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

NucPred

Fetching Q8BZN6 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MAGERTRRFTRSLLRPGQAAELRHSAASAAAVAVSSRQQQRQEKPRLLDP    50
  51  LDYETVIEELEKTYRDDPLQDLLFFPSDDFSTATVSWDIRTLYSTVPEEA   100
 101  EHRAESLLVKEACKFYSSQWYVVNYKYEQYSGDIRQLPRAEHKPEKLPSH   150
 151  SFEVDHEDADKDEDTTSHSSSKGGGGAGGTGVFKSGWLYKGNFNSTVNNT   200
 201  VTVRSFKKRYFQLTQLPDNSYIMNFYKDEKISKEPKGCIFLDSCTGVVQN   250
 251  NRLRKYAFELKMNDLTYFVLAAETESDMDEWIHTLNRILQISPEGPLQGR   300
 301  KSAELAELGLDPLDNCVTCECTLEETDSSENSLHPDFAKYLTETEDTVKT   350
 351  TRNMGRLNLFSLDPDIDTLKLQKRDSFENELMIKPFEEKAAKRIMIICRA   400
 401  LNFNLQGCVTENEYDPVTNIEPFFVSVALYDLRDNRKISADFHVDLNHPA   450
 451  VRQMLSGTPPALENGNIDTGTPRQSEEPHIKGLPEEWLKFPKQAVFSVSD   500
 501  PHSEIVLVAKVEKVLMGNIGSGAEPYIKNPDSNKFAQKILKSNRQFCSKL   550
 551  GKYRMPFAWAVRSVFKDNQGNVDRDSRFSPLYRQESSKMSSEDLLKLVSD   600
 601  YRRADRISKMQSIPGSLDIAVDNIPLEHPNCVTSSFIPVKPFNVSAQSEP   650
 651  TVEVEEFIYDSTKYCRPYRVYKNQIYVYPKHLKYDSQKCFNKARNITVCI   700
 701  EFKNSDDDGAKPMKCIYGKPGGPLFTSSAYTAVLHHSQNPDFSDEVKIEL   750
 751  PTQLHGKHHLLFSFYHITCDINAKANAKKKEALETSVGYAWLPLMKHDQI   800
 801  ASQEYNIPIATTLPPNYLSIQDPTSAKHGGSDIKWVDGGKPLFKVSTFVV   850
 851  STVNTQDPHVNAFFRQCQKREKDMSQSPTSSFVRACKNLLNVDKIHSIMS   900
 901  FLPIILNQLFKILVQNEEDEITATVTRVLADIVAKCHEEQLDHSVQSYIK   950
 951  FVFKTKSYKERTIHEELAKNLSDLLKSNDSTIVKHVLEHSWFFFAIILKS  1000
1001  MAQHLIDTNKIQLPRAQRFPESYQSELDNLVMGLCDHVIWKCKEAPEETK  1050
1051  RANHSVARFLKRCFTFMDRGFVFKMVNNYISMFSSGEFKTLCQYKFDFLQ  1100
1101  EVCQHEHFIPLCLPIRSANIPDPLTPSESIRELHASDMPEYSVTNEFCRK  1150
1151  HFLIGILLREVGFALQEDQDIRHLALAVLKNLMAKHSFDDRYREPRKQAQ  1200
1201  IASLYMPLYGMLLDNMPRIYLKDLYPFTVNTSNQGSRDDLSTNGGFQTQT  1250
1251  SMKHATSVDTSFSKDVLNSIAAFSSIAISTVNHADSRASLASLDSNPSTT  1300
1301  EKSSEKTDNCEKIPRPLSLIGSTLRFDKLDQAETRSLLMCFLHIMKTISD  1350
1351  ETLIAYWQRAPSPEVSDFFSILDVCLQNFRYLGKRNIIRKIAAAFKFVQS  1400
1401  TQNNGTLKGSNPSCQTSGLLSQWMHTTSGHEGHKQHRSQTLPIIRGKNAL  1450
1451  SNPKLLQMLDNSMNSNSNEIDIVHHVDTEANIATEVCLTILDLLSLFTQV  1500
1501  HQRQLQQSDCQNSLMKRVFDTYMLFFQVNQSASALKHVFASLRLFVCKFP  1550
1551  SAFFQGPADLCGSFCYEVLKCCNHRSRLTQMEASALLYFFMRKNFEFNKQ  1600
1601  KSIVRSHLQLIKAVSQLIADAGIGGSRFQHSLAITNNFANGDKQMKNSNF  1650
1651  PAEVKDLTKRIRTVLMATAQMKEHEKDPEMLVDLQYSLANSYASTPELRR  1700
1701  TWLESMAKIHARNGDLSEAAMCYIHIAALIAEYLKRKGYWKMEKICTPPL  1750
1751  LPEDTQPCDSNLLLTTPGGGSMFSMGWPAFLSITPNIKEEGAMKEDSGMQ  1800
1801  DTPYNENILVEQLYMCVEFLWKSERYELIADVNKPIIAVFEKQRDFKKLS  1850
1851  DLYYDIHRSYLKVAEVVNSEKRLFGRYYRVAFYGQGFFEEEEGKEYIYKE  1900
1901  PKLTGLSEISQRLLKLYADKFGADNVKIIQDSNKVNPKDLDPKYAYIQVT  1950
1951  YVTPFFEEKEIEDRKTDFEMHHNINRFVFETPFTLSGKKHGGVAEQCKRR  2000
2001  TVLTTSHLFPYVKKRIQVISQSSTELNPIEVAIDEMSRKVSELNQLCTTE  2050
2051  EVDMIRLQLKLQGSVSVKVNAGPMAYARAFLEETNAKKYPDNQVKLLKEI  2100
2101  FRQFADACGQALDVNERLIKEDQLEYQEELRSHYKDMLSELSAIMNEQIT  2150
2151  GRDDPAKCGVERPYTTRVTSKGTAAVPVVSISSSAEV               2187

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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