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

NucPred

Fetching Q9TXQ1 from www.uniprot.org...

The NucPred score for your sequence is 0.77 (see score help below)

   1  MARRVNKKKSPVKAARKIDGQIGRRVVDGVRAKSSRQRHQAVLYQAPTPT    50
  51  VIRRKTTKTAIVKKTVVVVKKGGKVVKKSSKTGQKVKAVKAPKVKAPSKK   100
 101  GNDRLTPRVITEYQENPFFYDPQVPEYISASVYHRWITRAVRNGNMKEIK   150
 151  DYYKSKKCQKSAIYTSFAYSFDTSACDEALRQDIKFATEFFKMNNKMEVD   200
 201  NSYHPGKEPNLLQKKTTGRKNYYMLGRHTRQIEMGRGGKEGNNALLNYDT   250
 251  RTDEPNPLTKLIEDNVTYTKLYQLCKIPDGPIVEHHIEMHFVTAVRMGHR   300
 301  DLASALAQGPVKMHCNDLHRATLKDQKLPAKILPVSVAKKAYMNKNITPL   350
 351  HTAAISNSTHMLEAMRAVYPTINIPDQDNWYTMHYAACAPGTAPMEFLLK   400
 401  NGGSVTMLTKQTETPLHVAARAGRAVNCTFLMKEMLDLEKGDDGESTIRA   450
 451  DRSIINARTRSGNSALHLAVLRNNLDVVDALLAEPTIVVDNPTSTGQNRL   500
 501  TPLMMACGKGYLEMAKKLVEKGALVEGKDKKKRTPLIHAMLNGQIHTAAF   550
 551  LLAKGASLTLADSSGNTAAHYAAAYGFLDCLKLLASIDDNILSEPNDWQL   600
 601  YPLSVAYLKGHYGIVTWLLEGPHKDKANINAKDNNGATLLSNLLSYADET   650
 651  MHKELLSQIEYLVARKADASLADSSGQTPLHLFSMQRIILKGSGEAAEND   700
 701  AMRMTLDNYKKCFNTLIKAGAKVDVYDHEDNTPLHYALTNGNLMLFNLML   750
 751  DKVANKRNLFEKWANHQNFLHEILALPMKVYGDQVLWKGETLTKPAYDVL   800
 801  PILKELHENLPDLFEKWISEVNKAGYSPIVEAIKQYQALAANKKLRGEAD   850
 851  QNGNPGFGNAIARGRVHNQFGRDRMNQSQAPHCDSYELKTFISTVNELFE   900
 901  WVIRLGPFQLTQKYINSENSAAVTLANLAMSIPIECGRHQQNQLALFKIL   950
 951  IKLSKEFNKVDEFLTQKNEKDDVLIVQAIMFDKPNVVELILDTASEMHLI  1000
1001  HGTHNAIKENELEVVVHKTIIMYMIEMRMWELIPKVNASSEFWKSKDAKG  1050
1051  NSVWHYAARVNSHKTVGLFKMIESKGVRRETNDDGRSVLHVATLACDGSA  1100
1101  DSVLEPIAWLSTRCPIDAVDKFNRTALHYAFGNENDFKEGNVPFGESDPI  1150
1151  AVVSLLSSLIRPEQIEIADVNGNTILHLAAIKNSTICLMTLIRKKCHVDL  1200
1201  KNKDGNTPLALAVHHGRQSSALTLIQANADVTEKIFVPALKPTSDFDQNS  1250
1251  SGTEAEKFWKWHGKEKKVLEDLHTTIPASVVSKGGSWEAMVYVLLDVLGQ  1300
1301  NTGSMAQLTDAALRRGQLNLANQLLKSIEALIDGAVLNSSYDLLDTFAEK  1350
1351  CFGALTSEETIEKTVLNRIILTRGLGLKQPETMKIIRTALQNGNWNLLNF  1400
1401  LKSEMGTAWKNQKIETPTENPIRSLLIYMNEKSVSSEAIGFLEELRQMRG  1450
1451  VNIDALCQLEIPGKFKKILDYGLIPPISFAVLQENPNMIRALRNAGASLK  1500
1501  TQDDYGRTPLMYAIMTNNRSVVDAIVGDGKLAVVLHKQKAVATGPRCVAV  1550
1551  PMRFGATSRAFIPAAAFASVPARVESDEEEEDNSGSESGEDGAASENKSE  1600
1601  HGSENGESGNGSDDEDDDDDDSSPPPAKKSRIAKEAAGPSTGPKRKKLVI  1650
1651  TDPSLFSARDHKENNPLHYFIEPLAWENVELLGDLAAANKTAIVQCLIDK  1700
1701  RSPNPIELAAMKMNRRMKSEMLKIVKNAAFPRPIKETKLTLQQVHIEPLS  1750
1751  DVDEDAAKFLAKWVEEKDKKKTSEAPKPHKSSTYSTNGLVSFCDETQQYF  1800
1801  DVLMNKTDLMYGRCGFHNFYRMQIIKRRDAELFILFTNWGRIGSGMGEFQ  1850
1851  TTPFNSLELAAKEFKSIFKSKSGNEWAPLANFRDMPKKYRLVETDSTPTS  1900
1901  LAEIELTWKKNTEKDPIRRMIADISDAKTLKTYASQVQMYGGSSQPFGRF  1950
1951  TKENIEKAKLVLDKLEKNANRIKQMVEAQTGVVESNLLDAYITTSELSGD  2000
2001  YYSLIPSGEYEFSNLTRLDNVEEIARHRARLNRCQEIETATRLLCAAEFR  2050
2051  QDLDRVDYIRSAIQCEYRLETPDSDISQRLLQWIHNSGGKQAKVKMILEI  2100
2101  SPMLSTEKFEPFVNDDNQKFLWHGTKATNLMSILKNGFLIDPPSACKNGN  2150
2151  LFGSGIYLADSFEKSTHYCQPSAGGINYMLVCQTALGKVRTLDTIPYHYM  2200
2201  NQSSSSAEKYEDTLHYIGDRFPAGSLTNDGVGMPLLPLRKRDPIQGSNYG  2250
2251  FGTLDFSEYIVRNPNRVLPKYIVMYK                          2276

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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