 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q8BRH4 from www.uniprot.org...
The NucPred score for your sequence is 0.98 (see score help below)
1 MSSEEDRSAEQQQPPPAPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQR 50
51 ARKKPRSRGKSTVEDEDSMDGLETTETENIVETEIKEQSVEEDAETEVDS 100
101 SKQPVSALQRSVSEESANSLVSVGVEAKISEQLCAFCYCGEKSSLGQGDL 150
151 KQFRVTPGLTLPWKDQPSNKDIDDNSSGTCEKIQNYAPRKQRGQRKERPP 200
201 QQSAVSCVSVSTQTACEDQAGKLWDELSLVGLPDAIDVQALFDSTGTCWA 250
251 HHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEK 300
301 CTQMYHYPCAAGAGTFQDFSHFFLLCPEHIDQAPERSKEDANCAVCDSPG 350
351 DLLDQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECKVCQNCKQSGEDS 400
401 KMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCRICIECGTRSSTQWHH 450
451 NCLICDTCYQQQDNLCPFCGKCYHPELQKDMLHCNMCKRWVHLECDKPTD 500
501 QELDSQLKEDYICMYCKHLGAEIDPLHPGNEVEMPELPTDYASGMEIEGT 550
551 EDEVVFLEQTVNKDVSDHQCRPGIVPDVQVYTEEPQKSNPLESPDTVGLI 600
601 TSESSDNKMNPDLANEIAHEVDTEKTEMLSKGRHVCEEDQNEDRMEVTEN 650
651 IEVLPHQTIVPQEDLLLSEDSEVASKELSPPKSAPETAAPEALLSPHSER 700
701 SLSCKEPLLTERVQEEMEQKENSEFSTGCVDFEMTLAVDSCDKDSSCQGD 750
751 KYVELPAEEESTFSSATDLNKADVSSSSTLCSDLPSCDMLHGYPPAFNSA 800
801 AGSIMPTTYISVTPKIGMGKPAITKRKFSPGRPRSKQGAWSNHNTVSPPS 850
851 WAPDTSEGREIFKPRQLSGSAIWSIKVGRGSGFPGKRRPRGAGLSGRGGR 900
901 GRSKLKSGIGAVVLPGVSAADISSNKDEEENSMHNTVVLFSSSDKFTLQQ 950
951 DMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLEC 1000
1001 TVCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCVWC 1050
1051 RHCGATSAGLRCEWQNNYTQCAPCASLSSCPVCCRNYREEDLILQCRQCD 1100
1101 RWMHAVCQNLNTEEEVENVADIGFDCSMCRPYMPVSNVPSSDCCDSSLVA 1150
1151 QIVTKVKELDPPKTYTQDGVCLTESGMSQLQSLTVTAPRRKRTKPKLKLK 1200
1201 IINQNSVAVLQTPPDIQSEHSRDGEMDDSREGELMDCDGKSESSPEREAG 1250
1251 DDETKGIEGTDAIKKRKRKPYRPGIGGFMVRQRSRTGQGKAKRSVVRKDS 1300
1301 SGSISEQLPSRDDGWREQLPDTLVDEPVSVAENTDKIKKRYRKRKNKLEE 1350
1351 TFPAYLQEAFFGKDLLDTSRQNKLSVDNLSEDAAQLSFKTGFLDPSSDPL 1400
1401 LSSSSTSAKPGTQGTADDPLADISEVLNTDDDILGIISDDLAKSVDHSDI 1450
1451 GPTTADASSLPQPGVSQSSRPLTEEQLDGILSPELDKMVTDGAILGKLYK 1500
1501 IPELGGKDVEDLFTAVLSPATTQPAPLPQPPPPPQLLPMHNQDVFSRMPL 1550
1551 MNGLIGPSPHLPHNSLPPGSGLGTFPAIAQSPYTDVRDKSPAFNAIASDP 1600
