 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q8SX83 from www.uniprot.org...
The NucPred score for your sequence is 0.98 (see score help below)
1 MFRCRNMVRDNSRNICFGKLAETTTTQQQQQQQQFVVDSSTIINNNNNNN 50
51 NNNNNQKLKRSTEEPPTNSFERNYYDRTTSRLVTQYQANNSTSLANSNSS 100
101 PSSVSASASVFATAAGGSSERSRNRDRPYRNGSASVQGGGINSSNTTTTT 150
151 AACTAGGSGSGAIGTGTGGLVGSGPGGVPQALGDRSSTQNIHQNHQSARV 200
201 APPQSWYEAATAATTAQLKSSGGSGNAGASAAVGFTMSSSPINHHPHQHP 250
251 HLQNPQHPHYTSSPVVGAGSCPSAAQGQPQIQSQSQTTAVHRSVAYAGSA 300
301 ADDLLNTATSRNMLLHSSKLNKLLKGAGATGSGGERSGSESPGRAGGATP 350
351 LTTTSTITNNSFSSNSLNNTITTATPTMPTIASGAAGSVGLGSGAEAGVC 400
401 SNSGTASGDILNVAAVLAAAVDNGVPTHPIRTRHNLHGRSTTSSSRSHSR 450
451 SPSSYSSSHSSSSSSHSSSHSHASSPVQSSGNCAMAEGRSSRTVNSVTVT 500
501 SNSSNPSGTAVTVSSAGVGGGCGSSSSSSSSSSSSGSSCLTANPVVHSED 550
551 NRPLAIRVRNLPARSSDTSLKDGLFHEYKKHGKVTWVKVVGQNSERYALV 600
601 CFKKPDDVEKALEVSHDKHFFGCKIEVEPYQGYDVEDNEFRPYEAELDEY 650
651 HPKSTRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGLNAYAFCQY 700
701 SDIVSVVKAMRKMDGEHLGSNRIKLGFGKSMPTNCVWIDGVDEKVSESFL 750
751 QSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQ 800
801 VDFASRECQDAFYDKQEKQQQQSSGSNPRFSRYESSASSLQSRSRASSFS 850
851 RHQNNSNDDCSPINTPGGASSGISSASNLINQSTSINISNIGTNACSAMP 900
901 APSLASAVVSCNVNASGTVPASTSMPSGVSSSSSSLPMSPAALAQRHRMV 950
951 RNARQTVDCDFNEVGRLRFRSSEEVSGGAGNSTQFEDVRCDSPVTARQGS 1000
1001 AVNCFTGPTAAVGESIDGTLNNNQITGGAEGFTGSGGSILSRRRCGKTPK 1050
1051 DLHPVHNQRIQLAEQVEECPSSGDEGVVSPRKRIKMDYHHHHHHSNASGV 1100
1101 ESTGEHSSINKPSPLLLSNCDVIHDPLNRKSEIRRVSETPSGSPSIKFPG 1150
1151 HLPSAPQSLMLSCRRPSIDVGALSALSSSSAFRHGIVGASSMDQQHMMNA 1200
1201 SAAAKRRRVTTTMQQPSSSSTTNSSSGSGLGGISSLTPADEYHHHVSRGR 1250
1251 GHQLHSHHSHEASGGESADGSRPGTPLCDERPEVLPTEPRRLPPPRERVR 1300
1301 ERTRDVMWLPLPKFGVLFFQQQQSRSSGGGGAGNSYLQQQLGGGSTGGLG 1350
1351 CIGAASSSACSLNNSSLNASQGMGSCSGSTFLPSPSSRYWRSSSHHQNQQ 1400
1401 NNHQQQSQQLHGSSSSNTCLMASPARPRSLSSNSSDSDVPGQNAGGSPSL 1450
1451 DERLRNFEENYERWSGGSSREHISGHTPSSATPSWQLSMHMNLSTGLNSH 1500
1501 QTSSASGNSNSSSGTVSSSASNSRHKFLDIDELQPSDIVKSVLAKKSVFD 1550
1551 DDFQRLNKNQWYDPSSSDFALGSSSNIVTGSSLVANVSRHPGGPCSGNTS 1600
1601 PALPNLAATKATPIIGNCSGGLGNSTGSKSAGLLQRLSSLSPMNSPQASM 1650
1651 SPYNSPSPSPSVGGVTACLGQLTKPAAPGTASAGLSGGTAASSSSPAANS 1700
1701 GPTKGLQYPFPSHPPLPNTAAPPPAVQPAPPPLPEMGKQSRLTGQSSGNN 1750
1751 LTKSLSVPDGPQSSPARVQLQKSASVPGSTNVGAPSSLSLDSTTASVETS 1800
