 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q9QYP1 from www.uniprot.org...
The NucPred score for your sequence is 0.59 (see score help below)
1 MRRWWGALLLGALLCAHGTASNLECACGRSHFTCAVSALGECTCIPAQWQ 50
51 CDGDNDCGDHSDEDGCTLPTCSPLDFHCDNGKCIRRSWVCDGDNDCEDDS 100
101 DEQDCPPRECEEDEFPCQNGYCIRSLWHCDGDNDCGDNSDEQCDMRKCSD 150
151 KEFRCSDGSCIAEHWYCDGDTDCKDGSDEESCPSAVPSPPCNLEEFQCAY 200
201 GRCILDIYHCDGDDDCGDWSDESDCSSHQPCRSGEFMCDSGLCVNAGWRC 250
251 DGDADCDDQSDERNCTTSMCTAEQFRCRSGRCVRLSWRCDGEDDCADNSD 300
301 EENCENTGSPQCASDQFLCWNGRCIGQRKLCNGVNDCGDNSDESPQQNCR 350
351 PRTGEENCNVNNGGCAQKCQMIRGAVQCTCHTGYRLTEDGRTCQDVNECA 400
401 EEGYCSQGCTNSEGAFQCWCEAGYELRPDRRSCKALGPEPVLLFANRIDI 450
451 RQVLPHRSEYTLLLNNLENAIALDFHHRRELVFWSDVTLDRILRANLNGS 500
501 NVEEVVSTGLESPGGLAVDWVHDKLYWTDSGTSRIEVANLDGAHRKVLLW 550
551 QSLEKPRAIALHPMEGTIYWTDWGNTPRIEASSMDGSGRRIIADTHLFWP 600
601 NGLTIDYAGRRMYWVDAKHHVIERANLDGSHRKAVISQGLPHPFAITVFE 650
651 DSLYWTDWHTKSINSANKFTGKNQEIIRNKLHFPMDIHTLHPQRQPAGKN 700
701 RCGDNNGGCTHLCLPSGQNYTCACPTGFRKINSHACAQSLDKFLLFARRM 750
751 DIRRISFDTEDLSDDVIPLADVRSAVALDWDSRDDHVYWTDVSTDTISRA 800
801 KWDGTGQKVVVDTSLESPAGLAIDWVTNKLYWTDAGTDRIEVANTDGSMR 850
851 TVLIWENLDRPRDIVVEPMGGYMYWTDWGASPKIERAGMDASNRQVIISS 900
901 NLTWPNGLAIDYGSQRLYWADAGMKTIEFAGLDGSKRKVLIGSQLPHPFG 950
951 LTLYGQRIYWTDWQTKSIQSADRLTGLDRETLQENLENLMDIHVFHRQRP 1000
1001 PVTTPCAVENGGCSHLCLRSPSPSGFSCTCPTGINLLLDGKTCSPGMNSF 1050
1051 LIFARRIDVRMVSLDIPYFADVVVPINMTMKNTIAIGVDPLEGKVYWSDS 1100
1101 TLHRISRASLDGSQHEDIITTGLQTTDGLAVDAIGRKVYWTDTGTNRIEV 1150
1151 GNLDGSMRKVLVWQNLDSPRAIVLYHEMGFMYWTDWGENAKLERSGMDGS 1200
1201 DRTVLINNNLGWPNGLTVDKTSSQLLWADAHTERIEVADLNGANRHTLVS 1250
1251 PVQHPYGLTLLDSYIYWTDWQTRSIHRADKSTGSNVILVRSNLPGLMDIQ 1300
1301 AVDRAQPLGFNKCGSRNGGCSHLCLPRPSGFSCACPTGIQLKGDGKTCDP 1350
1351 SPETYLLFSSRGSIRRISLDTDDHTDVHVPVPGLNNVISLDYDSVDGKVY 1400
1401 YTDVFLDVIRRADLNGSNMETVIGHGLKTTDGLAVDWVARNLYWTDTGRN 1450
1451 TIEASRLDGSCRKVLINNSLDEPRAIAVFPRKGYLFWTDWGHIAKIERAN 1500
1501 LDGSERKVLINADLGWPNGLTLDYDTRRIYWVDAHLDRIESADLNGKLRQ 1550
1551 VLVSHVSHPFALTQQDRWIYWTDWQTKSIQRVDKYSGRNKETVLANVEGL 1600
1601 MDIIVVSPQRQTGTNACGVNNGGCSHLCFARASDFVCACPDEPDSHPCSL 1650
1651 VPGLMPPAPRATSLNEKSPVLPNTLPTTLHSSTTRTRTSPEGAEGRCSER 1700
1701 DAQLGLCAHSNEAVPAAPGEGLHVSYAVGGLLSVLLILLVTAALMLYRHR 1750
1751 KSKFTDPGMGNLTYSNPSYRTSTQEVKIEAAPKPAMYNQLCYKKEGGPDH 1800
1801 SYTKEKIKIVEGIHLLAGHDAEWGDLKQLRSSRGGLLRDHVCMKTDTVSI 1850
1851 QASSGSLDDTETEQLLQEEQSECSSVHTATTPERRGSLPDTGWKHERKLS 1900
1901 SESQV 1905
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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