1601 NSSWAPTTPSMEGENDTLSNAQRSTLKWEKEEALGEMATVAPVLYTNINF 1650
1651 PNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQM 1700
1701 SNDSMKRQQQQDSIDPSSRIDSDLFKDPLKQRESEHEQEWKFRQQMRQKS 1750
1751 KQQAKIEATQKLEQVKNEQQQQQQQQQQQQQQQLASQHLLVAPGSDTPSS 1800
1801 GAQSPLTPQAGNGNVSPAQTFHKDLFSKHLPGTPASTPSDGVFVKPQPPP 1850
1851 PPSTPSRIPVQESLSQSQNSQPPSPQMFSPGSSHSRPPSPVDPYAKMVGT 1900
1901 PRPPPGGHSFPRRNSVTPVENCVPLSSVPRPIHMNETSATRPSPARDLCA 1950
1951 SSMTNSDPYAKPPDTPRPMMTDQFSKPFSLPRSPVISEQSTKGPLTTGTS 2000
2001 DHFTKPSPRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTPLHPPPSQDPY 2050
2051 GSVSQTSRRLSVDPYERPALTPRPVDNFSHSQSNDPYSHPPLTPHPAMTE 2100
2101 SFTHASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNPD 2150
2151 PYSQPPGTPRPNTIDPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYTHHL 2200
2201 GPPRPGISVPYSQPPAVPRPRTSEGFTRPSSARPALMPNQDPFLQAAQNR 2250
2251 VPGLPGPLIRPPDTCSQTPRPPGPGRIDTFTHASSSAVRDPYDQPPVTPR 2300
2301 PHSESFGTSQVVHDLVDRPVPGSEGNFSTSSNLPVSSQGQQFSSVSQLPG 2350
2351 PVPTSGGTDTQNTVNMSQADTEKLRQRQKLREIILQQQQQKKIASRQEKG 2400
2401 PQDTAVVPHPVPLPHWQPESINQAFTRPPPPYPGSTRSPVIPPLGPRYAV 2450
2451 FPKDQRGPYPPEVAGMGMRPHGFRFGFPGAGHGPMPSQDRFHVPQQIQGS 2500
2501 GIPPHIRRPMSMEMPRPSNNPPLNNPVGLPQHFPPQGLPVQQHNILGQAF 2550
2551 IELRHRAPDGRSRLPFAASPSSVIESPSHPRHGNFLPRPDFPGPRHTDPI 2600
2601 RQPSQCLSNQLPVHPNLEQVPPSQQEQGHPAHQSSIVMRPLNHPLSGEFS 2650
2651 EAPLSTSTPAETSPDNLEIAGQSSAGLEEKLDSDDPSVKELDVKDLEGVE 2700
2701 VKDLDDEDLENLNLDTEDGKGDDLDTLDNLETNDPNLDDLLRSGEFDIIA 2750
2751 YTDPELDLGDKKSMFNEELDLNVPIDDKLDNQCASVEPKTRDQGDKTMVL 2800
2801 EDKDLPQRKSSVSSEIKTEALSPYSKEEIQSEIKNHDDSRGDADTACSQA 2850
2851 ASAQTNHSDRGKTALLTTDQDMLEKRCNQENAGPVVSAIQGSTPLPARDV 2900
2901 MNSCDITGSTPVLSSLLSNEKCDDSDIRPSGSSPPSLPISPSTHGSSLPP 2950
2951 TLIVPPSPLLDNTVNSNVTVVPRINHAFSQGVPVNPGFIQGQSSVNHNLG 3000
3001 TGKPTNQTVPLTNQSSTMSGPQQLMIPQTLAQQNRERPLLLEEQPLLLQD 3050
3051 LLDQERQEQQQQRQMQAMIRQRSEPFFPNIDFDAITDPIMKAKMVALKGI 3100
3101 NKVMAQNSLGMPPMVMSRFPFMGPSVAGTQNNDGQTLVPQAVAQDGSITH 3150
3151 QISRPNPPNFGPGFVNDSQRKQYEEWLQETQQLLQMQQKYLEEQIGAHRK 3200
3201 SKKALSAKQRTAKKAGREFPEEDAEQLKHVTEQQSMVQKQLEQIRKQQKE 3250
3251 HAELIEDYRIKQQQQQQQCALAPPILMPGVQPQPPLVPGATSLTMSQPNF 3300
3301 PMVPQQLQHQQHTAVISGHTSPARMPSLPGWQSNSASAHLPLNPPRIQPP 3350
