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

NucPred

Fetching Q08378 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MDGASAEQDGLQEDRSHSGPSSLPEAPLKPPGPLVPPDQQDKVQCAEVNR    50
  51  ASTEGESPDGPGQGGLCQNGPTPPFPDPPSSLDPTTSPVGPDASPGVAGF   100
 101  HDNLRKSQGTSAEGSVRKEALQSLRLSLPMQETQLCSTDSPLPLEKEEQV   150
 151  RLQARKWLEEQLKQYRVKRQQERSSQPATKTRLFSTLDPELMLNPENLPR   200
 201  ASTLAMTKEYSFLRTSVPRGPKVGSLGLPAHPREKKTSKSSKIRSLADYR   250
 251  TEDSNAGNSGGNVPAPDSTKGSLKQNRSSAASVVSEISLSPDTDDRLENT   300
 301  SLAGDSVSEVDGNDSDSSSYSSASTRGTYGILSKTVGTQDTPYMVNGQEI   350
 351  PADTLGQFPSIKDVLQAAAAEHQDQGQEVNGEVRSRRDSICSSVSLESSA   400
 401  AETQEEMLQVLKEKMRLEGQLEALSLEASQALKEKAELQAQLAALSTKLQ   450
 451  AQVECSHSSQQRQDSLSSEVDTLKQSCWDLERAMTDLQNMLEAKNASLAS   500
 501  SNNDLQVAEEQYQRLMAKVEDMQRSMLSKDNTVHDLRQQMTALQSQLQQV   550
 551  QLERTTLTSKLKASQAEISSLQSVRQWYQQQLALAQEARVRLQGEMAHIQ   600
 601  VGQMTQAGLLEHLKLENVSLSQQLTETQHRSMKEKGRIAAQLQGIEADML   650
 651  DQEAAFMQIQEAKTMVEEDLQRRLEEFEGERERLQRMADSAASLEQQLEQ   700
 701  VKLTLLQRDQQLEALQQEHLDLMKQLTLTQEALQSREQSLDALQTHYDEL   750
 751  QARLGELQGEAASREDTICLLQNEKIILEAALQAAKSGKEELDRGARRLE   800
 801  EGTEETSETLEKLREELAIKSGQVEHLQQETAALKKQMQKIKEQFLQQKV   850
 851  MVEAYRRDATSKDQLISELKATRKRLDSELKELRQELMQVHGEKRTAEAE   900
 901  LSRLHREVAQVRQHMADLEGHLQSAQKERDEMETHLQSLQFDKEQMVAVT   950
 951  EANEALKKQIEELQQEARKAITEQKQKMRRLGSDLTSAQKEMKTKHKAYE  1000
1001  NAVGILSRRLQEALAAKEAADAELGQLRAQGGSSDSSLALHERIQALEAE  1050
1051  LQAVSHSKTLLEKELQEVIALTSQELEESREKVLELEDELQESRGFRKKI  1100
1101  KRLEESNKKLALELEHEKGKLTGLGQSNAALREHNSILETALAKREADLV  1150
1151  QLNLQVQAVLQRKEEEDRQMKHLVQALQASLEKEKEKVNSLKEQVAAAKV  1200
1201  EAGHNRRHFKAASLELSEVKKELQAKEHLVQKLQAEADDLQIREGKHSQE  1250
1251  IAQFQAELAEARAQLQLLQKQLDEQLSKQPVGNQEMENLKWEVDQKEREI  1300
1301  QSLKQQLDLTEQQGRKELEGLQQLLQNVKSELEMAQEDLSMTQKDKFMLQ  1350
1351  AKVSELKNNMKTLLQQNQQLKLDLRRGAAKTRKEPKGEASSSNPATPIKI  1400
1401  PDCPVPASLLEELLRPPPAVSKEPLKNLNSCLQQLKQEMDSLQRQMEEHA  1450
1451  LTVHESLSSWTPLEPATASPVPPGGHAGPRGDPQRHSQSRASKEGPGE    1498

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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