 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q61001 from www.uniprot.org...
The NucPred score for your sequence is 0.60 (see score help below)
1 MAKRGGQLCAGSAPGALGPRSPAPRPLLLLLAGLALVGEARTPGGDGFSL 50
51 HPPYFNLAEGARITASATCGEEAPTRSVSRPTEDLYCKLVGGPVAGGDPN 100
101 QTIQGQYCDICTAANSNKAHPVSNAIDGTERWWQSPPLSRGLEYNEVNVT 150
151 LDLGQVFHVAYVLIKFANSPRPDLWVLERSTDFGHTYQPWQFFASSKRDC 200
201 LERFGPRTLERITQDDDVICTTEYSRIVPLENGEIVVSLVNGRPGALNFS 250
251 YSPLLRDFTKATNIRLRFLRTNTLLGHLMGKALRDPTVTRRYYYSIKDIS 300
301 IGGRCVCHGHADVCDAKDPLDPFRLQCACQHNTCGGSCDRCCPGFNQQPW 350
351 KPATTDSANECQSCNCHGHAYDCYYDPEVDRRNASQNQDNVYQGGGVCLD 400
401 CQHHTTGINCERCLPGFFRAPDQPLDSPHVCRPCDCESDFTDGTCEDLTG 450
451 RCYCRPNFTGELCAACAEGYTDFPHCYPLPSFPHNDTREQVLPAGQIVNC 500
501 DCNAAGTQGNACRKDPRLGRCVCKPNFRGAHCELCAPGFHGPSCHPCQCS 550
551 SPGVANSLCDPESGQCMCRTGFEGDRCDHCALGYFHFPLCQLCGCSPAGT 600
601 LPEGCDEAGRCQCRPGFDGPHCDRCLPGYHGYPDCHACACDPRGALDQQC 650
651 GVGGLCHCRPGYTGATCQECSPGFYGFPSCIPCHCSADGSLHTTCDPTTG 700
701 QCRCRPRVTGLHCDMCVPGAYNFPYCEAGSCHPAGLAPANPALPETQAPC 750
751 MCRAHVEGPSCDRCKPGYWGLSASNPEGCTRCSCDPRGTLGGVTECQGNG 800
801 QCFCKAHVCGKTCAACKDGFFGLDYADYFGCRSCRCDVGGALGQGCEPKT 850
851 GACRCRPNTQGPTCSEPAKDHYLPDLHHMRLELEEAATPEGHAVRFGFNP 900
901 LEFENFSWRGYAHMMAIQPRIVARLNVTSPDLFRLVFRYVNRGSTSVNGQ 950
951 ISVREEGKLSSCTNCTEQSQPVAFPPSTEPAFVTVPQRGFGEPFVLNPGI 1000
1001 WALLVEAEGVLLDYVVLLPSTYYEAALLQHRVTEACTYRPSALHSTENCL 1050
1051 VYAHLPLDGFPSAAGTEALCRHDNSLPRPCPTEQLSPSHPPLATCFGSDV 1100
1101 DIQLEMAVPQPGQYVLVVEYVGEDSHQEMGVAVHTPQRAPQQGVLNLHPC 1150
1151 PYSSLCRSPARDTQHHLAIFYLDSEASIRLTAEQAHFFLHSVTLVPVEEF 1200
1201 STEFVEPRVFCVSSHGTFNPSSAACLASRFPKPPQPIILKDCQVLPLPPD 1250
1251 LPLTQSQELSPGAPPEGPQPRPPTAVDPNAEPTLLRHPQGTVVFTTQVPT 1300
1301 LGRYAFLLHGYQPVHPSFPVEVLINGGRIWQGHANASFCPHGYGCRTLVL 1350
1351 CEGQTMLDVTDNELTVTVRVPEGRWLWLDYVLIVPEDAYSSSYLQEEPLD 1400
1401 KSYDFISHCATQGYHISPSSSSPFCRNAATSLSLFYNNGALPCGCHEVGA 1450
1451 VSPTCEPFGGQCPCRGHVIGRDCSRCATGYWGFPNCRPCDCGARLCDELT 1500
1501 GQCICPPRTVPPDCLVCQPQSFGCHPLVGCEECNCSGPGVQELTDPTCDM 1550
1551 DSGQCRCRPNVAGRRCDTCAPGFYGYPSCRPCDCHEAGTMASVCDPLTGQ 1600
1601 CHCKENVQGSRCDQCRVGTFSLDAANPKGCTRCFCFGATERCGNSNLARH 1650
1651 EFVDMEGWVLLSSDRQVVPHEHRPEIELLHADLRSVADTFSELYWQAPPS 1700
1701 YLGDRVSSYGGTLHYELHSETQRGDIFIPYESRPDVVLQGNQMSIAFLEL 1750
1751 AYPPPGQVHRGQLQLVEGNFRHLETHNPVSREELMMVLAGLEQLQIRALF 1800
1801 SQTSSSVSLRRVVLEVASEAGRGPPASNVELCMCPANYRGDSCQECAPGY 1850