3351 IAQLSLKTCTPAPGTVSSANPQNGPPPRVEFDDNNPFSESFQERERKERL 3400
3401 REQQERQRVQLMQEVDRQRALQQRMEMEQHCLMGAELANRTPVSQMPFYG 3450
3451 SDRPCDFLQPPRPLQQSPQHQQQIGPVLQQQNVQQGSVNSPPNQTFMQTN 3500
3501 EQRQVGPPSFVPDSPSASGGSPNFHSVKPGHGNLPGSSFQQSPLRPPFTP 3550
3551 ILPGTSPVANSNVPCGQDPAVTQGQNYSGSSQSLIQLYSDIIPEEKGKKK 3600
3601 RTRKKKKDDDAESGKAPSTPHSDCAAPLTPGLSETTSTPAVSSPSELPQQ 3650
3651 RQQEPVEPVPVPTPNVSAGQPCIESENKLPNSEFIKETSNQQTHVNAEAD 3700
3701 KPSVETPNKTEEIKLEKAETQPSQEDTKVEEKTGNKIKDIVAGPVSSIQC 3750
3751 PSHPVGTPTTKGDTGNELLKHLLKNKKASSLLTQKPEGTLSSDESSTKDG 3800
3801 KLIEKQSPAEGLQTLGAQMQGGFGGGNSQLPKTDGASENKKQRSKRTQRT 3850
3851 GEKAAPRSKKRKKDEEEKQAMYSSSDSFTHLKQQNNLSNPPTPPASLPPT 3900
3901 PPPMACQKMANGFATTEELAGKAGVLVSHEVARALGPKPFQLPFRPQDDL 3950
3951 LARAIAQGPKTVDVPASLPTPPHNNHEELRIQDHYGDRDTPDSFVPSSSP 4000
4001 ESVVGVEVNKYPDLSLVKEEPPEPVPSPIIPILPSISGKNSESRRNDIKT 4050
4051 EPGTLFFTSPFGSSPNGPRSGLISVAITLHPTAAENISSVVAAFSDLLHV 4100
4101 RIPNSYEVSNAPDVPPMGLVSSHRVNPSLEYRQHLLLRGPPPGSANPPRL 4150
4151 ATSYRLKQPNVPFPPTSNGLSGYKDSSHGPAEGASLRPQWCCHCKVVILG 4200
4201 SGVRKSCKDLTFVNKGSRENTKRMEKDIVFCSNNCFILYSSAAQAKNSDN 4250
4251 KESLPSLPQSPMKEPSKAFHQYSNNISTLDVHCLPQFQEKVSPPASPPIS 4300
4301 FPPAFEAAKVESKPDELKVTVKLKPRLRTVPVGLEDCRPLNKKWRGMKWK 4350
4351 KWSIHIVIPKGTFKPPCEDEIDEFLKKLGTCLKPDPVPKDCRKCCFCHEE 4400
4401 GDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGL 4450
4451 QMKCVFCHKTGATSGCHRFRCTNIYHFTCATKAQCMFFKDKTMLCPMHKP 4500
4501 KGIHEQQLSYFAVFRRVYVQRDEVRQIASIVQRGERDHTFRVGSLIFHTI 4550
4551 GQLLPQQMQAFHSPKALFPVGYEASRLYWSTRYANRRCRYLCSIEEKDGR 4600
4601 PVFVIRIVEQGHEDLVLSDSSPKDVWDKILEPVACVRKKSEMLQLFPAYL 4650
4651 KGEDLFGLTVSAVARIAESLPGVEACENYTFRYGRNPLMELPLAVNPTGC 4700
4701 ARSEPKMSAHVKRFVLRPHTLNSTSTSKSFQSTVTGELNAPYSKQFVHSK 4750
4751 SSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNE 4800
4801 VANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAE 4850
4851 VVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRK 4900
4901 WMN 4903
Positively and negatively influencing subsequences are coloured according to the following scale:
(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)
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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