 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q61329 from www.uniprot.org...
The NucPred score for your sequence is 0.92 (see score help below)
1 MEGCDSPVVSGKDNGCGIPQHRQWTELNSAHLPDKPSSMEQPTGESHGPL 50
51 DSLRAPFNERLADSSTSAGPPAEPASKEVSCNECSASFSSLQTYMEHHCP 100
101 GTHPPPALREESASDTSEEGEEESDVENLAGEIVYQPDGSAYIVESLSQL 150
151 AQSGAACGSSSGSGAVPSLFLNSLPGVGGKQGDPSCAAPVYPQIINTSHI 200
201 ASSFGKWFEGSDPAFPNTSALAGLSPVLHSFRVFDVRHKSNKDYLNSDGS 250
251 AKSSCVSKDVPNNVDLSKFDGFVLYGKRKPILMCFLCKLSFGYVRSFVTH 300
301 AVHDHRMTLSEEERKLLSNKNISAIIQGIGKDKEPLVSFLEPKNKNFQHP 350
351 LVSTGNLIGPGHSFYGKFSGIRMEGEEALPAVAAAGPEQPQAGLLTPSTL 400
401 LNLGGLTSSVLKTPITSVPLGPLASSPTKSSEGKDSGAAEGDKQESGGHQ 450
451 DCFSEKVEPAEEEEAEEEEEEEEEAEEEEEEEEEEEEEEEEASKGLFPND 500
501 LEEELEDSPSEESGPPAGGTTKKDLALSNPSISNSPLMPNVLQTLSRGPA 550
551 STTSNSASNFVVFDGANRRSRLSFNSEGVRANVAEGRRLDFADESANKDS 600
601 ATAPEPNESTEGDDGGFVPHHQHAGSLCELGVGESPSGSGVECPKCDTVL 650
651 GSSRSLGGHMTMMHSRNSCKTLKCPKCNWHYKYQQTLEAHMKEKHPEPGG 700
701 SCVYCKSGQPHPRLARGESYTCGYKPFRCEVCNYSTTTKGNLSIHMQSDK 750
751 HLNNMQNLQNGGGEQVFSHSAGAAAAAAAAAAAAANIGSSWGAPSPTKPK 800
801 TKPTWRCEVCDYETNVARNLRIHMTSEKHMHNMMLLQQNMTQIQHNRHLG 850
851 LGSLPSPAEAELYQYYLAQNMNLPNLKMDSTASDAQFMMSGFQLDPTGPM 900
901 AAMTPALVGGEIPLDMRLGGGQLVSEELMNLGESFIQTNDPSLKLFQCAV 950
951 CNKFTTDNLDMLGLHMNVERSLSEDEWKAVMGDSYQCKLCRYNTQLKANF 1000
1001 QLHCKTDKHVQKYQLVAHIKEGGKANEWRLKCVAIGNPVHLKCNACDYYT 1050
1051 NSLEKLRLHTVNSRHEASLKLYKHLQQHESGVEGESCYYHCVLCNYSTKA 1100
1101 KLNLIQHVRSMKHQRSESLRKLQRLQKGLPEEDEDLGQIFTIRRCPSTDP 1150
1151 EEPVEDAEGPSEASADPEELAKDQGSGSEEGQSKRAASSSQAEKELTDSP 1200
1201 ATTKRTSFPGSSETPLSSKRPKASEEIKPEQMYQCPYCKYSNADVNRLRV 1250
1251 HAMTQHSVQPLLRCPLCQDMLNNKIHLQLHLTHLHSVAPDCVEKLIMTVT 1300
1301 APEMVMPSSMFLPAAAADRDGNSTLEEVGKQPEASEDPGKNILPPASMEH 1350
1351 GGDLKPTSADPSCGREDSGFLCWKKGCNQVFKTSATLQTHFNEVHAKRPQ 1400
1401 LPVSDRHVYKYRCNQCSLAFKTIEKLQLHSQYHVIRAATMCCLCQRSFRT 1450
1451 FQALKKHLETSHLELSEADIQQLYGGLLANGDLLAMGDPTLAEDHTIIVE 1500
1501 EDKEEESDLEDKQSPTGSDSGSVQEDSGSEPKRALPFRKGPNFTMEKFLD 1550
1551 PSRPYKCTVCKESFTQKNILLVHYNSVSHLHKLKRALQESATGQPEPTSS 1600
1601 PDNKPFKCNTCNVAYSQSSTLEIHMRSVLHQTKARAAKLEAASGNSNGTG 1650
1651 NSGGVSLSSSTPSPVGSSGANNTFTATNPSSAAMAPSVNALSQVPPESVV 1700
1701 MPPLGNPISANIASPSEPKEANRKKLADMIASRQQQQQQQQQQQQQAQTL 1750
1751 AQAQAQVQAHLQQELQQQAALIQSQLFNPTLLPHFPMTTETLLQLQQQQH 1800
1801 LLFPFYIPSAEFQLNPEVSLPVTSGALTLTGSGPGLLEDLKVQVQIPQQS 1850
