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

NucPred

Fetching P56715 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MSDTPSTGFSIIHPTSSEGQVPPPRHLSLTHPVVAKRISFYKSGDPQFGG    50
  51  VRVVVNPRSFKSFDALLDNLSRKVPLPFGVRNISTPRGRHSITRLEELED   100
 101  GESYLCSHGRKVQPVDLDKARRRPRPWLSSRAISAHSPPHPVAVAAPGMP   150
 151  RPPRSLVVFRNGDPKTRRAVLLSRRVTQSFEAFLQHLTEVMQRPVVKLYA   200
 201  TDGRRVPSLQAVILSSGAVVAAGREPFKPGNYDIQKYLLPARLPGISQRV   250
 251  YPKGNAKSESRKISTHMSSSSRSQIYSVSSEKTHNNDCYLDYSFVPEKYL   300
 301  ALEKNDSQNLPIYPSEDDIEKSIIFNQDGTMTVEMKVRFRIKEEETIKWT   350
 351  TTVSKTGPSNNDEKSEMSFPGRTESRSSGLKLAACSFSADVSPMERSSNQ   400
 401  EGSLAEEINIQMTDQVAETCSSASWENATVDTDIIQGTQDQAKHRFYRPP   450
 451  TPGLRRVRQKKSVIGSVTLVSETEVQEKMIGQFSYSEERESGENKSEYHM   500
 501  FTHSCSKMSSVSNKPVLVQINNNDQMEESSLERKKENSLLKSSAISAGVI   550
 551  EITSQKMLEMSHNNGLPSTISNNSIVEEDVVDCVVLDNKTGIKNFKTYGN   600
 601  TNDRFSPISADATHFSSNNSGTDKNISEAPASEASSTVTARIDRLINEFA   650
 651  QCGLTKLPKNEKKILSSVASKKKKKSRQQAINSRYQDGQLATKGILNKNE   700
 701  RINTKGRITKEMIVQDSDSPLKGGILCEEDLQKSDTVIESNTFCSKSNLN   750
 751  STISKNFHRNKLNTTQNSKVQGLLTKRKSRSLNKISLGAPKKREIGQRDK   800
 801  VFPHNESKYCKSTFENKSLFHVFNILEQKPKDFYAPQSQAEVASGYLRGM   850
 851  AKKSLVSKVTDSHITLKSQKKRKGDKVKASAILSKQHATTRANSLASLKK   900
 901  PDFPEAIAHHSIQNYIQSWLQNINPYPTLKPIKSAPVCRNETSVVNCSNN   950
 951  SFSGNDPHTNSGKISNFVMESNKHITKIAGLTGDNLCKEGDKSFIANDTG  1000
1001  EEDLHETQVGSLNDAYLVPLHEHCTLSQSAINDHNTKSHIAAEKSGPEKK  1050
1051  LVYQEINLARKRQSVEAAIQVDPIEEETPKDLLPVLMLHQLQASVPGIHK  1100
1101  TQNGVVQMPGSLAGVPFHSAICNSSTNLLLAWLLVLNLKGSMNSFCQVDA  1150
1151  HKATNKSSETLALLEILKHIAITEEADDLKAAVANLVESTTSHFGLSEKE  1200
1201  QDMVPIDLSANCSTVNIQSVPKCSENERTQGISSLDGGCSASEACAPEVC  1250
1251  VLEVTCSPCEMCTVNKAYSPKETCNPSDTFFPSDGYGVDQTSMNKACFLG  1300
1301  EVCSLTDTVFSDKACAQKENHTYEGACPIDETYVPVNVCNTIDFLNSKEN  1350
1351  TYTDNLDSTEELERGDDIQKDLNILTDPEYKNGFNTLVSHQNVSNLSSCG  1400
1401  LCLSEKEAELDKKHSSLDDFENCSLRKFQDENAYTSFDMEEPRTSEEPGS  1450
1451  ITNSMTSSERNISELESFEELENHDTDIFNTVVNGGEQATEELIQEEVEA  1500
1501  SKTLELIDISSKNIMEEKRMNGIIYEIISKRLATPPSLDFCYDSKQNSEK  1550
1551  ETNEGETKMVKMMVKTMETGSYSESSPDLKKCIKSPVTSDWSDYRPDSDS  1600
1601  EQPYKTSSDDPNDSGELTQEKEYNIGFVKRAIEKLYGKADIIKPSFFPGS  1650
1651  TRKSQVCPYNSVEFQCSRKASLYDSEGQSFGSSEQVSSSSSMLQEFQEER  1700
1701  QDKCDVSAVRDNYCRGDIVEPGTKQNDDSRILTDIEEGVLIDKGKWLLKE  1750
1751  NHLLRMSSENPGMCGNADTTSVDTLLDNNSSEVPYSHFGNLAPGPTMDEL  1800
1801  SSSELEELTQPLELKCNYFNMPHGSDSEPFHEDLLDVRNETCAKERIANH  1850
1851  HTEEKGSHQSERVCTSVTHSFISAGNKVYPVSDDAIKNQPLPGSNMIHGT  1900
1901  LQEADSLDKLYALCGQHCPILTVIIQPMNEEDRGFAYRKESDIENFLGFY  1950
1951  LWMKIHPYLLQTDKNVFREENNKASMRQNLIDNAIGDIFDQFYFSNTFDL  2000
2001  MGKRRKQKRINFLGLEEEGNLKKFQPDLKERFCMNFLHTSLLVVGNVDSN  2050
2051  TQDLSGQTNEIFKAVDENNNLLNNRFQGSRTNLNQVVRENINCHYFFEML  2100
2101  GQACLLDICQVETSLNISNRNILELCMFEGENLFIWEEEDILNLTDLESS  2150
2151  REQEDL                                              2156

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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