 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q9QXS1 from www.uniprot.org...
The NucPred score for your sequence is 0.85 (see score help below)
1 MVAGMLMPLDRLRAIYEVLFREGVMVAKKDRRPRSLHPHVPGVTNLQVMR 50
51 AMASLKARGLVRETFAWCHFYWYLTNEGIDHLRQYLHLPPEIVPASLQRV 100
101 RRPVAMVIPARRRSPHVQTMQGPLGCPPKRGPLPAEDPAREERQVYRRKE 150
151 REEGAPETPVVSATTVGTLARPGPEPAPATDERDRVQKKTFTKWVNKHLI 200
201 KHWRAEAQRHISDLYEDLRDGHNLISLLEVLSGDSLPREKGRMRFHKLQN 250
251 VQIALDYLRHRQVKLVNIRNDDIADGNPKLTLGLIWTIILHFQISDIQVS 300
301 GQSEDMTAKEKLLLWSQRMVEGYQGLRCDNFTTSWRDGRLFNAIIHRHKP 350
351 MLIDMNKVYRQTNLENLDQAFSVAERDLGVTRLLDPEDVDVPQPDEKSII 400
401 TYVSSLYDAMPRVPGAQDGVRANELQLRWQEYRELVLLLLQWIRHHTAAF 450
451 EERKFPSSFEEIEILWCQFLKFKETELPAKEADKNRSKVIYQSLEGAVQA 500
501 GQLKIPPGYHPLDVEKEWGKLHVAILEREKQLRSEFERLECLQRIVSKLQ 550
551 MEAGLCEEQLNQADALLQSDIRLLASGKVAQRAGEVERDLDKADGMIRLL 600
601 FNDVQTLKDGRHPQGEQMYRRVYRLHERLVAIRTEYNLRLKAGVGAPVTQ 650
651 VTLQSTQRRPELEDSTLRYLQDLLAWVEENQRRIDSAEWGVDLPSVEAQL 700
701 GSHRGMHQSIEEFRAKIERARNDESQLSPATRGAYRDCLGRLDLQYAKLL 750
751 NSSKARLRSLESLHGFVAAATKELMWLNEKEEEEVGFDWSDRNTNMAAKK 800
801 ESYSALMRELEMKEKKIKEIQNTGDRLLREDHPARPTVESFQAALQTQWS 850
851 WMLQLCCCIEAHLKENTAYFQFFSDVREAEEQLQKLQETLRRKYSCDRTI 900
901 TVTRLEDLLQDAQDEKEQLNEYKGHLSGLAKRAKAIVQLKPRNPAHPVRG 950
951 HVPLIAVCDYKQVEVTVHKGDQCQLVGPAQPSHWKVLSGSSSEAAVPSVC 1000
1001 FLVPPPNQEAQEAVARLEAQHQALVTLWHQLHVDMKSLLAWQSLSRDIQL 1050
1051 IRSWSLVTFRTLKPEEQRQALRNLELHYQAFLRDSQDAGGFGPEDRLVAE 1100
1101 REYGSCSRHYQQLLQSLEQGEQEESRCQRCISELKDIRLQLEACETRTVH 1150
1151 RLRLPLDKDPARECAQRIAEQQKAQAEVEGLGKGVARLSAEAEKVLALPE 1200
1201 PSPAAPTLRSELELTLGKLEQVRSLSAIYLEKLKTISLVIRSTQGAEEVL 1250
1251 KTHEEQLKEAQAVPATLQELEATKASLKKLRAQAEAQQPVFNTLRDELRG 1300
1301 AQEVGERLQQRHGERDVEVERWRERVTQLLERWQAVLAQTDVRQRELEQL 1350
1351 GRQLRYYRESADPLSAWLQDAKRRQEQIQAVPIANCQAAREQLRQEKALL 1400
1401 EEIERHGEKVEECQKFAKQYINAIKDYELQLITYKAQLEPVASPAKKPKV 1450
1451 QSGSESVIQEYVDLRTRYSELTTLTSQYIKFISETLRRMEEEERLAEQQR 1500
1501 AEERERLAEVEAALEKQRQLAEAHAQAKAQAELEAQELQRRMQEEVARRE 1550