1851 HQQILQQQQQQSQLSLSQSHSALLQPSQHPEKKNKVVIKEKDKESQRERE 1900
1901 GPEGAEGNTGPQESLPDASKAKEKKDLAPGGGSEGTMLPPRIASDARGNA 1950
1951 TKALLENFGFELVIQYNENKQKAQKKNGKAEQGGESLEKLECDSCGKLFS 2000
2001 NILILKSHQEHVHQNYFPFKQLERFAKQYREHYDKLYPLRPQTPEPPPPP 2050
2051 PPPPPPPLPTAPPQPASAPAIPASAPPITSPTIAPAQPSVPLTQLSMPME 2100
2101 LPIFSPLMMQTMPLQTLPAQLPPQLGPVEPLPADLAQLYQHQLNPTLLQQ 2150
2151 QNKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWF 2200
2201 RNTLFKERQRNKDSPYNFSNPPITSLEELKIDSRPPSPEPQKQEYWGSKR 2250
2251 SSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNA 2300
2301 RQKARKNYENQGEGKDGERRELTNDRYIRTSNLNYQCKKCSLVFQRIFDL 2350
2351 IKHQKKLCYKDEDEEGQDDSQNEDSMDAMEILTPTSSSCSTPMPSQAYST 2400
2401 PAPSAAAANTAPSAFLQLTAETDELATFNSKAEASDEKPKQADPPSAQPN 2450
2451 QTQEKQGQPKPEMQQQLEQLEQKTNAPQPKLPQPAAPSLPQPPPQAPPPQ 2500
2501 CPLPQSSPSPSQLSHLPLKPLHTSTPQQLANLPPQLIPYQCDQCKLAFPS 2550
2551 FEHWQEHQQLHFLSAQNQFIHPQFLDRSLDMPFMLFDPSNPLLASQLLSG 2600
2601 AIPQIPASSATSPSTPTSTMNTLKRKLEEKASASPGENDSGTGGEEPQRD 2650
2651 KRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQN 2700
2701 TRARERKGQFRAVGPAQAHRRCPFCRALFKAKTALEAHIRSRHWHEAKRA 2750
2751 GYNLTLSAMLLDCDGGLQMKGDIFDGTSFSHLPPSSSDGQGVPLSPVSKT 2800
2801 MELSPRTLLSPSSIKVEGIEDFESPSMSSVNLNFDQTKLDNDDCSSVNTA 2850
2851 ITDTTTGDEGNADNDSATGIATETKSSAPNEGLTKAAMMAMSEYEDRLSS 2900
2901 GLVSPAPSFYSKEYDNEGTVDYSETSSLADPCSPSPGASGSAGKSGDGGD 2950
2951 RPGQKRFRTQMTNLQLKVLKSCFNDYRTPTMLECEVLGNDIGLPKRVVQV 3000
3001 WFQNARAKEKKSKLSMAKHFGINQTSYEGPKTECTLCGIKYSARLSVRDH 3050
3051 IFSQQHISKVKDTIGSQLDKEKEYFDPATVRQLMAQQELDRIKKANEVLG 3100
3101 LAAQQQGMFDNAPLQALNLPTTYPALQGIPPVLLPGLNRPSLPGFTPANT 3150
3151 ALTSPKPNLMGLPSTTVPSPGLPTSGLPNKPSSASLSSPTPAQATMAMAP 3200
3201 QPPPQPQQPQPPVQQPPPPPAAQQIPAPQLTPQQQRKDKDGEKGKEKEKA 3250
3251 HKGKGEPLPVPKKEKGEAPPAGTGTISAPLPAMEYAVDPAQLQALQAALT 3300
3301 SDPTALLTSQFLPYFVPGFSPYYAPQIPGALQSGYLQPMYGMEGLFPYSP 3350
3351 ALSRPLMGLSPGSLLQQYQQYQQSLQEAIQQQQQQQQQQQQQQQQQQRQL 3400
3401 QQQQQQQQQKVQQQQQQQQQPKASQTPVPQGAASPDKDPAKESPKPEEQK 3450
3451 NVPRELSPLLPKPPEEPEAESKSASADSLCDPFIVPKVQYKLVCRKCQAG 3500
3501 FGDEEAARSHLKSLCCFGQSVVNLQEMVLHVPTGSGGGGGGGGGSGGGGG 3550
3551 SYHCLACESALCGEEALSQHLESALHKHRTITRAARNAKEHPSLLPHSAC 3600
3601 FPDPSTASTSQSAAHSNDSPPPPSAAPSSSASPHASRKSWPPVGSRASAA 3650
3651 KPPSFPPLSSSSTVTSSSCSTSGVQPSMPTDDYSEESDTDLSQKSDGPAS 3700
3701 PVEGPKDPSCPKDSGLTSVGTDTFRL 3726
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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