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

NucPred

Fetching Q8CIZ8 from www.uniprot.org...

The NucPred score for your sequence is 0.69 (see score help below)

   1  MNPFRYEICLLVLALTWPGTLCTEKPRDRPSTARCSLFGDDFINTFDETM    50
  51  YSFAGGCSYLLAGDCQKRSFSILGNFQDGKRMSLSVYLGEFFDIHLFANG   100
 101  TVMQGDQSISMPYASQGLYLELEAGYYKLSSETFGFAARIDGNGNFQVLM   150
 151  SDRHFNKTCGLCGDFNIFAEDDFRTQEGTLTSDPYDFANSWALSSEEQRC   200
 201  KRASPPSRNCESSSGDMHQAMWEQCQLLKTASVFARCHPLVDPESFVALC   250
 251  EKILCTCATGPECACPVLLEYARTCAQEGMVLYGWTDHSACRPACPAGME   300
 301  YKECVSPCPRTCQSLSINEVCQQQCVDGCSCPEGELLDEDRCVQSSDCPC   350
 351  VHAGKRYPPGTSLSQDCNTCICRNSLWICSNEECPGECLVTGQSHFKSFD   400
 401  NRYFTFSGICQYLLARDCEDHTFSIVIETMQCADDPDAVCTRSVSVRLSA   450
 451  LHNSLVKLKHGGAVGIDGQDVQLPFLQGDLRIQHTVMASVRLSYAEDLQM   500
 501  DWDGRGRLLVKLSPVYSGKTCGLCGNYNGNKGDDFLTPAGLVEPLVVDFG   550
 551  NAWKLQGDCSDLRRQHSDPCSLNPRLTRFAEEACALLTSSKFEACHHAVS   600
 601  PLPYLQNCRYDVCSCSDSRDCLCNAVANYAAECARKGVHIGWREPGFCAL   650
 651  GCPQGQVYLQCGNSCNLTCRSLSLPDEECSEVCLEGCYCPPGLYQDERGD   700
 701  CVPKAQCPCYYDGELFQPADIFSDHHTMCYCEDGFMHCTTSGTLGSLLPD   750
 751  TVLSSPLSHRSKRSLSCRPPMVKLVCPADNPRAQGLECAKTCQNYDLERM   800
 801  SLGCVSGCLCPPGMVRHENKCVALERCPCFHQGAEYAPGDTVKIGCNTCV   850
 851  CRERKWNCTNHVCDATRSAIGMAHYLTFDGLKYLFPGECQYVLVYDYCGS   900
 901  NPGTFQILVGNEGCSYPSVKCRKRVTILVDGGELELFDGEVNVKRPLRDE   950
 951  SHFEVVESGRYVILLLGQALSVVWDHHLSISVVLKHTYQEQVCGLCGNFD  1000
1001  GIQNNDSTTSSLQVEEDPVNFGNSWKVSSQCADTRKLSLDVSPATCHNNI  1050
1051  MKQTMVDSACRILTSDVFQGCNRLVDPEPYLDICIYDTCSCESIGDCACF  1100
1101  CDTIAAYAHVCAQHGQVVAWRTPTLCPQSCEEKNVRENGYECEWRYNSCA  1150
1151  PACPVTCQHPEPLACPVQCVEGCHAHCPPGRILDELLQTCVDPQDCPVCE  1200
1201  VAGRRLAPGKKITLSPDDPAHCQNCHCDGVNLTCEACQEPGGLVAPPTDA  1250
1251  PVSSTTPYVEDTPEPPLHNFYCSKLLDLVFLLDGSSMLSEAEFEVLKAFV  1300
1301  VGMMERLHISQKRIRVAVVEYHDGSRAYLELKARKRPSELRRITSQIKYT  1350
1351  GSQVASTSEVLKYTLFQIFGKIDRPEASHITLLLTASQEPPRMARNLVRY  1400
