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
Q9MAB9 UniProt NPD GO	Y3105_ARATH	Protein At3g01050	0.02	-	nuc	0				1SE9	117
Q8RW98 UniProt NPD GO	BRK1_MAIZE	Protein BRICK1	0.02	-	cyt	0					84
Q94JY4 UniProt NPD GO	BRK1_ARATH	Protein BRICK1 (AtBRK1)	0.02	-	cyt	0					85
Q9H7C9 UniProt NPD GO	CK067_HUMAN	Protein C11orf67	0.02	-	cyt	0				2AB1	122
Q502H1 UniProt NPD GO	CK067_BRARE	Protein C11orf67 homolog	0.02	-	cyt	0					122
Q8R0P4 UniProt NPD GO	CK067_MOUSE	Protein C11orf67 homolog	0.02	-	cyt	0					122
Q8C436 UniProt NPD GO	CN138_MOUSE	Protein C14orf138 homolog	0.02	-	cyt	0					89
Q9BXV9 UniProt NPD GO	CN142_HUMAN	Protein C14orf142	0.02	-	mit	0					71
Q9UN11 UniProt NPD GO	CT040_HUMAN	Protein C20orf40 precursor	0.02	-	mit	0					62
Q9Y6Z2 UniProt NPD GO	CF123_HUMAN	Protein C6orf123 (HGC6.2 protein)	0.02	-	nuc	0					57
Q9D7X8 UniProt NPD GO	CG024_MOUSE	Protein C7orf24 homolog	0.02	-	cyt	0					188
Q96EH3 UniProt NPD GO	CG030_HUMAN	Protein C7orf30	0.02	-	mit	0					234
Q9UGQ2 UniProt NPD GO	CI007_HUMAN	Protein C9orf7	0.02	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				172
Q8BG21 UniProt NPD GO	CI007_MOUSE	Protein C9orf7 homolog	0.02	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				171
Q9CQ89 UniProt NPD GO	CUTA_MOUSE	Protein CutA precursor (Brain acetylcholinesterase putative membrane anchor)	0.02	-	end	1 *					177
Q6MGD0 UniProt NPD GO	CUTA_RAT	Protein CutA precursor (Brain acetylcholinesterase putative membrane anchor)	0.02	-	end	1 *		membrane [ISS]		1OSC	177
O88767 UniProt NPD GO	PARK7_RAT	Protein DJ-1 (Contraception-associated protein 1) (Protein CAP1) (Fertility protein SP22)	0.02	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Associated with mitochondria in some cells, part ...				189
P39704 UniProt NPD GO	ERP2_YEAST	Protein ERP2 precursor	0.02	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	ER to Golgi transport vesicle [IDA]			215
Q7TPG5 UniProt NPD GO	F19A4_MOUSE	Protein FAM19A4 precursor (Chemokine-like protein TAFA-4)	0.02	-	mit	1 *	Secreted protein (By similarity)				135
Q91VU0 UniProt NPD GO	FAM3C_MOUSE	Protein FAM3C precursor	0.02	-	end	1 *	Secreted protein (Potential)	extracellular region [ISS]			227
Q9NPR9 UniProt NPD GO	GP108_HUMAN	Protein GPR108 precursor	0.02	-	end	7	Membrane; multi-pass membrane protein				543
O75562 UniProt NPD GO	HFS1_HUMAN	Protein HFSE-1	0.02	-	cyt	0					157
Q07764 UniProt NPD GO	HVA22_HORVU	Protein HVA22	0.02	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				130
Q14165 UniProt NPD GO	K0152_HUMAN	Protein KIAA0152 precursor	0.02	-	end	1	Membrane; single-pass type I membrane protein (Potential)				292
Q8K4G6 UniProt NPD GO	LRP16_RAT	Protein LRP16 (Fragment)	0.02	-	cyt	0					258
Q5BK62 UniProt NPD GO	MPV17_RAT	Protein Mpv17	0.02	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				176
Q66GV0 UniProt NPD GO	MPV17_XENLA	Protein Mpv17	0.02	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				177
Q9Z2L9 UniProt NPD GO	NDRG4_RAT	Protein NDRG4 (Brain development-related molecule 1)	0.02	-	mit	1					352
Q9ULP0 UniProt NPD GO	NDRG4_HUMAN	Protein NDRG4 (Brain development-related molecule 1) (Vascular smooth muscle cell-associated protein ...	0.02	-	mit	0		cytoplasm [NAS]			352
