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

NucPred

Fetching Q96HP0 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MAASERRAFAHKINRTVAAEVRKQVSRERSGSPHSSRRCSSSLGVPLTEV    50
  51  VEPLDFEDVLLSRPPDAEPGPLRDLVEFPADDLELLLQPRECRTTEPGIP   100
 101  KDEKLDAQVRAAVEMYIEDWVIVHRRYQYLSAAYSPVTTDTQRERQKGLP   150
 151  RQVFEQDASGDERSGPEDSNDSRRGSGSPEDTPRSSGASSIFDLRNLAAD   200
 201  SLLPSLLERAAPEDVDRRNETLRRQHRPPALLTLYPAPDEDEAVERCSRP   250
 251  EPPREHFGQRILVKCLSLKFEIEIEPIFGILALYDVREKKKISENFYFDL   300
 301  NSDSMKGLLRAHGTHPAISTLARSAIFSVTYPSPDIFLVIKLEKVLQQGD   350
 351  ISECCEPYMVLKEVDTAKNKEKLEKLRLAAEQFCTRLGRYRMPFAWTAVH   400
 401  LANIVSSAGQLDRDSDSEGERRPAWTDRRRRGPQDRASSGDDACSFSGFR   450
 451  PATLTVTNFFKQEAERLSDEDLFKFLADMRRPSSLLRRLRPVTAQLKIDI   500
 501  SPAPENPHFCLSPELLHIKPYPDPRGRPTKEILEFPAREVYAPHTSYRNL   550
 551  LYVYPHSLNFSSRQGSVRNLAVRVQYMTGEDPSQALPVIFGKSSCSEFTR   600
 601  EAFTPVVYHNKSPEFYEEFKLHLPACVTENHHLLFTFYHVSCQPRPGTAL   650
 651  ETPVGFTWIPLLQHGRLRTGPFCLPVSVDQPPPSYSVLTPDVALPGMRWV   700
 701  DGHKGVFSVELTAVSSVHPQDPYLDKFFTLVHVLEEGAFPFRLKDTVLSE   750
 751  GNVEQELRASLAALRLASPEPLVAFSHHVLDKLVRLVIRPPIISGQIVNL   800
 801  GRGAFEAMAHVVSLVHRSLEAAQDARGHCPQLAAYVHYAFRLPGTEPSLP   850
 851  DGAPPVTVQAATLARGSGRPASLYLARSKSISSSNPDLAVAPGSVDDEVS   900
 901  RILASKLLHEELALQWVVSSSAVREAILQHAWFFFQLMVKSMALHLLLGQ   950
 951  RLDTPRKLRFPGRFLDDITALVGSVGLEVITRVHKDVELAEHLNASLAFF  1000
1001  LSDLLSLVDRGFVFSLVRAHYKQVATRLQSSPNPAALLTLRMEFTRILCS  1050
1051  HEHYVTLNLPCCPLSPPASPSPSVSSTTSQSSTFSSQAPDPKVTSMFELS  1100
1101  GPFRQQHFLAGLLLTELALALEPEAEGAFLLHKKAISAVHSLLCGHDTDP  1150
1151  RYAEATVKARVAELYLPLLSIARDTLPRLHDFAEGPGQRSRLASMLDSDT  1200
1201  EGEGDIAGTINPSVAMAIAGGPLAPGSRASISQGPPTASRAGCALSAESS  1250
1251  RTLLACVLWVLKNTEPALLQRWATDLTLPQLGRLLDLLYLCLAAFEYKGK  1300
1301  KAFERINSLTFKKSLDMKARLEEAILGTIGARQEMVRRSRERSPFGNPEN  1350
1351  VRWRKSVTHWKQTSDRVDKTKDEMEHEALVEGNLATEASLVVLDTLEIIV  1400
1401  QTVMLSEARESVLGAVLKVVLYSLGSAQSALFLQHGLATQRALVSKFPEL  1450
1451  LFEEDTELCADLCLRLLRHCGSRISTIRTHASASLYLLMRQNFEIGHNFA  1500
1501  RVKMQVTMSLSSLVGTTQNFSEEHLRRSLKTILTYAEEDMGLRDSTFAEQ  1550
1551  VQDLMFNLHMILTDTVKMKEHQEDPEMLIDLMYRIARGYQGSPDLRLTWL  1600
1601  QNMAGKHAELGNHAEAAQCMVHAAALVAEYLALLEDHRHLPVGCVSFQNI  1650
1651  SSNVLEESAISDDILSPDEEGFCSGKHFTELGLVGLLEQAAGYFTMGGLY  1700
1701  EAVNEVYKNLIPILEAHRDYKKLAAVHGKLQEAFTKIMHQSSGWERVFGT  1750
1751  YFRVGFYGAHFGDLDEQEFVYKEPSITKLAEISHRLEEFYTERFGDDVVE  1800
1801  IIKDSNPVDKSKLDSQKAYIQITYVEPYFDTYELKDRVTYFDRNYGLRTF  1850
1851  LFCTPFTPDGRAHGELPEQHKRKTLLSTDHAFPYIKTRIRVCHREETVLT  1900
1901  PVEVAIEDMQKKTRELAFATEQDPPDAKMLQMVLQGSVGPTVNQGPLEVA  1950
1951  QVFLAEIPEDPKLFRHHNKLRLCFKDFCKKCEDALRKNKALIGPDQKEYH  2000
2001  RELERNYCRLREALQPLLTQRLPQLMAPTPPGLRNSLNRASFRKADL     2047

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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