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

NucPred

Fetching Q8K0T7 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MVASLFKSLILAYIHKLCKGMFTKKLGNTTKKKENRQQKKDQDFPTAGHT    50
  51  KPPKLSNALKSTVKKIAKCSSTRNFSIEDEEGHKDFSLSPTFSYRVAIAN   100
 101  GLQTAVTNSDEDLLQELSSIESSYSESFNELRSSTENQVQSTHTMPVRRN   150
 151  RKSSSSLAPSEGSSDGERTLHTLKLGALRKLRKWKKSQECVSSDSELSTV   200
 201  KKTWGIRSKSLDRTARNPKTNVLEPGFSSSGCISQTHDVMEMIFKELQGI   250
 251  SQIETELSELRGHVNALKYSIDEISSSVEVVQSEIEQLRTGFVQARRETR   300
 301  DIHDYIKHLGHMGSKVSLRFLNVPEERHEYVESVVYQILIDKMGFSDVPN   350
 351  AIKIEFAQRIGQQRDCPNAKPRPILVYFETPQQRDSVLKKSYKLKGTGIG   400
 401  ISTDILTYDIRERKEKGVLPSSQTYESMDMKLSTPEPKAKKNAWLSPNDS   450
 451  DRELESDLSRSSYADSPAKGSSSKSSSKSHSARSKNKAANSRTSQKSDYN   500
 501  KRPSQPPASSTPEKQTPHYVEATPPLWHSQSDFFTLKLSRSESDFSKLCQ   550
 551  SYSEDFSESQFFCRTNGSSLLSSSDRELWQRKQEGMPALYHRLQDQGLDE   600
 601  TIPAVPGQAEIENTETVDSGMSNSMVCASGDRSNYSGSQLSLHEDLSPWK   650
 651  EWNQAGQGTDDVGLDSSTQEPFDYDTNSLSDQQLDLSSKDLDDLGKCHSD   700
 701  LQDDSESYDLTQDDNSSPCPGLDNEPQGQWVGQYDSYQEANSNDLYPNQS   750
 751  HPSMMYRSQSELQSDDSEGAQPKSWHSRLSIDLSDKTFKFPKFGSTLQRA   800
 801  KSALEVVWNKSTQSLSGCEDSGSSLMGRFRTLSQSTANESSTTLDSDIYT   850
 851  EPYYYKAEEEEDYCEPVADSETDYVEVMEQVLAKLENRTSITEVNEHIKD   900
 901  YDHPSYETPYETPQDEGYDGQADDIISEGELETLNEPAVEMELAEDENQN   950
 951  LPAESLEVMKPKRIRPSFKEAALRAYKKQMAELEEKILAGDSSSMDEKAR  1000
1001  IVSGNDLDASKFSALQVFGGAGRGLYGIDSMPDLRRKKTLPIVRDVAMTL  1050
1051  AARKSGLSLAMVIRTSLNNEELKMHVFRKTLQALIYPISSTTPHNFEVWT  1100
1101  ATTPTYCYECEGLLWGIARQGMKCLECGVKCHEKCQDLLNADCLQRAAEK  1150
1151  SSKHGAEDKTQTIITAMKERMKIRERNRPEVFEVIQEMFQISKEDFVQYT  1200
1201  KAAKQSVLDGTSKWSAKITITVVSAQGLQAKDKTGSSDPYVTVQVGKNKR  1250
1251  RTKTIFGNLNPVWDEKFFFECHNSTDRIKVRVWDEDDDIKSRVKQHFKKE  1300
1301  SDDFLGQTIVEVRTLSGEMDVWYNLEKRTDKSAVSGAIRLKINVEIKGEE  1350
1351  KVAPYHIQYTCLHENLFHYLTEVKSNGSVKIPEVKGDEAWKVFFDDASQE  1400
1401  IVDEFAMRYGVESIYQAMTHFSCLSSKYMCPGVPAVMSALLANINAFYAH  1450
1451  TTVSTNVQVSASDRFAATNFGREKFIKLLDQLHNSLRIDLSKYRENFPAS  1500
1501  NSERLQDLKSTVDLLTSITFFRMKVLELQSPPKASAVVKDCVRACLDSTY  1550
1551  KYIFDNCHELYSQLIDPSKKQDVPREDQGPTTKNLDFWPQLITLMVTIID  1600
1601  EDKTAYTPVLNQFPQELNMGKISAEIMWSLFALDMKYALEEHEKQRLCKS  1650
1651  TDYMNLHFKVKWFYNEYVRELPAFKDAVPEYSLWFEPFVMQWLDENEDVS  1700
1701  MEFLHGALGRDKKDGFQQTSDHALFSCSVVDVFAQLNQSFEIIKKLECPN  1750
1751  PEALSHLMRRFAKTINKVLVQYAAIVSNDFSSYCDKETVPCILMNNIQQL  1800
1801  RVQLEKMFESMGGKELDPEASTILKELQIKLNGVLDALSITYGESFQLTI  1850
1851  EECIKQMGAELNQMRANGNSTANKNSAAMDAEIVLRPLMDFLDKTLSLSA  1900
1901  KICEKTVLKRVLKELWKLVLNKIEKQIVLPPLTDQTGPQMIFIAAKDLGQ  1950
1951  LSKLKEHMIREDAKGLTPRQCAIVEVVLATIKQYFHAGGNGLKKNFLEKS  2000
2001  PDLHSLRYALSLYTQTTDALIKKFIETQGSQSRSSKDAVGQISVHVDVTT  2050
2051  TPGTGDHKVTVKVIAINDLNWQTTAMFRPFVEVCMLGPSLGDKKRKQGTK  2100
2101  TKSNTWSPKYNETFQFILGNENRPGAYELHLSVKDYCFAREDRIIGMTVI  2150
2151  QLQNIAEKGSYGAWYPLLKNLSMDETGLTILRILSQRTSDDVAKEFVRLK  2200
2201  SETRSIEESA                                          2210

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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