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
Q56JY0 UniProt NPD GO	CK073_BOVIN	Protein C11orf73 homolog	0.04	-	cyt	0	Cytoplasm (By similarity)				197
Q9DD02 UniProt NPD GO	CK073_MOUSE	Protein C11orf73 homolog (Lethal gene on chromosome 7 Rinchik 6 protein)	0.04	-	cyt	0	Cytoplasm				197
Q8BH86 UniProt NPD GO	CN159_MOUSE	Protein C14orf159 homolog, mitochondrial precursor	0.04	-	mit	0	Mitochondrion (Potential)				617
Q7Z5M8 UniProt NPD GO	CN029_HUMAN	Protein C14orf29	0.04	-	cyt	0					362
O13780 UniProt NPD GO	YEO2_SCHPO	Protein C17G6.02c in chromosome I	0.04	-	end	7 *	Membrane; multi-pass membrane protein				324
Q5M8N0 UniProt NPD GO	CB032_MOUSE	Protein C2orf32 homolog	0.04	-	cyt	0					164
Q5M7A7 UniProt NPD GO	CB032_RAT	Protein C2orf32 homolog	0.04	-	cyt	0					164
Q3U4G3 UniProt NPD GO	CC021_MOUSE	Protein C3orf21 homolog	0.04	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				392
Q6AXS2 UniProt NPD GO	CI071_RAT	Protein C9orf71 homolog	0.04	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				185
Q9BTM9 UniProt NPD GO	CI074_HUMAN	Protein C9orf74	0.04	-	cyt	0					101
Q5JZQ7 UniProt NPD GO	CLN8_CANFA	Protein CLN8	0.04	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				288
Q5RAX6 UniProt NPD GO	CX040_PONPY	Protein CXorf40 homolog	0.04	-	cyt	0					158
Q8TE69 UniProt NPD GO	CX04A_HUMAN	Protein CXorf40A (Endothelial-overexpressed lipopolysaccharide-associated factor 1)	0.04	-	cyt	0					158
Q12123 UniProt NPD GO	DCS2_YEAST	Protein DCS2 (Histidine triad protein)	0.04	-	cyt	0	Cytoplasm. Predominantly	cytoplasm [IDA]			352
Q99765 UniProt NPD GO	YV02_HUMAN	Protein DJ1104E15.3	0.04	-	mit	0					158
Q8N3H0 UniProt NPD GO	F19A2_HUMAN	Protein FAM19A2 precursor (Chemokine-like protein TAFA-2)	0.04	-	mit	0	Cytoplasm				131
Q5R6N2 UniProt NPD GO	F19A2_PONPY	Protein FAM19A2 precursor (Chemokine-like protein TAFA-2)	0.04	-	mit	0	Cytoplasm (By similarity)				131
Q5R5C3 UniProt NPD GO	FAM3A_PONPY	Protein FAM3A precursor	0.04	-	end	1 *	Secreted protein (Potential)				230
P98173 UniProt NPD GO	FAM3A_HUMAN	Protein FAM3A precursor (2-19 protein)	0.04	-	end	1 *	Secreted protein (Potential)		300492		230
P97805 UniProt NPD GO	FAM3D_MOUSE	Protein FAM3D precursor (Oncoprotein-induced protein 1) (Protein EF-7)	0.04	-	mit	1 *	Secreted protein (Potential)	extracellular region [ISS]			223
P14065 UniProt NPD GO	GCY_YEAST	Protein GCY (EC 1.1.1.-)	0.04	-	cyt	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			312
P37020 UniProt NPD GO	GEF1_YEAST	Protein GEF1 (Voltage-gated chloride channel) (ClC-Y1) (ClC-A)	0.04	-	end	11	Membrane; multi-pass membrane protein	endosome [IDA] Golgi apparatus [IDA] Golgi-associated vesicle [TAS]			779
Q753I3 UniProt NPD GO	HSD1_ASHGO	Protein HSD1	0.04	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				317
Q7ZX75 UniProt NPD GO	LMBRL_XENLA	Protein LMBR1L	0.04	-	end	9 *	Cell membrane; multi-pass membrane protein (By similarity)				483