1551 EAAVDAQQQKRSIQEELQHLRQSSEAEIQAKAQQVEAAERSRMRIEEEIR 1600
1601 VVRLQLETTERQRGGAEGELQALRARAEEAEAQKRQAQEEAERLRRQVQD 1650
1651 ESQRKRQAEAELALRVKAEAEAAREKQRALQALDELRLQAEEAERRLRQA 1700
1701 EAERARQVQVALETAQRSAEVELQSKRASFAEKTAQLERTLQEEHVTVAQ 1750
1751 LREEAERRAQQQAEAERAREEAERELERWQLKANEALRLRLQAEEVAQQK 1800
1801 SLAQADAEKQKEEAEREARRRGKAEEQAVRQRELAEQELEKQRQLAEGTA 1850
1851 QQRLAAEQELIRLRAETEQGEQQRQLLEEELARLQHEATAATQKRQELEA 1900
1901 ELAKVRAEMEVLLASKARAEEESRSTSEKSKQRLEAEAGRFRELAEEAAR 1950
1951 LRALAEEAKRQRQLAEEDAARQRAEAERVLTEKLAAISEATRLKTEAEIA 2000
2001 LKEKEAENERLRRLAEDEAFQRRRLEEQAALHKADIEERLAQLRKASESE 2050
2051 LERQKGLVEDTLRQRRQVEEEIMALKVSFEKAAAGKAELELELGRIRSNA 2100
2101 EDTMRSKEQAELEAARQRQLAAEEEQRRREAEERVQRSLAAEEEAARQRK 2150
2151 VALEEVERLKAKVEEARRLRERAEQESARQLQLAQEAAQKRLQAEEKAHA 2200
2201 FVVQQREEELQQTLQQEQNMLDRLRSEAEAARRAAEEAEEAREQAEREAA 2250
2251 QSRKQVEEAERLKQSAEEQAQAQAQAQAAAEKLRKEAEQEAARRAQAEQA 2300
2301 ALKQKQAADAEMEKHKKFAEQTLRQKAQVEQELTTLRLQLEETDHQKSIL 2350
2351 DEELQRLKAEVTEAARQRSQVEEELFSVRVQMEELGKLKARIEAENRALI 2400
2401 LRDKDNTQRFLEEEAEKMKQVAEEAARLSVAAQEAARLRQLAEEDLAQQR 2450
2451 ALAEKMLKEKMQAVQEATRLKAEAELLQQQKELAQEQARRLQEDKEQMAQ 2500
2501 QLVEETQGFQRTLEAERQRQLEMSAEAERLKLRMAEMSRAQARAEEDAQR 2550
2551 FRKQAEEIGEKLHRTELATQEKVTLVQTLEIQRQQSDHDAERLREAIAEL 2600
2601 EREKEKLKQEAKLLQLKSEEMQTVQQEQILQETQALQKSFLSEKDSLLQR 2650
2651 ERFIEQEKAKLEQLFQDEVAKAKQLREEQQRQQQQMEQEKQELMASMEEA 2700
2701 RRRQREAEEGVRRKQEELQHLEQQRQQQEKLLAEENQRLRERLQRLEEEH 2750
2751 RAALAHSEIATTQAASTKALPNGRDAPDGPSVEAEPEYTFEGLRQKVPAQ 2800
2801 QLQEAGILSQEELQRLAQGHTTVAELTQREDVYRYLKGRSSIAGLLLKPT 2850
2851 NEKLSVYTALQRQLLSPGTALILLEAQAASGFLLDPVRNRRLTVNEAVKE 2900
2901 GVVGPELHHKLLSAERAVTGYKDPYTGEQISLFQAMKKDLIVRDHGVRLL 2950
2951 EAQIATGGIIDPVHSHRVPVDVAYKRGYFDEEMNRILSDPSDDTKGFFDP 3000
3001 NTHENLTYLQLLERCVEDPETGLRLLPLTDKAAKGGELVYTDTEARDVFE 3050
3051 KATVSAPFGKFQGRTVTIWEIINSEYFTAEQRRDLLQQFRTGHITVEKII 3100
3101 KIVITVVEEHERKGQLCFEGLRALVPAAELLDSGVISHELYQQLQRGERS 3150
