NucPred on Proteomes

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

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q9H367 UniProt NPD GO	CN057_HUMAN	Uncharacterized protein C14orf57	0.26	-	mit	0					127
Q6P656 UniProt NPD GO	CO026_HUMAN	Uncharacterized protein C15orf26	0.26	-	cyt	0					301
Q9NYP8 UniProt NPD GO	CU062_HUMAN	Uncharacterized protein C21orf62 (B37)	0.26	-	exc	0					247
Q5JPI3 UniProt NPD GO	CC038_HUMAN	Uncharacterized protein C3orf38	0.26	-	cyt	0					329
Q3TTL0 UniProt NPD GO	CC038_MOUSE	Uncharacterized protein C3orf38 homolog	0.26	-	cyt	0					348
Q8CE93 UniProt NPD GO	CF078_MOUSE	Uncharacterized protein C6orf78 homolog	0.26	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				315
P39564 UniProt NPD GO	YAN8_YEAST	Uncharacterized protein YAR068W	0.26	-	nuc	0					161
P37263 UniProt NPD GO	YC16_YEAST	Uncharacterized protein YCR087C-A	0.26	-	nuc	0		nucleolus [IDA]			153
Q3E7Z7 UniProt NPD GO	YD003_YEAST	Uncharacterized protein YDR003W-A	0.26	-	nuc	0					40
P36114 UniProt NPD GO	YKZ8_YEAST	Uncharacterized protein YKR018C	0.26	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			725
Q99325 UniProt NPD GO	YO152_YEAST	Uncharacterized protein YOR152C precursor	0.26	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)	membrane fraction [IDA]			256
P56575 UniProt NPD GO	UH09_RAT	Unknown protein from 2D-PAGE of heart tissue (Spot P9) (Fragment)	0.26	-		0					8
P46201 UniProt NPD GO	UTMP_BOVIN	Uterine milk protein precursor (UTMP)	0.26	-	end	1 *					459
Q2HJD1 UniProt NPD GO	LMA2L_BOVIN	VIP36-like protein precursor (Lectin, mannose-binding 2-like) (LMAN2-like protein)	0.26	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein. Predomin ...				348
P59481 UniProt NPD GO	LMA2L_MOUSE	VIP36-like protein precursor (Lectin, mannose-binding 2-like) (LMAN2-like protein)	0.26	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	endoplasmic reticulum membrane [ISS] ER to Golgi transport vesicle [ISS] Golgi apparatus [ISS] integral to membrane [ISS]			347
Q9SZH0 UniProt NPD GO	VATG3_ARATH	Vacuolar ATP synthase subunit G 3 (EC 3.6.3.14) (V-ATPase G subunit 3) (Vacuolar proton pump G subun ...	0.26	-	nuc	0					108
Q9C0U3 UniProt NPD GO	YEAJ_SCHPO	Very hypothetical protein CUNK4.19 in chromosome I	0.26	-	mit	0					109
Q04502 UniProt NPD GO	YMI9_YEAST	Very hypothetical protein YML089C	0.26	-	cyt	0					122
P23763 UniProt NPD GO	VAMP1_HUMAN	Vesicle-associated membrane protein 1 (VAMP-1) (Synaptobrevin-1)	0.26	-	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass type IV membrane protein. Neuronal synaptic ...	integral to plasma membrane [TAS]	185880		118
P81721 UniProt NPD GO	VACHT_TORCA	Vesicular acetylcholine transporter (VAChT) (TorVAChT)	0.26	-	end	10 *	Membrane; multi-pass membrane protein				515
P42660 UniProt NPD GO	VCP_AEDAE	Vitellogenic carboxypeptidase precursor (EC 3.4.16.-)	0.26	-	end	0					471
O54929 UniProt NPD GO	WSB2_MOUSE	WD repeat and SOCS box-containing protein 2 (WSB-2) (SOCS box-containing WD protein SWiP-2)	0.26	-	cyt	0					404
Q5MNZ9 UniProt NPD GO	WIPI1_HUMAN	WD repeat domain phosphoinositide-interacting protein 1 (WIPI-1) (WD40 repeat protein interacting wi ...	0.26	-	nuc	0	Trans elements of the Golgi and peripheral endosomes. Dynamically cycles through these compartments ...		609224		446
Q7ZWU5 UniProt NPD GO	WIPI2_XENLA	WD repeat domain phosphoinositide-interacting protein 2 (WIPI-2)	0.26	-	nuc	0					435
Q499N3 UniProt NPD GO	WDR18_RAT	WD repeat protein 18	0.26	-	cyt	0					431
