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

NucPred

Fetching O88279 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MALTPQRGSSSGLSRPELWLLLWAAAWRLGATACPALCTCTGTTVDCHGT    50
  51  GLQAIPKNIPRNTERLELNGNNITRIHKNDFAGLKQLRVLQLMENQIGAV   100
 101  ERGAFDDMKELERLRLNRNQLQVLPELLFQNNQALSRLDLSENSLQAVPR   150
 151  KAFRGATDLKNLQLDKNQISCIEEGAFRALRGLEVLTLNNNNITTIPVSS   200
 201  FNHMPKLRTFRLHSNHLFCDCHLAWLSQWLRQRPTIGLFTQCSGPASLRG   250
 251  LNVAEVQKSEFSCSGQGEAAQVPACTLSSGSCPAMCSCSNGIVDCRGKGL   300
 301  TAIPANLPETMTEIRLELNGIKSIPPGAFSPYRKLRRIDLSNNQIAEIAP   350
 351  DAFQGLRSLNSLVLYGNKITDLPRGVFGGLYTLQLLLLNANKINCIRPDA   400
 401  FQDLQNLSLLSLYDNKIQSLAKGTFTSLRAIQTLHLAQNPFICDCNLKWL   450
 451  ADFLRTNPIETTGARCASPRRLANKRIGQIKSKKFRCSAKEQYFIPGTED   500
 501  YHLNSECTSDVACPHKCRCEASVVECSGLKLSKIPERIPQSTTELRLNNN   550
 551  EISILEATGLFKKLSHLKKINLSNNKVSEIEDGTFEGATSVSELHLTANQ   600
 601  LESVRSGMFRGLDGLRTLMLRNNRISCIHNDSFTGLRNVRLLSLYDNHIT   650
 651  TISPGAFDTLQALSTLNLLANPFNCNCQLAWLGDWLRKRKIVTGNPRCQN   700
 701  PDFLRQIPLQDVAFPDFRCEEGQEEVGCLPRPQCPQECACLDTVVRCSNK   750
 751  HLQALPKGIPKNVTELYLDGNQFTLVPGQLSTFKYLQLVDLSNNKISSLS   800
 801  NSSFTNMSQLTTLILSYNALQCIPPLAFQGLRSLRLLSLHGNDVSTLQEG   850
 851  IFADVTSLSHLAIGANPLYCDCHLRWLSSWVKTGYKEPGIARCAGPPEME   900
 901  GKLLLTTPAKKFECQGPPSLAVQAKCDPCLSSPCQNQGTCHNDPLEVYRC   950
 951  TCPSGYKGRNCEVSLDSCSSNPCGNGGTCHAQEGEDAGFTCSCPSGFEGL  1000
1001  TCGMNTDDCVKHDCVNGGVCVDGIGNYTCQCPLQYTGRACEQLVDFCSPD  1050
1051  LNPCQHEAQCVGTPEGPRCECVPGYTGDNCSKNQDDCKDHQCQNGAQCVD  1100
1101  EINSYACLCAEGYSGQLCEIPPAPRNSCEGTECQNGANCVDQGSRPVCQC  1150
1151  LPGFGGPECEKLLSVNFVDRDTYLQFTDLQNWPRANITLQVSTAEDNGIL  1200
1201  LYNGDNDHIAVELYQGHVRVSYDPGSYPSSAIYSAETINDGQFHTVELVT  1250
1251  FDQMVNLSIDGGSPMTMDNFGKHYTLNSEAPLYVGGMPVDVNSAAFRLWQ  1300
1301  ILNGTSFHGCIRNLYINNELQDFTKTQMKPGVVPGCEPCRKLYCLHGICQ  1350
1351  PNATPGPVCHCEAGWGGLHCDQPVDGPCHGHKCVHGKCVPLDALAYSCQC  1400
1401  QDGYSGALCNQVGAVAEPCGGLQCLHGHCQASATRGAHCVCSPGFSGELC  1450
1451  EQESECRGDPVRDFHRVQRGYAICQTTRPLSWVECRGACPGQGCCQGLRL  1500
1501  KRRKLTFECSDGTSFAEEVEKPTKCGCAPCA                     1531

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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