1801 ASISSSTSNGNSSLTSAAIHVQKPQQSTFVEEEHTKKSGTSTSQSSSSSS 1850
1851 KKISSTHDKLHSKHNNRSESDKKIKKSDKNASSSDKRKNSSTSQSSKSAT 1900
1901 PRIEDDSSEADDTADKAEKNQRHEKEKKERQEKREKDLRKQVEREEKDRK 1950
1951 AQQEEREKEDRKAKEEEKEREREKKAQEDREKKEREERELREKEQRDKEQ 2000
2001 KEKEIREKDLREKEQRERDNREKELRDKDLREKEMREKEQREKELHREKD 2050
2051 QREREHREKEQSRRAMDVEQEGRGGRMRELSSYQKSKMDIAGEASSLTAI 2100
2101 DCQHNKENAMDTIAQGTPGASPSTPSDNTPKERSRKLSRNSPVRLHKRRL 2150
2151 SSQESNHSAGGGGSCGGSSHQIHHEDYVKRIRMENSQNISVHSSNQRLND 2200
2201 RRDSKEHKSSSFKEDKNSSSHISRPHGCGGSSASSSKHHHRRDKHHQKGS 2250
2251 ASSIETNSSIEVVVDPISQTKHNLNTSEEELQSHQPKREKEREHFSSHAN 2300
2301 SSSSRHKSKRDHHHHREKKRHSVAESTNTDEEHTPQQHNPHRRISAAGSG 2350
2351 SAGELSSAATNTSSGKLHHQHHRRSVERKSSRGSDEGHHSSSKSLRAKLM 2400
2401 MLSSADSDDTDDASKKHSIFDIPDDCPNVSMYDKVKARSCKNMQRQAEEK 2450
2451 KIKAKFSQLKQSRAKKKRSTSYDGDSDTEFEDRQHRNSGSSSFHGRYPGL 2500
2501 SSSDDDDDEETHQRRISSDSDAEHGGQDNQGASTLADANRVRQMQQNLRR 2550
2551 LCDGDDSSEDEIRRNVMKHSHFGKRNSNSTRIASDSESQSQPAPDLTIKQ 2600
2601 EHPIAPAQEIKREQLSDEEQKFKSRHDSNSSIEERKLKTEREIKTELGDF 2650
2651 YNSSEYTYTGKLKEYSPETRKKHKKSKRRLKSSSTADTSAAQTPLVMTPL 2700
2701 TPSIFDVHSSSECKTKFDNFDDLKTECSSIPLEISAGERRKHKERKEKKR 2750
2751 EKLRNMTEATVPNSPTTNDTSSEKLSKEERHRLKKSKKSKSMDNSCNTKI 2800
2801 YNSSGAHPSTSPSLPATPTSAPSTAQTSKRGEDKMEFIFGIISDEEESQF 2850
2851 PEQAETNKDIIPSSVSTTGPIVSAALQTYKQEPSTPNSKNEEAHIQLTVH 2900
2901 EPEQQQQLERSRLSGGSSSSSHADRERHRREKREKKRREKSQREQQNQIH 2950
2951 QKSSKVETKVDDDNSVDMDEAGRALEAQLMSDFDTKPISEEATPSTAATY 3000
3001 RSDMTDVFRFSDNEDNNSVDMTKQGVKSEQQEQHKSKDKKKKKKRSKEEK 3050
3051 QEKLLQQQRRESLPNVASTSSAPPTPGKLTVNVQAASKHADLQLDAKHIS 3100
3101 SPPVCKPSPSLPCLIGDDDDDALHTPKAKPTTPSSRGNDGLTPSREKPRL 3150
3151 ISPIPKTPTIANSSTLSTQSAETPVSSGTVISSSALATTPTSSTAAGVSA 3200
3201 APGLDNSPTSASAQCKKKESFIPGFDGQLDDRISESAVQSISAEFNSTSL 3250
3251 LDNIADEPKIPVASPPRATKPLDKLEESKSRVTISQEETESAVSALLGES 3300
3301 FGTSSTTDYSLDGMDEMSSVNELETPTLVIAEPDEEAALAAKAIETAGEP 3350
3351 ASILEEPEMEPEREAEPDPDPEAEIESEPVVEVLDPEELNKAVQSLKHED 3400
3401 MMDIKADTPQSERDLQIDTDTEENPDEADSSGPSLKIDETVQSSSSPEKS 3450
3451 ISNNSPTPRETANIDIPNVESQPKLSNESTPQPSVITKLPFLDTPKTVPA 3500
3501 GLPPSPVKIEPPTISKLQQPLVQPVQTVLPAPHSTGSGISANSVINLDLS 3550
3551 NVISSCSNTSAASATASASASISFGSPTASQNAMPQASTPKQGPITPQQA 3600
3601 IRTQSLIMQPPTISIPEQTPHFAVPQMVLSPQSHHPQQPGTYMVGIRAPS 3650
3651 PHSPLHSPGRGVAQSRLVGQLSPVGRPMVSQPSPQQQVQQTQQQHALITS 3700
3701 PQSSNISPLASPTTRVLSSSNSPTTSKVNSYQPRNQQVPQQPSPKSVAEV 3750