1401  VQGLKKKKVIVIPVGIGPHASLKQIRLIEKQAPENKAFLLSGVDELEQRR  1450
1451  DEIVSYLCDLAPEAPAPTQPPQVAHVTVSPGIAGISSPGPKRKSMVLDVV  1500
1501  FVLEGSDEVGEANFNKSKEFVEEVIQRMDVSPDATRISVLQYSYTVTMEY  1550
1551  AFNGAQSKEEVLRHVREIRYQGGNRTNTGQALQYLSEHSFSPSQGDRVEA  1600
1601  PNLVYMVTGNPASDEIKRLPGDIQVVPIGVGPHANMQELERISRPIAPIF  1650
1651  IRDFETLPREAPDLVLQTCCSKEGLQLPTLPPLPDCSQPLDVVLLLDGSS  1700
1701  SLPESSFDKMKSFAKAFISKANIGPHLTQVSVIQYGSINTIDVPWNVVQE  1750
1751  KAHLQSLVDLMQQEGGPSQIGDALAFAVRYVTSQIHGARPGASKAVVIII  1800
1801  MDTSLDPVDTAADAARSNRVAVFPVGVGDRYDEAQLRILAGPGASSNVVK  1850
1851  LQQVEDLSTMATLGNSFFHKLCSGFSGVCVDEDGNEKRPGDVWTLPDQCH  1900
1901  TVTCLANGQTLLQSHRVNCDHGPRPSCANSQSPVRVEETCGCRWTCPCVC  1950
1951  TGSSTRHIVTFDGQNFKLTGSCSYVIFQNKEQDLEVLLHNGACSPGAKQA  2000
2001  CMKSIEIKHAGVSAELHSNMEMAVDGRLVLAPYVGENMEVSIYGAIMYEV  2050
2051  RFTHLGHILTYTPQNNEFQLQLSPKTFASKMHGLCGICDENGANDFTLRD  2100
2101  GTVTTDWKRLVQEWTVQQPGYTCQAVPEEQCPVSDSSHCQVLLSASFAEC  2150
2151  HKVIAPATFHTICQQDSCHQERVCEVIASYAHLCRTSGVCVDWRTTDFCA  2200
2201  MSCPPSLVYNHCERGCPRHCDGNTSFCGDHPSEGCFCPQHQVFLEGSCVP  2250
2251  EEACTQCVGEDGVRHQFLETWVPDHQPCQICMCLSGRKINCTAQPCPTAR  2300
2301  APTCGPCEVARLKQSTNLCCPEYECVCDLFNCNLPPVPPCEGGLQPTLTN  2350
2351  PGECRPTFTCDCRKEECKRVSPPSCPPHRTPTLRKTQCCDEYECACSCVN  2400
2401  STLSCPLGYLASATTNDCGCTTTTCLPDKVCVHRGTVYPVGQFWEEGCDT  2450
2451  CTCTDMEDTVVGLRVVQCSQRPCEDSCQPGFSYVLHEGECCGRCLPSACK  2500
2501  VVAGSLRGDSHSSWKSVGSRWAVPENPCLVNECVRVEDAVFVQQRNISCP  2550
2551  QLAVPTCPTGFQLNCETSECCPSCHCEPVEACLLNGTIIGPGKSVMVDLC  2600
2601  TTCRCIVQTDAISRFKLECRKTTCEACPMGYREEKSQGECCGRCLPTACT  2650
2651  IQLRGGRIMTLKQDETFQDGCDSHLCRVNERGEYIWEKRVTGCPPFDEHK  2700
2701  CLAEGGKIVKIPGTCCDTCEEPDCKDITAKVQYIKVGDCKSQEEVDIHYC  2750
2751  QGKCASKAVYSIDIEDVQEQCSCCLPSRTEPMRVPLHCTNGSVVYHEVIN  2800
2801  AMQCRCSPRNCSK                                       2813

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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