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

NucPred

Fetching Q8MJ03 from www.uniprot.org...

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

   1  MSDTPSTGFSMIHPTSSEGQVPSPRHLSLTHPVVAKRISFYKSGDPQFGG    50
  51  VRVVVNPRSFKSFDALLDNLSRKVPLPFGVRNISTPRGRHSITRLEELED   100
 101  GESYLCSHGRKVQPVDLDKARRRPRPWLSSRAVSTHAPPHSVAAPGMPRA   150
 151  PRSLVVFRNGDPKTRRAVLLSRKVTQSFEAFLQHLTEVMQRPVVKLYATD   200
 201  GRRVPSLQAVILSSGAVVAAGREPFKPGNYDIQKYLLPARLPGISQRVYP   250
 251  KGNGKSESRKISTHMASSSRSQIYSVSSEKTHNNDCYLDYSFVPENYLAL   300
 301  EKNDSQNLPIYPSEDDVEKSIIFNQDGTMTVEMKVRFRIKEEETIKWTTT   350
 351  VSKTGPSNNDEKSEMSFPGRTESRSSGLKLAACSFSADVSPTERSSNQEG   400
 401  SLAEEINIQMTDQEAETCSSASWENATVDTDIIQGTQDQAKHRFYRPPTP   450
 451  GLRRVRQKKSVIGSVTLVSETEVQEKMIGQFSYSEERESGENKSEYHMFT   500
 501  HSCSKMSSVSNKPVLVQINNSDQMEESSLERKKENRLLKSSAISAGVIEI   550
 551  TSQKMLELSHNNGLPSTISNNSIVEEDVVDSVVSDNKTGIKNLRTYGNTS   600
 601  DRFSPVSADATHFSSNKSRADKNISEAPASVASSTVTARIDRLINEFAQC   650
 651  GLTKLPKTEKKILSSVASKKKKKKSQQQAINSRYQDGQLATTGILNKNER   700
 701  INAGGRITKEMILQDSDSPLKGGVLCEEDLRTSETVIESNTFCSKSNLNP   750
 751  MISKNFHRNKLNTTQNSKVQGLLTKRKSRPLRKISLGTPKKREIGQGDKV   800
 801  FPHNESKYSKSTCENKSLFHVFNLLEQKPKHFSGPRSQAEVASGYLRGMA   850
 851  KKSLVSKVTDSHITLKSQKKQKGDKLKASAILSKQHAATRANSLASLKKP   900
 901  DFPEDIAHPSVQTYIQNWLHNINPYPTLKPIKSAPVCKNEISVVNCNNSF   950
 951  SGNDPHTSSGKINNFVMESNKHITKIASLTGDNLCKEGDKSFIANDTGED  1000
1001  LCETQVGSLNDAYLVSLHEHCTSPQSAINDRNTKSRISPEKSGPEINLVY  1050
1051  QEINLAKKRQSVEAAIQVDPIEEDTPKDLLPVLMLHQLQASVPSTPKTQN  1100
1101  GVVRMPGSLADVSFPSAICNSSTNLLLAWLLVLNLKGSMNSFCQGDAHKT  1150
1151  TNKSSETLALLEILKHIAITEEADDLKAAVANLVESTTNHFGLSEKEQDT  1200
1201  VPIDLSANCSIVNIQSVPKCNENEGTQGIFSFDGGCSAVEACAPEVCVLE  1250
1251  LTYPPREVCTVNKAYVPKETCNLSDTFFPSDGYTVDRTSMNKACFVGEVC  1300
1301  SLTDTVFSDKACAQKENHIYEGACATDETCVPVDVCNTTGFLNSKQNTYT  1350
1351  DNLESTEELERGDDVQKDLNILTDPEYKNGFNTLVSHQNVSNLSPCGLCV  1400
1401  SEEAEFDKKHSSADDFKNCSLNLFQDKNAYTSFDMEEPRTSEEPGSVTNS  1450
1451  VTSSERNISELESFEELENQDTDIFNTEINVGEKATEEFIQEEIEASKTL  1500
1501  ELLDISSKNIMVEERKNGIIYETISKRLATPPSLVFCYDSKQNNEKETNE  1550
1551  GETNMVKMMVKSMETGSYSESSPDMKKCIKSPVTSDWSDYRPDSDSEQAY  1600
1601  KTSSDDPNDSGELEKEYNIGFVKRAIEKLYGKADIIKPSFFPGSTRKSQV  1650
1651  CPYNSVEFQCTRRASLYDSEGQSFGSSERVSSSSPVLQEFQEEGQDKCDI  1700
1701  NHVRNNYCGGDIVEPGTKENDHSRVLTDIEEGVLIDKGKWLLKENHLLRM  1750
1751  SYENPGVCGNADTTSVDTLLDNNSSEVPYSHFGNLAPGPTMDELSSSELE  1800
1801  ELTQPLELKCNYFKMPHGSDSEPFHEDLLGVHNETCDKERIANHHTEEKC  1850
1851  PHQSERICTSVTHSFMSAGNKVYPVSDDAIKNQPLPGSNMIHGTLQETDS  1900
1901  LDKLYALCGQHCPILTVTIQPVNEEDRGFAYRKESDIENFLGFYLWMKIH  1950
1951  PYLLQTDKNMFREENNKASMRKNLINNATGDIFDEFYFSNIFDLMDKRRK  2000
2001  QKRINFLELQEAGNLKKFQPDLKERFCMYFLHTSSLVVGNMNSNTQDLSS  2050
2051  QTNEIFKAVDENNNLLNNRFQGSRTNLNQVVRENISRYFFEMLGQACLLD  2100
2101  ICQVETSLNISNRNILEELCMFEDENIFIWEEEDILNLTDLESSREQDL   2149

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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