Q8BTG7 UniProt NPD GO	NDRG4_MOUSE	Protein NDRG4 (Protein Ndr4)	0.02	-	mit	0					352
O00057 UniProt NPD GO	NMT1_UROFA	Protein NMT1 homolog (Planta-induced rust protein 1)	0.02	-	cyt	0					341
Q9CQE1 UniProt NPD GO	NPS3A_MOUSE	Protein NipSnap3A (NipSnap-related protein)	0.02	-	mit	0	Cytoplasm; cytosol. May be part of some vesicular structure distinct from lysosomal vesicles (By sim ...	mitochondrion [IDA]			247
P25096 UniProt NPD GO	P21_SOYBN	Protein P21	0.02	-	nuc	0					202
Q6FLC9 UniProt NPD GO	PNS1_CANGA	Protein PNS1	0.02	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				557
P83367 UniProt NPD GO	PL5_LUPLU	Protein PR-L5 (Fragment)	0.02	-		0					20
Q8SPU5 UniProt NPD GO	PLUNC_BOVIN	Protein Plunc precursor (Palate lung and nasal epithelium clone protein)	0.02	-	exc	0	Secreted protein (By similarity). Found in the nasal mucus (By similarity). Apical side of airway ep ...	extracellular region [ISS]			255
Q8K4I4 UniProt NPD GO	PLUNC_RAT	Protein Plunc precursor (Palate lung and nasal epithelium clone protein)	0.02	-	cyt	0	Secreted protein. Found in the nasal mucus. Apical side of airway epithelial cells. Detected in nasa ...	extracellular region [ISS] microvillus [IDA]			270
Q5XW65 UniProt NPD GO	PLUNC_PIG	Protein Plunc precursor (Palate lung and nasal epithelium clone protein) (Lung and nasal epithelium ...	0.02	-	mit	0	Secreted protein (By similarity). Found in the nasal mucus (By similarity). Apical side of airway ep ...				249
P52499 UniProt NPD GO	RCC1_CANAL	Protein RCC1	0.02	-	nuc	0	Nucleus (By similarity)				464
O77791 UniProt NPD GO	S10AC_RABIT	Protein S100-A12 (S100 calcium-binding protein A12) (Calgranulin-C) (CAGC) (Fragment)	0.02	-	cyt	0					81
P29034 UniProt NPD GO	S10A2_HUMAN	Protein S100-A2 (S100 calcium-binding protein A2) (Protein S-100L) (CAN19)	0.02	-	cyt	0			176993		97
P51964 UniProt NPD GO	S100G_CHICK	Protein S100-G (S100 calcium-binding protein G) (Vitamin D-dependent calcium-binding protein, intest ...	0.02	-	nuc	0					50
Q4IPX8 UniProt NPD GO	SYM1_GIBZE	Protein SYM1	0.02	-	mit	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				175
Q04189 UniProt NPD GO	TAP1_ANTMA	Protein TAP1 precursor	0.02	-	mit	1 *					107
Q6IE41 UniProt NPD GO	WFDC9_RAT	Protein WFDC9 precursor	0.02	-	mit	0	Secreted protein (Potential)				74
P28108 UniProt NPD GO	WNT4_CHECA	Protein Wnt-4 (Fragment)	0.02	-	cyt	0	Secreted protein; extracellular space; extracellular matrix				119
P28127 UniProt NPD GO	WNT4_MELGA	Protein Wnt-4 (Fragment)	0.02	-	cyt	0	Secreted protein; extracellular space; extracellular matrix				119
P28143 UniProt NPD GO	WNT4_SCEOC	Protein Wnt-4 (Fragment)	0.02	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				119
Q3T196 UniProt NPD GO	YIF1A_BOVIN	Protein YIF1A (YIP1-interacting factor homolog A)	0.02	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				293
Q6PC24 UniProt NPD GO	YIF1A_BRARE	Protein YIF1A (YIP1-interacting factor homolog A)	0.02	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				307

You are viewing entries 85301 to 85350 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.