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

NucPred

Fetching P30182 from www.uniprot.org...

The NucPred score for your sequence is 0.58 (see score help below)

   1  MATKLPLQNSNAANVAKAPAKSRAAAGGKTIEEMYQKKSQLEHILLRPDT    50
  51  YIGSIEKHTQTLWVYEKDEMVQRPVTYVPGLYKIFDEILVNAADNKQRDA   100
 101  KMDSVQVVIDVEQNLISVCNSGAGVPVEIHQEEGIYVPEMIFGHLLTSSN   150
 151  YDDNVKKTTGGRNGYGAKLTNIFSTEFIIETADGKRLKKYKQVFENNMGK   200
 201  KSEPVITKCNKSENWTKVTFKPDLKKFNMTELEDDVVALMSKRVFDIAGC   250
 251  LGKSVKVELNGKQIPVKSFTDYVDLYLSAANKSRTEDPLPRLTEKVNDRW   300
 301  EVCVSLSEGQFQQVSFVNSIATIKGGTHVDYVTSQITNHIVAAVNKKNKN   350
 351  ANVKAHNVKNHLWVFVNALIDNPAFDSQTKETLTLRQSSFGSKCELSEDF   400
 401  LKKVGKSGVVENLLSWADFKQNKDLKKSDGAKTGRVLVEKLDDAAEAGGK   450
 451  NSRLCTLILTEGDSAKSLALAGRSVLGNNYCGVFPLRGKLLNVREASTTQ   500
 501  ITNNKEIENLKKILGLKQNMKYENVNSLRYGQMMIMTDQDHDGSHIKGLL   550
 551  INFIHSFWPSLLQVPSFLVEFITPIVKATRKGTKKVLSFYSMPEYEEWKE   600
 601  SLKGNATGWDIKYYKGLGTSTAEEGKEYFSNLGLHKKDFVWEDEQDGEAI   650
 651  ELAFSKKKIEARKNWLSSYVPGNHLDQRQPKVTYSDFVNKELILFSMADL   700
 701  QRSIPSMVDGLKPGQRKILFVAFKKIARKEMKVAQLVGYVSLLSAYHHGE   750
 751  QSLASAIIGMAQDYVGSNNINLLLPNGQFGTRTSGGKDSASARYIFTKLS   800
 801  PVTRILFPKDDDLLLDYLNEDGQRIEPTWYMPIIPTVLVNGAEGIGTGWS   850
 851  TFIPNYNPREIVANVRRLLNGESMVPMDPWYRGFKGTIEKTASKEGGCTY   900
 901  TITGLYEEVDETTIRITELPIRRWNDDYKNFLQSLKTDNGAPFFQDVKAY   950
 951  NDEKSVDFDLILSEENMLAARQEGFLKKFKLTTTIATSNMHLFDKKGVIK  1000
1001  KYVTPEQILEEFFDLRFEYYEKRKETVVKNMEIELLKLENKARFILAVLS  1050
1051  GEIIVNKRKKADIVEDLRQKGFTPFPRKAESVEAAIAGAVDDDAAEEPEE  1100
1101  ILVDPESSSSYIPGSEYDYLLAMAIASLTIEKVEELLADRDKMIIAVADM  1150
1151  KKTTPKSLWLSDLESLDKELEKLDLKDAQVQQAIEAAQKKIRAKSGAAVK  1200
1201  VKRQAPKKPAPKKTTKKASESETTEASYSAMDTDNNVAEVVKPKARQGAK  1250
1251  KKASESETTEASHSAMDTDNNVAEVVKPKGRQGAKKKAPAAAKEVEEDEM  1300
1301  LDLAQRLAQYNFGSAPADSSKTAETSKAIAVDDDDDDVVVEVAPVKKGGR  1350
1351  KPAATKAAKPPAAPRKRGKQTVASTEVLAIGVSPEKKVRKMRSSPFNKKS  1400
1401  SSVMSRLADNKEEESSENVAGNSSSEKSGGDVSAISRPQRANRRKMTYVL  1450
1451  SDSESESANDSEFDDIEDDEDDE                             1473

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.)

Go back to the NucPred Home Page.