSGSRSGSRRGSF 2850
2851 DATGNSSYSYSYSFSSSSIGH 2871

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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