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

NucPred

Fetching Q6CJ38 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MPEVRDWRQLAKTRLEYELLTNELFHLWEFTSLVEYDPLFRNTSNSFKTF    50
  51  LQERGLDVESSLEQDDMKESNASRRLKRRNVISGTADSSSDKNNIWGQVM   100
 101  PLVDQEYSELQEKLRASVCGRRGRKRTQQVASVPAESEEDVAVPRPNKKR   150
 151  QTVVTAQGSAQNKLNTPVVSSPKKSLKQTADKKSKLNKRDSSTNDISVES   200
 201  EDPPVKDITNTGQGKSKARLKSSKAKSKKRAVKSQTELVRKQSPEIKNES   250
 251  KRTKADPTHTNDDGNDNRKTNNKSKNIINNNESGLKTSLNTTGDIIDDEE   300
 301  YYFTSSSEDDDNEKPRTALQKKSLPNRLKVKLHVNAPRQTITNPLHVLKP   350
 351  EYADVHSFLQSYKSLDEDVSLEEYDSYIKEQRKTAKLIRIGFERGAIKYD   400
 401  PQTDSLQSLSLRDVMPPSNAAEPISVYYKEQSKHTFQDHLVNQGIVLSKS   450
 451  FQDSRRSQIAKARRVAQIIESHFKHIAGAEERKLKEEEKRKKNLARFAMQ   500
 501  AVKKRWTMAEKAYKVLKKDELDQLERIQGKQHLTEMLEQSTQLLGAQLNQ   550
 551  LDSCTYPSEASDASSEFSANEESDGNSDIDDEMMSTSSCDSDKEGNTERI   600
 601  GNDMELSVEELRSKYAQLNKINDFGNETSKSAADESIFDEASDSVSDSME   650
 651  DSLSSSESETEDADASAQEDTPGLSALLGNIDENEEDVEADVNFDADSSS   700
 701  DDGLDGDSSGAENNSKTEELPSPPKSDNELKDEKAETTESVTSPAAADPL   750
 751  AVSDVPVPSLLRGTLRIYQKQGLNWLASLYNNKTNGILADEMGLGKTIQT   800
 801  ISLLAYLACEKENWGPHLIVVPTSVLLNWEMEFKRFAPGFKVLTYYGSPQ   850
 851  QRREKRKGWNKPDAFHVCITSYQLVVHDQHSFKRKKWQYMILDEAHNIKN   900
 901  FRSTRWQALLNFNTERRLLLTGTPLQNNLAELWSLLYFLMPQTALENGKV   950
 951  SGFADLDAFQQWFGRPVDKIVETGENYEQDEETKKTVSKLHQVLRPYLLR  1000
1001  RLKADVEKQMPGKYEHIIYCRLSKRQRFLYDDFMSRAQTKETLASGNFMS  1050
1051  IINCLMQLRKVCNHPDLFEVRPILTSFCIEDSVSKSYCDLNNYVYNRLHE  1100
1101  NQFETSVDLSNLNFQFTSNDKTLSTNHSEKISELQCVQPILKEISRLKQL  1150
1151  NENDSPVTQPDFQDLNQYYSYAKHNKINEIIGQLEHLNYMNNLRCNRRPM  1200
1201  YGSNIVKLLTVGPKKFIDCELTQESIKPLETRLLEGKETIEKFAVITPPV  1250
1251  VTLDIRERAVGVDDNNKRFEESVKHHLVSQMRSLENPFHQLQTKLSVAFP  1300
1301  DKSLLQYDCGKLQKLAQLLQNLKDNGHRALIFTQMTKVLDILEQFLNFHG  1350
1351  YLYMRLDGATKIEDRQILTERFNSDPRITVFILSSRSGGLGINLTGADTV  1400
1401  IFYDSDWNPAMDKQCQDRCHRIGQTRDVHIYRFVSDHTIESNILKKANQK  1450
1451  RHLDNVVIQTGDFTTDYFTKLSVKDLLGAEAPEDIPDDKPLLQDQKNLNK  1500
1501  LLAQAEDEDDAKAAKSALREVNVDNEDFQEGSVAAQDGNSDNENNEDSED  1550
1551  EYGGTSHVEEYMVRFIANGFYY                              1572

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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