 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q94IN5 from www.uniprot.org...
The NucPred score for your sequence is 0.31 (see score help below)
1 MKQSVRPIISNVLRKEVALYSTIIGQDKGKEPTGRTYTSGPKPASHIEVP 50
51 HHVTVPATDRTPNPDAQFFQSVDGSQATSHVAYALSDTAFIYPITPSSVM 100
101 GELADVWMAQGRKNAFGQVVDVREMQSEAGAAGALHGALAAGAIATTFTA 150
151 SQGLLLMIPNMYKIAGELMPSVIHVAARELAGHALSIFGGHADVMAVRQT 200
201 GWAMLCSHTVQQSHDMALISHVATLKSSIPFVHFFDGFRTSHEVNKIKML 250
251 PYAELKKLVPPGTMEQHWARSLNPMHPTIRGTNQSADIYFQNMESANQYY 300
301 TDLAEVVQETMDEVAPYIGRHYKIFEYVGAPDAEEVTVLMGSGATTVNEA 350
351 VDLLVKRGKKVGAVLVHLYRPWSTKAFEKVLPKTVKRIAALDRCKEVTAL 400
401 GEPLYLDVSATLNLFPERQNVKVIGGRYGLGSKDFIPEHALAIYANLASE 450
451 NPIQRFTVGITDDVTGTSVPFVNERVDTLPEGTRQCVFWGIGSDGTVGAN 500
501 RSAVRIIGDNSDLMVQAYFQFDAFKSGGVTSSHLRFGPKPITAQYLVTNA 550
551 DYIACHFQEYVKRFDMLDAIREGGTFVLNSRWTTEDMEKEIPADFRRNVA 600
601 QKKVRFYNVDARKICDSFGLGKRINMLMQACFFKLSGVLPLAEAQRLLNE 650
651 SIVHEYGKKGGKVVEMNQAVVNAVFAGDLPQEVQVPAAWANAVDTSTRTP 700
701 TGIEFVDKIMRPLMDFKGDQLPVSVMTPGGTFPVGTTQYAKRAIAAFIPQ 750
751 WIPANCTQCNYCSYVCPHATIRPFVLTDQEVQLAPESFVTRKAKGDYQGM 800
801 NFRIQVAPEDCTGCQVCVETCPDDALEMTDAFTATPVQRTNWEFAIKVPN 850
851 RGTMTDRYSLKGSQFQQPLLEFSGACEGCGETPYVKLLTQLFGERTVIAN 900
901 ATGCSSIWGGTAGLAPYTTNAKGQGPAWGNSLFEDNAEFGFGIAVANAQK 950
951 RSRVRDCILQAVEKKVADEGLTTLLAQWLQDWNTGDKTLKYQDQIIAGLA 1000
1001 QQRSKDPLLEQIYGMKDMLPNISQWIIGGDGWANDIGFGGLDHVLASGQN 1050
1051 LNVLVLDTEMYSNTGGQASKSTHMASVAKFALGGKRTNKKNLTEMAMSYG 1100
1101 NVYVATVSHGNMAQCVKAFVEAESYDGPSLIVGYAPCIEHGLRAGMARMV 1150
1151 QESEAAIATGYWPLYRFDPRLATEGKNPFQLDSKRIKGNLQEYLDRQNRY 1200
1201 VNLKKNNPKGADLLKSQMADNITARFNRYRRMLEGPNTKAAAPSGNHVTI 1250
1251 LYGSETGNSEGLAKELATDFERREYSVAVQALDDIDVADLENMGFVVIAV 1300
1301 STCGQGQFPRNSQLFWRELQRDKPEGWLKNLKYTVFGLGDSTYYFYCHTA 1350
1351 KQIDARLAALGAQRVVPIGFGDDGDEDMFHTGFNNWIPSVWNELKTKTPE 1400
1401 EALFTPSIAVQLTPNATPQDFHFAKSTPVLSITGAERITPADHTRNFVTI 1450
1451 RWKTDLSYQVGDSLGVFPENTRSVVEEFLQYYGLNPKDVITIENKGSREL 1500
1501 PHCMAVGDLFTKVLDILGKPNNRFYKTLSYFAVDKAEKERLLKIAEMGPE 1550
1551 YSNILSEMYHYADIFHMFPSARPTLQYLIEMIPNIKPRYYSISSAPIHTP 1600
1601 GEVHSLVLIDTWITLSGKHRTGLTCTMLEHLQAGQVVDGCIHPTAMEFPD 1650
1651 HEKPVVMCAMGSGLAPFVAFLRERSTLRKQGKKTGNMALYFGNRYEKTEF 1700
1701 LMKEELKGHINDGLLTLRCAFSRDDPKKKVYVQDLIKMDEKMMYDYLVVQ 1750
1751 KGSMYCCGSRSFIKPVQESLKHCFMKAGGLTAEQAENEVIDMFTTGRYNI 1800
1801 EAW 1803
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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