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

NucPred

Fetching Q86UK0 from www.uniprot.org...

The NucPred score for your sequence is 0.82 (see score help below)

   1  MASLFHQLQILVWKNWLGVKRQPLWTLVLILWPVIIFIILAITRTKFPPT    50
  51  AKPTCYLAPRNLPSTGFFPFLQTLLCDTDSKCKDTPYGPQDLLRRKGIDD   100
 101  ALFKDSEILRKSSNLDKDSSLSFQSTQVPERRHASLATVFPSPSSDLEIP   150
 151  GTYTFNGSQVLARILGLEKLLKQNSTSEDIRRELCDSYSGYIVDDAFSWT   200
 201  FLGRNVFNKFCLSNMTLLESSLQELNKQFSQLSSDPNNQKIVFQEIVRML   250
 251  SFFSQVQEQKAVWQLLSSFPNVFQNDTSLSNLFDVLRKANSVLLVVQKVY   300
 301  PRFATNEGFRTLQKSVKHLLYTLDSPAQGDSDNITHVWNEDDGQTLSPSS   350
 351  LAAQLLILENFEDALLNISANSPYIPYLACVRNVTDSLARGSPENLRLLQ   400
 401  STIRFKKSFLRNGSYEDYFPPVPEVLKSKLSQLRNLTELLCESETFSLIE   450
 451  KSCQLSDMSFGSLCEESEFDLQLLEAAELGTEIAASLLYHDNVISKKVRD   500
 501  LLTGDPSKINLNMDQFLEQALQMNYLENITQLIPIIEAMLHVNNSADASE   550
 551  KPGQLLEMFKNVEELKEDLRRTTGMSNRTIDKLLAIPIPDNRAEIISQVF   600
 601  WLHSCDTNITTPKLEDAMKEFCNLSLSERSRQSYLIGLTLLHYLNIYNFT   650
 651  YKVFFPRKDQKPVEKMMELFIRLKEILNQMASGTHPLLDKMRSLKQMHLP   700
 701  RSVPLTQAMYRSNRMNTPQGSFSTISQALCSQGITTEYLTAMLPSSQRPK   750
 751  GNHTKDFLTYKLTKEQIASKYGIPINSTPFCFSLYKDIINMPAGPVIWAF   800
 801  LKPMLLGRILYAPYNPVTKAIMEKSNVTLRQLAELREKSQEWMDKSPLFM   850
 851  NSFHLLNQAIPMLQNTLRNPFVQVFVKFSVGLDAVELLKQIDELDILRLK   900
 901  LENNIDIIDQLNTLSSLTVNISSCVLYDRIQAAKTIDEMEREAKRLYKSN   950
 951  ELFGSVIFKLPSNRSWHRGYDSGNVFLPPVIKYTIRMSLKTAQTTRSLRT  1000
1001  KIWAPGPHNSPSHNQIYGRAFIYLQDSIERAIIELQTGRNSQEIAVQVQA  1050
1051  IPYPCFMKDNFLTSVSYSLPIVLMVAWVVFIAAFVKKLVYEKDLRLHEYM  1100
1101  KMMGVNSCSHFFAWLIESVGFLLVTIVILIIILKFGNILPKTNGFILFLY  1150
1151  FSDYSFSVIAMSYLISVFFNNTNIAALIGSLIYIIAFFPFIVLVTVENEL  1200
1201  SYVLKVFMSLLSPTAFSYASQYIARYEEQGIGLQWENMYTSPVQDDTTSF  1250
1251  GWLCCLILADSFIYFLIAWYVRNVFPGTYGMAAPWYFPILPSYWKERFGC  1300
1301  AEVKPEKSNGLMFTNIMMQNTNPSASPEYMFSSNIEPEPKDLTVGVALHG  1350
1351  VTKIYGSKVAVDNLNLNFYEGHITSLLGPNGAGKTTTISMLTGLFGASAG  1400
1401  TIFVYGKDIKTDLHTVRKNMGVCMQHDVLFSYLTTKEHLLLYGSIKVPHW  1450
1451  TKKQLHEEVKRTLKDTGLYSHRHKRVGTLSGGMKRKLSISIALIGGSRVV  1500
1501  ILDEPSTGVDPCSRRSIWDVISKNKTARTIILSTHHLDEAEVLSDRIAFL  1550
1551  EQGGLRCCGSPFYLKEAFGDGYHLTLTKKKSPNLNANAVCDTMAVTAMIQ  1600
1601  SHLPEAYLKEDIGGELVYVLPPFSTKVSGAYLSLLRALDNGMGDLNIGCY  1650
1651  GISDTTVEEVFLNLTKESQKNSAMSLEHLTQKKIGNSNANGISTPDDLSV  1700
1701  SSSNFTDRDDKILTRGERLDGFGLLLKKIMAILIKRFHHTRRNWKGLIAQ  1750
1751  VILPIVFVTTAMGLGTLRNSSNSYPEIQISPSLYGTSEQTAFYANYHPST  1800
1801  EALVSAMWDFPGIDNMCLNTSDLQCLNKDSLEKWNTSGEPITNFGVCSCS  1850
1851  ENVQECPKFNYSPPHRRTYSSQVIYNLTGQRVENYLISTANEFVQKRYGG  1900
1901  WSFGLPLTKDLRFDITGVPANRTLAKVWYDPEGYHSLPAYLNSLNNFLLR  1950
1951  VNMSKYDAARHGIIMYSHPYPGVQDQEQATISSLIDILVALSILMGYSVT  2000
2001  TASFVTYVVREHQTKAKQLQHISGIGVTCYWVTNFIYDMVFYLVPVAFSI  2050
2051  GIIAIFKLPAFYSENNLGAVSLLLLLFGYATFSWMYLLAGLFHETGMAFI  2100
2101  TYVCVNLFFGINSIVSLSVVYFLSKEKPNDPTLELISETLKRIFLIFPQF  2150
2151  CFGYGLIELSQQQSVLDFLKAYGVEYPNETFEMNKLGAMFVALVSQGTMF  2200
2201  FSLRLLINESLIKKLRLFFRKFNSSHVRETIDEDEDVRAERLRVESGAAE  2250
2251  FDLVQLYCLTKTYQLIHKKIIAVNNISIGIPAGECFGLLGVNGAGKTTIF  2300
2301  KMLTGDIIPSSGNILIRNKTGSLGHVDSHSSLVGYCPQEDALDDLVTVEE  2350
2351  HLYFYARVHGIPEKDIKETVHKLLRRLHLMPFKDRATSMCSYGTKRKLST  2400
2401  ALALIGKPSILLLDEPSSGMDPKSKRHLWKIISEEVQNKCSVILTSHSME  2450
2451  ECEALCTRLAIMVNGKFQCIGSLQHIKSRFGRGFTVKVHLKNNKVTMETL  2500
2501  TKFMQLHFPKTYLKDQHLSMLEYHVPVTAGGVANIFDLLETNKTALNITN  2550
2551  FLVSQTTLEEVFINFAKDQKSYETADTSSQGSTISVDSQDDQMES       2595

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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