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

NucPred

Fetching Q8VI59 from www.uniprot.org...

The NucPred score for your sequence is 0.78 (see score help below)

   1  MGSQVLQILRQGVWASLTGGWFFDPHQSTFSNCFHLYVWIFLLIFPFLLY    50
  51  MVLPPSLMVAGVYCLVVAVIFATIKTVNYRLHAMFDQGEIVEKRNSTMGE   100
 101  QEEEAAQGESSLPRDPGVEMTVFRKVSSTPPVRCSSQHSVFGFNQVSELL   150
 151  PRMEDSGPLRDIKELVREQGSNNVIVTSADREMLKLSSQEKLIGDLPQTP   200
 201  PGVVPDPSLPSTDSSERSPMAGDGVPWGGSGVADTPMSPLLKGSLSQELS   250
 251  KSFLTLTRPDRALVRTSSRREQCRGTGGYQPLDRRGSGDPMPQKAGSSDS   300
 301  CFSGTDRETLSSFKSEKTNSTHLDSPPGGHAPEGSDTDPPSEAELPASPD   350
 351  AGVPSDDTLRSFDTVIGAGTPPGQTEPLLVVRPKDLALLRPSKRRPPMRG   400
 401  HSPPGRTPRRPLLEGSGFFEDEDTSEGSELSPASSLRSQRRYSTDSSSST   450
 451  SCYSPESSQGAAGGPRKRRAPHGAEEGTAVPPKRPYGTQRTPSTASAKTH   500
 501  ARVLSMDGAGGDVLRAPLAGSKAELEAQPGMELAAGEPAVLPPEARRGPA   550
 551  ANQPGWRGELQEEGAVGGAPEETGQRECTSNVRRAQAIRRRHNAGSNPTP   600
 601  PASVMGSPPSSLQEAQRGRAASHSRALTLPSALHFASSLLLTRAGPNVHE   650
 651  ASNFDDTSEGAVHYFYDESGVRRSYTFGLAGGGYENPVSQPGEQAANGAW   700
 701  DRHSHSSSFHSADVPEATGGLNLLQPRPVVLQGMQVRRVPLEIPEEQTLM   750
 751  EEAPPRAQHSYKYWFLPGRWTSVRYERLALLALLDRTRGVMENIFGVGLS   800
 801  SLVAFLGYLLLLKGFFTDIWVFQFCLVIASCQYSLLKSVQPDAASPMHGH   850
 851  NWVIAYSRPVYFCICCLLIWLLDALGTAQPFPPVSLYGLTLFSASFFFCA   900
 901  RDVATVFTLCFPFVFLLGLLPQVNTCLMYLLEQIDMHGFGGTAATSPLTA   950
 951  VFSLTRSLLAAALLYGFCLGAIKTPWPEQHVPVLFSVFCGLLVAMSYHLS  1000
1001  RQSSDPTVLWSLVRSKLFPELEERSLETARVEPPDPLPEKMRQSVREVLH  1050
1051  SDLVMCVVIAVLTFAVSASTVFIALKSVLGFVLYALAGAVGFFTHYLLPQ  1100
1101  LRKQLPWFCLSQPVLKPLEYSQYEVRGAAQVMWFEKLYAGLQCAEKYLIY  1150
1151  PAVVLNALTVDAHTVVSHPDKFCLYCRALLMTVAGLKLLRSAFCCPPQQY  1200
1201  LTLAFTVLLFHFDYPRLSQGFLLDYFLMSLLCSKLWDLLYKLRFVLTYIA  1250
1251  PWQITWGSAFHAFAQPFAVPHSAMLFLQALLSGLFSTPLNPLLGSAVFIM  1300
1301  SYARPLKFWERDYNTKRVDHSNTRLVTQLDRNPGADDNNLNSIFYEHLTR  1350
1351  SLQHTLCGDLVLGRWGNYGPGDCFVLASDYLNALVHLIEVGNGLITFQLR  1400
1401  GLEFRGTYCQQREVEAITEGVEEDEGCCCCEPGHLPRVLSFNAAFGQRWL  1450
1451  AWEVTASKYVLEGYSISDNNAASMLQVFDLRKILVTYYVKSIIYYVSRSP  1500
1501  KLETWLNHEGIAAALRPVRALGYADSDPTFSLSVDEDYDLRLSGLSLPSF  1550
1551  CAVHLEWIQYCASRRSQPVDQDWNSPLVTLCFGLCVLGRRALGTASHSMS  1600
1601  ASLEPFLYGLHALFKGDFRITSPRDEWVFADMDLLHRVVAPGVRMALKLH  1650
1651  QDHFTSPDEYEEPAALYDAIAANEERLVISHEGDPAWRSAILSNTPSLLA  1700
1701  LRHVMDDASDEYKIIMLNRRHLSFRVIKVNRECVRGLWAGQQQELVFLRN  1750
1751  RNPERGSIQNAKQALRNMINSSCDQPLGYPIYVSPLTTSLAGSHPQLRAL  1800
1801  WGGPVSLGAIARWLLRSWERLHKGCGAGCNSGGNVDDSDCGGGGGLTSLS  1850
1851  NHPPLAHPTPENAAGSSEQPLPPGPSWGPRPSLSGSGDGRPPPLLQWPPP  1900
1901  RLPGPPPASPAPTEGPRPSRPSGPALLNSEGPSGKWSLGGRKGLGGPDGE  1950
1951  PASGSPKGGTPKSQAPLDLSLSPDVSSEASPARTTQDLPCLDSSIPEGCT  2000
2001  PSGAPGDWPVPAEERESPAAQPLLEHQY                        2028

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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