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

NucPred

Fetching Q9UIF8 from www.uniprot.org...

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

   1  MESGERLPSSAASSTTPTSSSTPSVASVVSKGGLSTGVASLSSTINPCGH    50
  51  LFRTAGDQPFNLSTVSSAFPMVSHPVFGLHSASSGHSEFGGLGTLGTPTA   100
 101  LAAHPQLASFPGAEWWRTTDAHTRTGATFFPPLLGIPPLFAPPAQNHDSS   150
 151  SFHSRTSGKSNRNGPEKGVNGSINGSNTSSVIGINTSVLSTTASSSMGQT   200
 201  KSTSSGGGNRKCNQEQSKNQPLDARVDKIKDKKPRKKAMESSSNSDSDSG   250
 251  TSSDTSSEGISSSDSDDLEEDEEEEDQSIEESEDDDSDSESEAQHKSNNQ   300
 301  VLLHGISDPKADGQKATEKAQEKRIHQPLPLASESQTHSFQSQQKQPQVL   350
 351  SQQLPFIFQSSQAKEESVNKHTSVIQSTGLVSNVKPLSLVNQAKKETYMK   400
 401  LIVPSPDVLKAGNKNTSEESSLLTSELRSKREQYKQAFPSQLKKQESSKS   450
 451  LKKVIAALSNPKATSSSPAHPKQTLENNHPNPFLTNALLGNHQPNGVIQS   500
 501  VIQEAPLALTTKTKMQSKINENIAAASSTPFSSPVNLSTSGRRTPGNQTP   550
 551  VMPSASPILHSQGKEKAVSNNVNPVKTQHHSHPAKSLVEQFRGTDSDIPS   600
 601  SKDSEDSNEDEEEDDEEEDEEDDEDDESDDSQSESDSNSESDTEGSEEED   650
 651  DDDKDQDESDSDTEGEKTSMKLNKTTSSVKSPSMSLTGHSTPRNLHIAKA   700
 701  PGSAPAALCSESQSPAFLGTSSSTLTSSPHSGTSKRRRVTDERELRIPLE   750
 751  YGWQRETRIRNFGGRLQGEVAYYAPCGKKLRQYPEVIKYLSRNGIMDISR   800
 801  DNFSFSAKIRVGDFYEARDGPQGMQWCLLKEEDVIPRIRAMEGRRGRPPN   850
 851  PDRQRAREESRMRRRKGRPPNVGNAEFLDNADAKLLRKLQAQEIARQAAQ   900
 901  IKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQIKIMKQQEKIKRI   950
 951  QQIRMEKELRAQQILEAKKKKKEEAANAKLLEAEKRIKEKEMRRQQAVLL  1000
1001  KHQERERRRQHMMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRR  1050
1051  LELEMAKELKKPNEDMCLADQKPLPELPRIPGLVLSGSTFSDCLMVVQFL  1100
1101  RNFGKVLGFDVNIDVPNLSVLQEGLLNIGDSMGEVQDLLVRLLSAAVCDP  1150
1151  GLITGYKAKTALGEHLLNVGVNRDNVSEILQIFMEAHCGQTELTESLKTK  1200
1201  AFQAHTPAQKASVLAFLINELACSKSVVSEIDKNIDYMSNLRRDKWVVEG  1250
1251  KLRKLRIIHAKKTGKRDTSGGIDLGEEQHPLGTPTPGRKRRRKGGDSDYD  1300
1301  DDDDDDSDDQGDEDDEDEEDKEDKKGKKTDICEDEDEGDQAASVEELEKQ  1350
1351  IEKLSKQQSQYRRKLFDASHSLRSVMFGQDRYRRRYWILPQCGGIFVEGM  1400
1401  ESGEGLEEIAKEREKLKKAESVQIKEEMFETSGDSLNCSNTDHCEQKEDL  1450
1451  KEKDNTNLFLQKPGSFSKLSKLLEVAKMPPESEVMTPKPNAGANGCTLSY  1500
1501  QNSGKHSLGSVQSTATQSNVEKADSNNLFNTGSSGPGKFYSPLPNDQLLK  1550
1551  TLTEKNRQWFSLLPRTPCDDTSLTHADMSTASLVTPQSQPPSKSPSPTPA  1600
1601  PLGSSAQNPVGLNPFALSPLQVKGGVSMMGLQFCGWPTGVVTSNIPFTSS  1650
1651  VPSLGSGLGLSEGNGNSFLTSNVASSKSESPVPQNEKATSAQPAAVEVAK  1700
1701  PVDFPSPKPIPEEMQFGWWRIIDPEDLKALLKVLHLRGIREKALQKQIQK  1750
1751  HLDYITQACLKNKDVAIIELNENEENQVTRDIVENWSVEEQAMEMDLSVL  1800
1801  QQVEDLERRVASASLQVKGWMCPEPASEREDLVYFEHKSFTKLCKEHDGE  1850
1851  FTGEDESSAHALERKSDNPLDIAVTRLADLERNIERRIEEDIAPGLRVWR  1900
1901  RALSEARSAAQVALCIQQLQKSIAWEKSIMKVYCQICRKGDNEELLLLCD  1950
1951  GCDKGCHTYCHRPKITTIPDGDWFCPACIAKASGQTLKIKKLHVKGKKTN  2000
2001  ESKKGKKVTLTGDTEDEDSASTSSSLKRGNKDLKKRKMEENTSINLSKQE  2050
2051  SFTSVKKPKRDDSKDLALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKV  2100
2101  IKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNEDDSDIGRAG  2150
2151  HNMRKYFEKKWTDTFKVS                                  2168

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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