SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q9U3V8 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MAEPRPGGYNYKTLLCRNIPELFLDKYVARSHFGRFGTLVNFVLRPRRMT    50
  51  CTVSYASEDEAARALLDGASFQGHLFDISYADNETAPAQKTEEWVDPDIQ   100
 101  AELSALQSGWRNEYGSGKPIKKPQNGSSGSGGSSMLPAIPVGPATAPVSR   150
 151  DRTPAQLRDLENMMRRPAHTSEEKFSVLDARDKLLRLNRTQHKLSGATQG   200
 201  HCADMCPEKERVLREFQRQVAYYELQPGSDELICHERALKQYSRSSADQE   250
 251  TPLPHELRNETALHMTMSYLMHEIMDISERQDPQSHMGDWFHFVWDRTRS   300
 301  IRKEITQQELCSLGAVKLVEQCARFHIHCAARLVDADPSVFDSKINAENL   350
 351  TKCLQTLKYMYHDLRIKGVPCPKEAEFRGYIVLLNLADANFLWDIGQLPA   400
 401  ELQSCPEVRQAIQFYLALQDTNFVRFFQLLADKDTSYLSACILVNYFTRL   450
 451  RVLGLHRLIQAYRSPRKDEVSSLPLSYIAELLSFASEQEAADFVQHYGLQ   500
 501  INEAGRVVLSRMHTVETEYKLPRQYELVEVKRVKSVGEVVSGEPLPPRDL   550
 551  YLNHRPHNSFDDYGMLKSIAWTAKDQLAGMQQEEMQPQMPSQPPAVSKHS   600
 601  DTLFKVPMQPDGTAAGFGVFAAAAVPPASSIDGFSFVLPKSRAQEFQEQA   650
 651  PATQQRRAQEEAKHQALQVAIAAAKKREAELMAIHEAKVAEAERVRQQKL   700
 701  RERQEQQRRQQQELEEQRQREQEKLQLEKERQLKLEQLFFVQQQEREAHK   750
 751  QTRTLELYQEIFQDTLAEICQSEFMSHSRACRSYESMLDSITRDLVERQM   800
 801  EQSIYELGVMRVCIRRWRKYRRTQQEKDTLFNQLPLSFGAENPEGVVNKR   850
 851  SMEDSLRLSRRYRLGEPCDYGKLLAGLEEHSWLKLDLWHVLDKCLPVAQP   900
 901  GARRFYKLLISLSGGQEGLQLNCDLDRGLLQQPQSPDARFVDGGYIRGFS   950
 951  QGIGLSVMKIRDDDHDWKATDLAEANGIICLIGLDDIRLLPDRLKPLLQA  1000
1001  SRCHDVAVIVQHPANTAFVQPDIPLQELCLRSFNIFRLRKSGNNRQRLMI  1050
1051  ALESAVKFLAKATERKRVGHLHQVETREYLLVNLGSELFRRLKYAAEHDT  1100
1101  AIRSDTQLNPQRCVDLFNEAVHRLQLVAGEDLSDWPQFPEELRVFVQPLP  1150
1151  IESSLNTNRLEHFEPGWHLPERRQRIVQLLERCKLPKMPVLPRSSSLAEA  1200
1201  QCQWVLDYAQISQQEDCVEQIALQAIKILQYDTDDYLNFVEYLAGERMQY  1250
1251  ILRQERNPPQGIVYNTKTLKRRFLSAWYYEFREPQIYEPVPAEENAQMLE  1300
1301  KQPSSQAEVQQLDFDEITSKAEAVLKRFHQRQDERHTLRELNRSHKSRKR  1350
1351  RDASDHKHAMSSLVSALKAARSDYQGKSSAVCRLVAQMVEADQVKYQWTP  1400
1401  NLTSLIDRKDASTRHQWRPHVNHSTRHARKLPVQSISFLSRCLAKKGEHA  1450
1451  GLTSCVLSVKTRYAPKTLHGRELLIWRQSSMRPLLLPSSNLWTGVLSKRH  1500
1501  YVPRLRPAEEDEEVERRAVPQLRITKEQSEEEEHQLQRRKDGSRLRNECS  1550
1551  EFYLPMGEQDYSEREEENRGHRQAYVPSELMTPELATKWQTTSVTDRDRQ  1600
1601  LLNLEQQMKTQPSVRMTTQTWFSGNHRRYRSRRSGAKRYHVVSELEGWRR  1650
1651  SSNHQPVPVFQGQPGEQEHLRHASHKASARSMPDGQERCQMVWEQKKRSP  1700
1701  WHRTEVTNSNKVRMPRIRAAKSAVMMAQEARNKHHRLITKKLVYRPRRTV  1750
1751  NAVQAEETEDQDTHHRHHGGGQKMSKRAPERALLKQHLADLLAVSKPEDS  1800
1801  FRIGYQPNAPTRQLLEQGKCYVSLRREQFIHLHPVRPNSLILAVNLEVKE  1850
1851  SPRQPVTTLHRRDGAKRPRLVEDVVKPSLITVIRQSAATWDHNGRKVPAK  1900
1901  KSNLVGMPSKEHAYQRRLVRNTSTLEAIVKAQAKPRSEPKSPSSATDYHR  1950
1951  VASQKLPHVTSKADISKAADPFKDLDKPRIKEKEVASSWKQAYVVRSKMY  2000
2001  DAITPYRRRAYPGKKCITKDKTDGYFLAKRSSAAAAGSSKKVKPPKQPVV  2050
2051  SPKVQVPSVLHKKKSRESLGPQTTKTGKL                       2079

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

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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