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

NucPred

Fetching Q9UKL3 from www.uniprot.org...

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

   1  MAADDDNGDGTSLFDVFSASPLKNNDEGSLDIYAGLDSAVSDSASKSCVP    50
  51  SRNCLDLYEEILTEEGTAKEATYNDLQVEYGKCQLQMKELMKKFKEIQTQ   100
 101  NFSLINENQSLKKNISALIKTARVEINRKDEEISNLHQRLSEFPHFRNNH   150
 151  KTARTFDTVKTKDLKSRSPHLDDCSKTDHRAKSDVSKDVHHSTSLPNLEK   200
 201  EGKPHSDKRSTSHLPTSVEKHCTNGVWSRSHYQVGEGSSNEDSRRGRKDI   250
 251  RHSQFNRGTERVRKDLSTGCGDGEPRILEASQRLQGHPEKYGKGEPKTES   300
 301  KSSKFKSNSDSDYKGERINSSWEKETPGERSHSRVDSQSDKKLERQSERS   350
 351  QNINRKEVKSQDKEERKVDQKPKSVVKDQDHWRRSERASLPHSKNEITFS   400
 401  HNSSKYHLEERRGWEDCKRDKSVNSHSFQDGRCPSSLSNSRTHKNIDSKE   450
 451  VDAMHQWENTPLKAERHRTEDKRKREQESKEENRHIRNEKRVPTEHLQKT   500
 501  NKETKKTTTDLKKQNEPKTDKGEVLDNGVSEGADNKELAMKAESGPNETK   550
 551  NKDLKLSFMKKLNLTLSPAKKQPVSQDNQHKITDIPKSSGVCDSESSMQV   600
 601  KTVAYVPSISEHILGEAAVSEHTMGETKSTLLEPKVALLAVTEPRIGISE   650
 651  TNKEDENSLLVRSVDNTMHCEEPICGTETSFPSPMEIQQTESLFPSTGMK   700
 701  QTINNGRAAAPVVMDVLQTDVSQNFGLELDTKRNDNSDYCGISEGMEMKV   750
 751  ALSTTVSETTESILQPSIEEADILPIMLSEDNNPKFEPSVIVTPLVESKS   800
 801  CHLEPCLPKETLDSSLQQTELMDHRMATGETNSVYHDDDNSVLSIDLNHL   850
 851  RPIPEAISPLNSPVRPVAKVLRNESPPQVPVYNNSHKDVFLPNSAHSTSK   900
 901  SQSDLNKENQKPIYKSDKCTEADTCKNSPLDELEEGEIRSDSETSKPQES   950
 951  FEKNSKRRVSADVRKSKTIPRRGKSTVCLDKDSRKTHVRIHQTNNKWNKR  1000
1001  PDKSSRSSKTEKKDKVMSTSSLEKIVPIIAVPSSEQEIMHMLRMIRKHVR  1050
1051  KNYMKFKAKFSLIQFHRIIESAILSFTSLIKHLNLHKISKSVTTLQKNLC  1100
1101  DIIESKLKQVKKNGIVDRLFEQQLPDMKKKLWKFVDDQLDYLFAKLKKIL  1150
1151  VCDSKSFGRDSDEGKLEKTSKQNAQYSNSQKRSVDNSNRELLKEKLSKSE  1200
1201  DPVHYKSLVGCKKSEENYQDQNNSSINTVKHDIKKNFNICFDNIKNSQSE  1250
1251  ERSLEVHCPSTPKSEKNEGSSIEDAQTSQHATLKPERSFEILTEQQASSL  1300
1301  TFNLVSDAQMGEIFKSLLQGSDLLDSSVNCTEKSEWELKTPEKQLLETLK  1350
1351  CESIPACTTEELVSGVASPCPKMISDDNWSLLSSEKGPSLSSGLSLPVHP  1400
1401  DVLDESCMFEVSTNLPLSKDNVCSVEKSKPCVSSILLEDLAVSLTVPSPL  1450
1451  KSDGHLSFLKPDMSSSSTPEEVISAHFSEDALLEEEDASEQDIHLALESD  1500
1501  NSSSKSSCSSSWTSRSVAPGFQYHPNLPMHAVIMEKSNDHFIVKIRRATP  1550
1551  STSSGLKQSMMPDELLTSLPRHGKEADEGPEKEYISCQNTVFKSVEELEN  1600
1601  SNKNVDGSKSTHEEQSSMIQTQVPDIYEFLKDASDKMGHSDEVADECFKL  1650
1651  HQVWETKVPESIEELPSMEEISHSVGEHLPNTYVDLTKDPVTETKNLGEF  1700
1701  IEVTVLHIDQLGCSGGNLNQSAQILDNSLQADTVGAFIDLTQDASSEAKS  1750
1751  EGNHPALAVEDLGCGVIQVDEDNCKEEKAQVANRPLKCIVEETYIDLTTE  1800
1801  SPSSCEVKKDELKSEPGSNCDNSELPGTLHNSHKKRRNISDLNHPHKKQR  1850
1851  KETDLTNKEKTKKPTQDSCENTEAHQKKASKKKAPPVTKDPSSLKATPGI  1900
1901  KDSSAALATSTSLSAKNVIKKKGEIIILWTRNDDREILLECQKRGPSFKT  1950
1951  FAYLAAKLDKNPNQVSERFQQLMKLFEKSKCR                    1982

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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