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

NucPred

Fetching Q62656 from www.uniprot.org...

The NucPred score for your sequence is 0.61 (see score help below)

   1  MRILQSFLACVQLLCVCRLDWAYGYYRQQRKLVEEIGWSYTGALNQKNWG    50
  51  KKYPICNSPKQSPINIDEDLTQVNVNLKKLKFQGWEKPSLENTFIHNTGK   100
 101  TVEINLTNDYYLSGGLSEKVFKASKMTFHWGKCNVSSEGSEHSLEGQKFP   150
 151  LEMQIYCFDADRFSSFEETVKGKGRLRALSILFEIGVEENLDYKAIIDGT   200
 201  ESVSRFGKQAALDPFILQNLLPNSTDKYYIYNGSLTSPPCTDTVEWIVFK   250
 251  DTVSISESQLAVFCEVLTMQQSGYVMLMDYLQNNFREQQYKFSRQVFSSY   300
 301  TGKEEIHEAVCSSEPENVQADPENYTSLLITWERPRVVYDTMIEKFAVLY   350
 351  QPLEGNDQTKHEFLTDGYQDLGAILNNLIPNMSYVLQIVAICSNGLYGKY   400
 401  SDQLIVDMPTEDAELDLFPELIGTEEIIKEENYGKGNEEDTGLNPGRDSA   450
 451  TNQIRKKEPQVSTTTHYNHMGTKYNEAKTNRSPTRGSEFSGKSDVLNTSL   500
 501  NPTSQQVAEFNPEREMSLPSQIGTNLPPHSVEGTSASLNSGSKTLLVFPQ   550
 551  MNLSGTAESLNMVSITEYKEVSADLSEEENLLTDFKLDSGADDSSGSSPA   600
 601  SSTVPFSTDNLSHGYTSSSDTPEAVTYDVLRPESTRNALEDSAPSGSEES   650
 651  LKDPSLEGSVWFPGSTDLTTQSETGSGREGFLQVNSTDFQVDESRETTET   700
 701  FSPDATASRGPSVTDMEMPHYSTFAYPPTEVTSHAFTPSSRPLDLAPTSN   750
 751  ILHSQTTQPVYNGETPLQPSYSSEVFPLVTPLLLDNQTLNTTPAASSSDS   800
 801  ALHATPVFPSVGVSFDSILSSYDDAPLLPFSSASFSSDLFHHLHTVSQTL   850
 851  PQVTSAAERDELSLHASLLVAGGDLLLEPSLVQYSDVMSHQVTIHAASDT   900
 901  LEFGSESAVLYKTSMVSQIESPSSDVVMHAYSSGPETSYAIEGSHHVLTV   950
 951  SSSSAIPVHDSVGVADQGSLLINPSHISLPESSFITPTASLLQLPPALSG  1000
1001  DGEWSGASSDSELLLPDTDGLRTLNMSSPVSVADFTYTTSVSGDDIKPLS  1050
1051  KGEMMYGNETELKMSSFSDMAYPSKSTVVPKMSDIVNKWSESLKETSVSV  1100
1101  SSINSVFTESLVYPITKVFDQEISRVPEIIFPVKPTHTASQASGDTWLKP  1150
1151  GLSTNSEPALSDTASSEVSHPSTQPLLYEAASPFNTEALLQPSFPASDVD  1200
1201  TLLKTALPSGPRDPVLTETPMVEQSSSSVSLPLASESASSKSTLHFTSVP  1250
1251  VLNMSPSDVHPTSLQRLTVPHSREEYFEQGLLKSKSPQQVLPSLHSHDEF  1300
1301  FQTAHLDISQAYPPKGRHAFATPILSINEPQNTLINRLVYSEDIFMHPEI  1350
1351  SITDKALTGLPTTVSDVLIATDHSVPLGSGPISMTTVSPNRDDSVTTTKL  1400
1401  LLPSKATSKPTHSARSDADLVGGGEDGDDYDDDDYDDIDSDRFPVNKCMS  1450
1451  CSPYRESQEKVMNDSDTQESSLVDQSDPISHLLSENTEEENGGTGVTRVD  1500
1501  KSPDKSPPPSMLPQKHNDGREDRDIQMGSAVLPHTPGSKAWAVLTSDEES  1550
1551  GSGQGTSDSLNDNETSTDFSFPDVNEKDADGVLEADDTGIAPGSPRSSTP  1600
1601  SVTSGHSGVSNSSEAEASNSSHESRIGLAEGLESEKKAVIPLVIVSALTF  1650
1651  ICLVVLVGILIYWRKCFQTAHFYLEDNTSPRVISTPPTPIFPISDDIGAI  1700
1701  PIKHFPKHVADLHASNGFTEEFETLKEFYQEVQSCTVDLGITADSSNHPD  1750
1751  NKHKNRYVNIVAYDHSRVKLTQLAEKDGKLTDYINANYVDGYNRPKAYIA  1800
1801  AQGPLKSTAEDFWRMIWEHNVEVIVMITNLVEKGRRKCDQYWPTDGSEEY  1850
1851  GSFLVNQKNVQVLAYYTVRNFTLRNTKIKKGSQKGRSSGRLVTQYHYTQW  1900
1901  PDMGVPEYSLPVLAFVRKTAQAKRHAVGPVVVHCSAGVGRTGTYIVLDSM  1950
1951  LQQIQHEGTVNIFGFLKHIRSQRNYLVQTEEQYVFIHDTLVEAILSKETE  2000
2001  VPDSHIHSYVNTLLIPGPSGKTKLEKQFQLLSQSNILQSDYSTALKQCNR  2050
2051  EKNRTSSIIPVERSRVGISSLSGEGTDYINASYIMGYYQSNEFIITQHPL  2100
2101  LHTIKDFWRMIWDHNAQLVVMIPDGQNMAEDEFVYWPNKDEPINCESFKV  2150
2151  TLMSEEHKCLSNEEKLIVQDFILEATQDDYVLEVRHFQCPKWPNPDSPIS  2200
2201  KTFELISIIKEEAANRDGPMIVHDEHGGVTAGTFCALTTLMHQLEKENSM  2250
2251  DVYQVAKMINLMRPGVFTDIEQYQFLYKVVLSLVSTRQEENPSTSLDSNG  2300
2301  AALPDGNIAESLESLV                                    2316

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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