3751 QTTPQLMTIPLQKMTPIQVPHHPTIISKVVTVQPQQATQSQVASSPPLGS 3800
3801 LPPHKNVHLNAHQNQQQPQVIAKMTAHQHQQHMQQFMHQQMIQRQQHMQQ 3850
3851 QQLHGQSQQITSAPQHQMHQQHQAQQQQQHHNQQHLNQQLHAQQHPTQKQ 3900
3901 HQAQQQFNQQIQQHQSQQQHQVQQQNQAQQQHLSQQQHQSQQQLNQQHQA 3950
3951 QQQQLQQIQKLQQMHGPQQQQKSPQGVGHLGGSTSIFASQQHNSQLPARG 4000
4001 VPQQQHPQQLSHSSPCKPNTLVSVNQGVQPPAILTRVGSHSQPNQQQQLP 4050
4051 HQQSSSGHPHQKQLSSPGANLPLQTPLNVIQNTPKIIVQQHIVAQNQVPP 4100
4101 PQTQGNAIHYPQNQGKDSTPPGHVEPTPAMSAQKTSESVSVIRTPTPTTG 4150
4151 LAVISANTVGSLLTEENLIKISQPKQDELIEQDSKEVDSDYWSAKEVNID 4200
4201 SVIKKLDTPLASKDAKRAVEMQAIAPAPIPNPQPGNQSMAQETALPTTSM 4250
4251 SVNNSNDHDTEDETETRQLPPAKPPIPTVGRPPGRGGSAKRGRQPRGAKK 4300
4301 VGGFPLNSVTAAPPGVDSLVVQPGDNGVQTRLRKPVTAPVTRGRKGRPPR 4350
4351 NLLLQQQQLQQQQLDIQRKGMEMVTSATSSTPLPTPIPTSSVLTAAEKKA 4400
4401 RNQALTQAQEQNQVASQVGTGQDIYEFHEDGGEEPKPKTISSVAPSAEDQ 4450
4451 RPRLILTINKTQPSIKNISEMEQTIQQQQQQQSEVISNTDPIGGDNSESC 4500
4501 NTRKSRRLQEKEDRSTVDDIIEDVVRNTNTPTGTGPHLPKGAQTPPRRSG 4550
4551 RNAQAKKTDAVQIINAVGRPRRSKDRKTIGEQTANLIEEVTASNATVAAS 4600
4601 HLAPPEGAGVESHVPQLDAKEVEPVSVVTPISTPAPVSVAAPVTVPVPAM 4650
4651 VPVKPTMPQHPKKKAIAAAEIESYQAINSSIPSGGLPMHQTAAPATQKIT 4700
4701 GGVADAVSKALVDPVTGVITAGMPQGKEGNLPAATAAAPANSSNEDGQAA 4750
4751 PPPQLQHQQQQQHPQQPPQQQANLQINTTLIPSGLPNPITALGKSVQLET 4800
4801 SAAALLNKPVSVLVKGNASQVIQQQQPQIVAPAKQPIILQQNPLPTVLHH 4850
4851 AQHTTVRPPQPLKAHVLNREKNIQQQLTPTKQAVAQPPQHAPHSGHMLLT 4900
4901 DTAGNQQLVQPQIIARHLQQQQHLQVNVPPPTAHSPHSPRIPSQQQQLGP 4950
4951 GASISPQQQQPQTVVIKQAASAAQPQILHVVSSKASVVPQPQQQQLPPTS 5000
5001 STGPHLQLAKPNYSYAPTVLTPTLPAVQQQQQQHLYKQNNQQKGAQIQMP 5050
5051 PHGIIMPTHPGMLLQQKLPAHLQPQQHQLNPSPPPGKPNPVLHGLQSGQI 5100
5101 MPGSVGSPPPVSAAVLKTAQQQVNSVVPVAGIRTAIPNISPQSQPRVSPL 5150
5151 VLPPGISGVPPFDASLHDLGAYVSGRRTQSPPPAHQQASPITPNDSTYRG 5200
5201 VTASRDFMLYQHHLMRGGDYDDKMGSSPPLELRRPGSGPPRTIAVPHSLQ 5250
5251 SPQDRTAADSPQMAQVYVHNTRIPPAHFSEIASRGLYDSGALQLEPPPAH 5300
5301 RPTATISVVVPQQMPAVSSGSPFIGRDGSVQPGSHHHPGKAMDMQLDEMD 5350
5351 RMSMIAAVVQQQQEHLPPALPAGMELASQQAPPAMAPPPGDSLVTLLQRY 5400
5401 PVMWQGLLALKTDQAAVQMHFVHGNPNVARASLPSLVETNTPLLRIAQRM 5450
5451 RLEQTQLEGVAKKMQVDKEHCMLLALPCGRDHADVLQHSRNLQTGFITYL 5500
5501 QQKMAAGIVNIPIPGSEQAAYVVHIFPSCDFANENLERAAPDLKNRVAEL 5550
5551 AHLLIVIATV 5560
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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