Q4R2Z6 UniProt NPD GO	WDR48_MACFA	WD repeat protein 48	0.26	-	nuc	0	Lysosome (By similarity)				622
P01401 UniProt NPD GO	TXW11_NAJHH	Weak toxin CM-11	0.26	-	nuc	0	Secreted protein				65
Q9SIT6 UniProt NPD GO	WBC5_ARATH	White-brown complex homolog protein 5	0.26	-	end	6	Membrane; multi-pass membrane protein (By similarity)				649
Q5GH76 UniProt NPD GO	XKR4_HUMAN	XK-related protein 4	0.26	-	end	10	Membrane; multi-pass membrane protein (Potential)				650
Q49LS4 UniProt NPD GO	XKR4_PANTR	XK-related protein 4	0.26	-	end	10	Membrane; multi-pass membrane protein (Potential)				650
P10351 UniProt NPD GO	XDH_DROME	Xanthine dehydrogenase (EC 1.17.1.4) (XD) (Protein rosy locus)	0.26	-	cyt	0	Peroxisome				1335
Q41638 UniProt NPD GO	XTHA_PHAAN	Xyloglucan endotransglucosylase/hydrolase protein A precursor (EC 2.4.1.207) (VaXTH1)	0.26	-	exc	0	Secreted protein; extracellular space; apoplast (Probable)				292
Q5XH48 UniProt NPD GO	YJDC_XENLA	YjeF domain-containing protein 1	0.26	-	nuc	0					505
Q6ZSS3 UniProt NPD GO	ZN621_HUMAN	Zinc finger protein 621	0.26	-	nuc	0	Nucleus (Potential)				439
Q7TM96 UniProt NPD GO	ZN622_RAT	Zinc finger protein 622 (Liver regeneration-related protein LRRG121)	0.26	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				386
Q8BQN6 UniProt NPD GO	OZF_MOUSE	Zinc finger protein OZF (Only zinc finger protein) (Zinc finger protein 146)	0.26	-	nuc	0	Nucleus (By similarity)				292
Q21180 UniProt NPD GO	NAS16_CAEEL	Zinc metalloproteinase nas-16 precursor (EC 3.4.24.21) (Nematode astacin 16)	0.26	-	nuc	0	Secreted protein (Potential)				451
P53849 UniProt NPD GO	GIS2_YEAST	Zinc-finger protein GIS2	0.26	-	nuc	0	Cytoplasm	cytoplasm [IDA]			153
O54767 UniProt NPD GO	ZP2_RAT	Zona pellucida sperm-binding protein 2 precursor (Zona pellucida glycoprotein ZP2) (Zona pellucida p ...	0.26	-	nuc	2 *	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				695
O13318 UniProt NPD GO	PHR2_CANAL	pH-responsive protein 2 precursor (pH-regulated protein 2)	0.26	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor (Potential)				546
Q00257 UniProt NPD GO	1A12_CUCMA	1-aminocyclopropane-1-carboxylate synthase CMA101 (EC 4.4.1.14) (ACC synthase) (S-adenosyl-L-methion ...	0.25	-	cyt	0					475
P17048 UniProt NPD GO	PRO2_ORYSA	13 kDa prolamin precursor	0.25	-	vac	0	In rice prolamin accumulates as type I protein body, which originates directly from the endoplasmic ...				156
Q6UFZ3 UniProt NPD GO	143G1_ONCMY	14-3-3 protein gamma-1 (Protein 14-3-3G1)	0.25	-	nuc	0	Cytoplasm (By similarity)				247
Q3SZI4 UniProt NPD GO	1433T_BOVIN	14-3-3 protein theta	0.25	-	nuc	0	Cytoplasm (By similarity)				245
Q5RFJ2 UniProt NPD GO	1433T_PONPY	14-3-3 protein theta	0.25	-	nuc	0	Cytoplasm (By similarity)				245
Q52M98 UniProt NPD GO	1433T_XENLA	14-3-3 protein theta	0.25	-	nuc	0	Cytoplasm (By similarity)				245
P68254 UniProt NPD GO	1433T_MOUSE	14-3-3 protein theta (14-3-3 protein tau)	0.25	-	nuc	0	Cytoplasm				245
Q6Q6X0 UniProt NPD GO	1433T_RABIT	14-3-3 protein theta (14-3-3 protein tau)	0.25	-	nuc	0	Cytoplasm (By similarity)				245
P68255 UniProt NPD GO	1433T_RAT	14-3-3 protein theta (14-3-3 protein tau)	0.25	-	nuc	0	Cytoplasm				245
P27348 UniProt NPD GO	1433T_HUMAN	14-3-3 protein theta (14-3-3 protein tau) (14-3-3 protein T-cell) (HS1 protein)	0.25	-	nuc	0	Cytoplasm. In neurons, axonally transported to the nerve terminals		609009	2BTP	245

You are viewing entries 44801 to 44850 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

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.)

Go back to the NucPred Home Page.