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

NucPred

Fetching Q6UVK1 from www.uniprot.org...

The NucPred score for your sequence is 0.41 (see score help below)

   1  MQSGPRPPLPAPGLALALTLTMLARLASAASFFGENHLEVPVATALTDID    50
  51  LQLQFSTSQPEALLLLAAGPADHLLLQLYSGRLQVRLVLGQEELRLQTPA   100
 101  ETLLSDSIPHTVVLTVVEGWATLSVDGFLNASSAVPGAPLEVPYGLFVGG   150
 151  TGTLGLPYLRGTSRPLRGCLHAATLNGRSLLRPLTPDVHEGCAEEFSASD   200
 201  DVALGFSGPHSLAAFPAWGTQDEGTLEFTLTTQSRQAPLAFQAGGRRGDF   250
 251  IYVDIFEGHLRAVVEKGQGTVLLHNSVPVADGQPHEVSVHINAHRLEISV   300
 301  DQYPTHTSNRGVLSYLEPRGSLLLGGLDAEASRHLQEHRLGLTPEATNAS   350
 351  LLGCMEDLSVNGQRRGLREALLTRNMAAGCRLEEEEYEDDAYGHYEAFST   400
 401  LAPEAWPAMELPEPCVPEPGLPPVFANFTQLLTISPLVVAEGGTAWLEWR   450
 451  HVQPTLDLMEAELRKSQVLFSVTRGARHGELELDIPGAQARKMFTLLDVV   500
 501  NRKARFIHDGSEDTSDQLVLEVSVTARVPMPSCLRRGQTYLLPIQVNPVN   550
 551  DPPHIIFPHGSLMVILEHTQKPLGPEVFQAYDPDSACEGLTFQVLGTSSG   600
 601  LPVERRDQPGEPATEFSCRELEAGSLVYVHRGGPAQDLTFRVSDGLQASP   650
 651  PATLKVVAIRPAIQIHRSTGLRLAQGSAMPILPANLSVETNAVGQDVSVL   700
 701  FRVTGALQFGELQKQGAGGVEGAEWWATQAFHQRDVEQGRVRYLSTDPQH   750
 751  HAYDTVENLALEVQVGQEILSNLSFPVTIQRATVWMLRLEPLHTQNTQQE   800
 801  TLTTAHLEATLEEAGPSPPTFHYEVVQAPRKGNLQLQGTRLSDGQGFTQD   850
 851  DIQAGRVTYGATARASEAVEDTFRFRVTAPPYFSPLYTFPIHIGGDPDAP   900
 901  VLTNVLLVVPEGGEGVLSADHLFVKSLNSASYLYEVMERPRHGRLAWRGT   950
 951  QDKTTMVTSFTNEDLLRGRLVYQHDDSETTEDDIPFVATRQGESSGDMAW  1000
1001  EEVRGVFRVAIQPVNDHAPVQTISRIFHVARGGRRLLTTDDVAFSDADSG  1050
1051  FADAQLVLTRKDLLFGSIVAVDEPTRPIYRFTQEDLRKRRVLFVHSGADR  1100
1101  GWIQLQVSDGQHQATALLEVQASEPYLRVANGSSLVVPQGGQGTIDTAVL  1150
1151  HLDTNLDIRSGDEVHYHVTAGPRWGQLVRAGQPATAFSQQDLLDGAVLYS  1200
1201  HNGSLSPRDTMAFSVEAGPVHTDATLQVTIALEGPLAPLKLVRHKKIYVF  1250
1251  QGEAAEIRRDQLEAAQEAVPPADIVFSVKSPPSAGYLVMVSRGALADEPP  1300
1301  SLDPVQSFSQEAVDTGRVLYLHSRPEAWSDAFSLDVASGLGAPLEGVLVE  1350
1351  LEVLPAAIPLEAQNFSVPEGGSLTLAPPLLRVSGPYFPTLLGLSLQVLEP  1400
1401  PQHGALQKEDGPQARTLSAFSWRMVEEQLIRYVHDGSETLTDSFVLMANA  1450
1451  SEMDRQSHPVAFTVTVLPVNDQPPILTTNTGLQMWEGATAPIPAEALRST  1500
1501  DGDSGSEDLVYTIEQPSNGRVVLRGAPGTEVRSFTQAQLDGGLVLFSHRG  1550
1551  TLDGGFRFRLSDGEHTSPGHFFRVTAQKQVLLSLKGSQTLTVCPGSVQPL  1600
1601  SSQTLRASSSAGTDPQLLLYRVVRGPQLGRLFHAQQDSTGEALVNFTQAE  1650
1651  VYAGNILYEHEMPPEPFWEAHDTLELQLSSPPARDVAATLAVAVSFEAAC  1700
1701  PQRPSHLWKNKGLWVPEGQRARITVAALDASNLLASVPSPQRSEHDVLFQ  1750
1751  VTQFPSRGQLLVSEEPLHAGQPHFLQSQLAAGQLVYAHGGGGTQQDGFHF  1800
1801  RAHLQGPAGASVAGPQTSEAFAITVRDVNERPPQPQASVPLRLTRGSRAP  1850
1851  ISRAQLSVVDPDSAPGEIEYEVQRAPHNGFLSLVGGGLGPVTRFTQADVD  1900
1901  SGRLAFVANGSSVAGIFQLSMSDGASPPLPMSLAVDILPSAIEVQLRAPL  1950
1951  EVPQALGRSSLSQQQLRVVSDREEPEAAYRLIQGPQYGHLLVGGRPTSAF  2000
2001  SQFQIDQGEVVFAFTNFSSSHDHFRVLALARGVNASAVVNVTVRALLHVW  2050
2051  AGGPWPQGATLRLDPTVLDAGELANRTGSVPRFRLLEGPRHGRVVRVPRA  2100
2101  RTEPGGSQLVEQFTQQDLEDGRLGLEVGRPEGRAPGPAGDSLTLELWAQG  2150
2151  VPPAVASLDFATEPYNAARPYSVALLSVPEAARTEAGKPESSTPTGEPGP  2200
2201  MASSPEPAVAKGGFLSFLEANMFSVIIPMCLVLLLLALILPLLFYLRKRN  2250
2251  KTGKHDVQVLTAKPRNGLAGDTETFRKVEPGQAIPLTAVPGQGPPPGGQP  2300
2301  DPELLQFCRTPNPALKNGQYWV                              2322

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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