 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q03376 from www.uniprot.org...
The NucPred score for your sequence is 0.58 (see score help below)
1 MKTLSSLLLVLAVNVLLIQASPDPDNRCPARKYWNERKQACVCKRENRCY 50
51 PIGAIFDPESCTFSMCQSKGCSAKQIFNKDKCACECRNDQPKDGCGAGRY 100
101 WCNQDCSCKCSTPMSAGGCSGSQIWCEKSCACVCPNADKCTAPQVWNKDT 150
151 CCCGCPVNMQEPADGCTKPLIWDKVDCRCECPLKKDCGKNRDWSDSSCSC 200
201 ECKGDGKCQGSKIWCKNNCRCICPTAEPAGGCSAPLKWDDDKCSCACPAK 250
251 MEEKKEKCVESGKIWNPNTCECGCAQLNCPDNKKANKETCQCECKEVKKC 300
301 NGGQVFCKDSCSCVCPGGDKDKTCTAPQVYDGVACSCSCPVNMQKPADGC 350
351 PRPQKWDKEECRCECPVKHDCKNGKVWDETICQCICPRDAPVCTAGKERC 400
401 GESCECKCINREPKEGCAKPLVWNENTCKCVCPADKQMSPGGCGSGKSFN 450
451 KLTCQCECDQSASKCGLKRWNADTCKCECQPGMPPEGCGKQTWISDKCKC 500
501 ECSPTITCQAPQILDLNTCECKCPVNMLAQKEKCKSPRQWTDSKCLCECS 550
551 TTPATCEGKQTWCGEACQCICPGGDKNCGNKKFFDKPSCECKCKNNPTCT 600
601 SPQVWDADDCECKCPKDKQKPQGGCDGGQKWNDRVCSCGCPVPRPDCTNG 650
651 QIYNINTCACGCGIDKPSCPKQQIYNWKTCDCECPNGMKEPVGGCGAKTW 700
701 LDDECQCDCVPGKPKGGCTGAQKWCDKTCKCKCEKEMPTGGCENNKKWCD 750
751 ETCDCVCPQKNTCIAPKVWDAKTCSCICVNPPKCNSPQVLKDTCCCGCQN 800
801 VKSCKAPQKFIENICDCACPNKKQCKAPLVWSDEFCDCVCPNSASMKTCL 850
851 SPKEWNKVTCTCDCNPPKPDCCPGTQKWMDDKCKCGCPNAQTDCAGGKKF 900
901 NDFTCSCGCPSGKLDCTGNTKWSAETCTCGCGDVNRNCGNLKNFNDNLCQ 950
951 CECKNKQEMANCKSPRTWNYDTCKCVCKNADDSDDCVKPQIWLDDQCKCG 1000
1001 CPASAQMTCPANKRFIEKSCSCECKSPMPSPIPQGKKWNEDKCVVECANV 1050
1051 KTCEGPQRWCDNQCKCICPQVNTKCSDKQKFIESKCECGCETQTQCKDGF 1100
1101 RWSNLECGCLCDDKKCPGKQVFDKNTCQCKCPNQKPGDTCGNGKDFCPLD 1150
1151 CSCKCKNPKPANGCTGVQEWNEEKCQCECPKDKPKKQCPGGQDWNNHQCQ 1200
1201 CGCPTPAPTCSNNQKYSNVSCSCGCNPGKPKNGCPGNQIWCDNTCRCVCP 1250
1251 KNMEKPADNCKTKWWNDEMCQCVCKPGCPEGGCKGVMKWNANTCSCECPA 1300
1301 DKAKPASCGDKKSWNDDSCSCQCKSKMPCGGCPPNQQWNEKDCECKCSAT 1350
1351 GNCPAGQTWNSQTCQCSCPATGKCTGAQVWCSKACKCVCPAQKKCDSPKT 1400
1401 WDENSCSCQCPKNMRPPTGGCNAGRTWDDATCSEKCAATPKCDSPKVFDP 1450
1451 TTCGCKCGNKPNKLDAGRTWDEQKCKMTCDLPAIPCCHYEGQVYDSNTCK 1500
1501 CGCPKEETCKQGFSFSPKSGCKCILECNKKDPGCGAKKIWCQETCKCECA 1550
1551 SEPPRMGCGPNRYWDKEDCACQCLKTKVCTDSDFSFFSHDTCDCECSNAK 1600
1601 DFILNCNQKLNKVSCQPQCIQRPPPEGCAEKFGEFFSWDPKACECKCIEQ 1650
1651 KTTVKGRVFDKATCNFKCTNEPKTNPKCANTAESWDSQICACKVCSTCKH 1700
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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