1851 YRDTKGLFLGRCVPCQCHGHSDRCLPGSGICVGCQHNTEGDQCERCRPGF 1900
1901 VSSDPSNPASPCVSCPCPLAVPSNNFADGCVLRNGRTQCLCRPGYAGASC 1950
1951 ERCAPGFFGNPLVLGSSCQPCDCSGNGDPNMIFSDCDPLTGACRGCLRHT 2000
2001 TGPHCERCAPGFYGNALLPGNCTRCDCSPCGTETCDPQSGRCLCKAGVTG 2050
2051 QRCDRCLEGYFGFEQCQGCRPCACGPAAKGSECHPQSGQCHCQPGTTGPQ 2100
2101 CLECAPGYWGLPEKGCRRCQCPRGHCDPHTGHCTCPPGLSGERCDTCSQQ 2150
2151 HQVPVPGKPGGHGIHCEVCDHCVVLLLDDLERAGALLPAIREQLQGINAS 2200
2201 SAAWARLHRLNASIADLQSKLRSPPGPRYQAAQQLQTLEQQSISLQQDTE 2250
2251 RLGSQATGVQGQAGQLLDTTESTLGRAQKLLESVRAVGRALNELASRMGQ 2300
2301 GSPGDALVPSGEQLRWALAEVERLLWDMRTRDLGAQGAVAEAELAEAQRL 2350
2351 MARVQEQLTSFWEENQSLATHIRDQLAQYESGLMDLREALNQAVNTTREA 2400
2401 EELNSRNQERLKEALQWKQELSQDNATLKATLQAASLILGHVSELLQGID 2450
2451 QAKEDLEHLAASLDGAWTPLLKRMQAFSPASSKVDLVEAAEAHAQKLNQL 2500
2501 AINLSGIILGINQDRFIQRAVEASNAYSSILQAVQAAEDAAGQALRQASR 2550
2551 TWEMVVQRGLAAGARQLLANSSALEETILGHQGRLGLAQGRLQAAGIQLH 2600
2601 NVWARKNQLAAQIQEAQAMLAMDTSETSEKIAHAKAVAAEALSTATHVQS 2650
2651 QLQGMQKNVERWQSQLGGLQGQDLSQVERDASSSVSTLEKTLPQLLAKLS 2700
2701 RLENRGVHNASLALSANIGRVRKLIAQARSAASKVKVSMKFNGRSGVRLR 2750
2751 TPRDLADLAAYTALKFHIQSPVPAPEPGKNTGDHFVLYMGSRQATGDYMG 2800
2801 VSLRNQKVHWVYRLGKAGPTTLSIDENIGEQFAAVSIDRTLQFGHMSVTV 2850
2851 EKQMVHEIKGDTVAPGSEGLLNLHPDDFVFYVGGYPSNFTPPEPLRFPGY 2900
2901 LGCIEMETLNEEVVSLYNFEQTFMLDTAVDKPCARSKATGDPWLTDGSYL 2950
2951 DGSGFARISFEKQFSNTKRFDQELRLVSYNGIIFFLKQESQFLCLAVQEG 3000
3001 TLVLFYDFGSGLKKADPLQPPQALTAASKAIQVFLLAGNRKRVLVRVERA 3050
3051 TVFSVDQDNMLEMADAYYLGGVPPEQLPLSLRQLFPSGGSVRGCIKGIKA 3100
3101 LGKYVDLKRLNTTGISFGCTADLLVGRTMTFHGHGFLPLALPDVAPITEV 3150
3151 VYSGFGFRGTQDNNLLYYRTSPDGPYQVSLREGHVTLRFMNQEVETQRVF 3200
3201 ADGAPHYVAFYSNVTGVWLYVDDQLQLVKSHERTTPMLQLQPEEPSRLLL 3250
3251 GGLPVSGTFHNFSGCISNVFVQRLRGPQRVFDLHQNMGSVNVSVGCTPAQ 3300
3301 LIETSRATAQKVSRRSRQPSQDLACTTPWLPGTIQDAYQFGGPLPSYLQF 3350
3351 VGISPSHRNRLHLSMLVRPHAASQGLLLSTAPMSGRSPSLVLFLNHGHFV 3400
3401 AQTEGPGPRLQVQSRQHSRAGQWHRVSVRWGMQQIQLVVDGSQTWSQKAL 3450
3451 HHRVPRAERPQPYTLSVGGLPASSYSSKLPVSVGFSGCLKKLQLDKRPLR 3500
3501 TPTQMVGVTPCVSGPLEDGLFFPGSEGVVTLELPKAKMPYVSLELEMRPL 3550
3551 AAAGLIFHLGQALATPYMQLKVLTEQVLLQANDGAGEFSTWVTYPKLCDG 3600
3601 RWHRVAVIMGRDTLRLEVDTQSNHTTGRLPESLAGSPALLHLGSLPKSST 3650
3651 ARPELPAYRGCLRKLLINGAPVNVTASVQIQGAVGMRGCPSGTLALSKQG 3700
3701 KALTQRQAKPSVSPLLWH 3718
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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