3151 VREVAEADSVRQALRGTNVIAGVWLEEAGQKLSIYEALKKDLLQPEVAVA 3200
3201 LLEAQAGTGHIIDPATSARLTVDEAVRAGLVGPELHEKLLSAEKAVTGYR 3250
3251 DPYSGQSVSLFQALKKGLIPREQGLRLLDAQLSTGGIVDPSKSHRVPLDV 3300
3301 AYARGYLDKETNRALTSPRDDARVYHDPSTQEPVTYSQLQQRCRSDQLTG 3350
3351 LSLLPLSEKAVRARQEEVYSELQARETLEQAKVEVPVGSFKGRAMTVWEL 3400
3401 ISSEYFTEEQRQELLRQFRTGKVTVEKVIKIVITIVEEVETRRQERLSFS 3450
3451 GLRAPVPASELLDAKILSRAQFDQLKDGKTSVKELSEVGSVRTLLQGSGC 3500
3501 LAGIYLEDSKEKVTIYEAMRRGLLRPSTATLLLEAQAATGFLVDPVRNQR 3550
3551 LYVHEAVKAGVVGPELHEKLLSAEKAVTGYKDPYSGNTISLFQAMKKGLV 3600
3601 LRDHAIRLLEAQVATGGIIDPVHSHRLPVDVAYQRGYFDEEMNRVLADPS 3650
3651 DDTKGFFDPNTHENLTYLQLLERCVEDPETGLRLLPLKGAEKTEVVETTQ 3700
3701 VYTEEETRRAFEETQIDIPGGGSHGGSSMSLWEVMQSNMIPEDQRARLMA 3750
3751 DFQAGRVTKERMIIIIIEIIEKTEIIRQQNLASYDYVRRRLTAEDLYEAR 3800
3801 IISLETYNLFREGTKNLREVLEMESAWRYLYGTGAVAGVYLPGSRQTLTI 3850
3851 YQALKKGLLSAEVARLLLEAQAATGFLLDPVKGERLTVDEAVRKGLVGPE 3900
3901 LHDRLLSAERAVTGYRDPYTEQTISLFQAMKKELIPAEEALRLLDAQLAT 3950
3951 GGIVDPRLGFHLPLEVAYQRGYLNKDTHDQLSEPSEVRSYVDPSTDERLS 4000
4001 YTQLLKRCRRDDPSGQMLLLLSDARKLTFRGLRKQITVEELVRSQVMDEA 4050
4051 TALQLQEGLTSIEEVTKNLQKFLEGTSCIAGVFVDATKERLSVYQAMKKG 4100
4101 IIRPGTAFELLEAQAATGYVIDPIKGLKLTVEEAVRMGIVGPEFKDKLLS 4150
4151 AERAVTGYKDPYSGKLISLFQAMKKGLILKDHGIRLLEAQIATGGIIDPE 4200
4201 ESHRLPVEVAYKRGLFDEEMNEILTDPSDDTKGFFDPNTEENLTYLQLME 4250
4251 RCITDPQTGLCLLPLKEKKRERKTSSKSSVRKRRVVIVDPETGKEMSVYE 4300
4301 AYRKGLIDHQTYLELSEQECEWEEITISSSDGVVKSMIIDRRSGRQYDID 4350
4351 DAITKNLIDRSALDQYRAGTLSITEFADMLSGNAGGFRSRSSSVGSSSSY 4400
4401 PISSAGPRTQLASWSDPTEETGPVAGILDTETLEKVSITEAMHRNLVDNI 4450
4451 TGQRLLEAQACTGGIIDPSTGERFPVTEAVNKGLVDKIMVDRINLAQKAF 4500
4501 CGFEDPRTKTKMSAAQALKKGWLYYEAGQRFLEVQYLTGGLIEPDTPGRV 4550
4551 SLDEALQRGTVDARTAQKLRDVSAYSKYLTCPKTKLKISYKDALDRSMVE 4600
4601 EGTGLRLLEAAAQSSKGYYSPYSVSGSGSTAGSRTGSRTGSRAGSRRGSF 4650
4651 DATGSGFSMTFSSSSYSSSGYGRRYASGPSASLGGPESAVA 4691
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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