Q922B1 UniProt NPD GO	LRP16_MOUSE	Protein LRP16	0.04	-	mit	0		mitochondrion [IDA]			323
P49283 UniProt NPD GO	MVL_DROME	Protein Malvolio	0.04	-	end	11	Membrane; multi-pass membrane protein (Probable)				596
Q9UFN0 UniProt NPD GO	NPS3A_HUMAN	Protein NipSnap3A (NipSnap4) (Target for Salmonella secreted protein C) (TassC)	0.04	-	mit	0	Cytoplasm; cytosol. May be part of some vesicular structure distinct from lysosomal vesicles		608871		247
Q9UKY4 UniProt NPD GO	POMT2_HUMAN	Protein O-mannosyl-transferase 2 (EC 2.4.1.109) (Dolichyl-phosphate-mannose--protein mannosyltransfe ...	0.04	-	end	10	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein		607439		750
Q4I8E9 UniProt NPD GO	PNS1_GIBZE	Protein PNS1	0.04	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				538
P32857 UniProt NPD GO	PTM1_YEAST	Protein PTM1 precursor	0.04	-	end	7	Membrane; multi-pass membrane protein (Potential)				531
P30801 UniProt NPD GO	S10A6_RABIT	Protein S100-A6 (S100 calcium-binding protein A6) (Calcyclin) (Lung 10 kDa protein)	0.04	-	cyt	0		nuclear envelope [ISS]		2CNP	90
P05964 UniProt NPD GO	S10A6_RAT	Protein S100-A6 (S100 calcium-binding protein A6) (Calcyclin) (Prolactin receptor-associated protein ...	0.04	-	cyt	0		nuclear envelope [ISS]			89
P14069 UniProt NPD GO	S10A6_MOUSE	Protein S100-A6 (S100 calcium-binding protein A6) (Calcyclin) (Prolactin receptor-associated protein ...	0.04	-	cyt	0		nuclear envelope [ISS]			89
P05109 UniProt NPD GO	S10A8_HUMAN	Protein S100-A8 (S100 calcium-binding protein A8) (Calgranulin-A) (Migration inhibitory factor-relat ...	0.04	-	cyt	0			123885	1XK4	93
P28782 UniProt NPD GO	S10A8_BOVIN	Protein S100-A8 (S100 calcium-binding protein A8) (Calgranulin-A) (Neutrophil cytosolic 7 kDa protei ...	0.04	-	cyt	0	Cytoplasm. Cytoskeleton. Loosely associated to the cytoskeleton				89
P28091 UniProt NPD GO	WNT6_EVATR	Protein Wnt-6 (Fragment)	0.04	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				117
Q91XB7 UniProt NPD GO	YIF1A_MOUSE	Protein YIF1A (YIP1-interacting factor homolog A)	0.04	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				293
Q5E9E8 UniProt NPD GO	YIPF5_BOVIN	Protein YIPF5 (YIP1 family member 5)	0.04	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				257
Q4R5M4 UniProt NPD GO	YIPF5_MACFA	Protein YIPF5 (YIP1 family member 5)	0.04	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				257
Q66KA5 UniProt NPD GO	YIPF5_XENTR	Protein YIPF5 (YIP1 family member 5)	0.04	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				256
Q6IQ85 UniProt NPD GO	YIPF6_BRARE	Protein YIPF6 (YIP1 family member 6)	0.04	-	end	5	Membrane; multi-pass membrane protein (Potential)				240
Q75A56 UniProt NPD GO	YOP1_ASHGO	Protein YOP1	0.04	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				189
Q99210 UniProt NPD GO	YO111_YEAST	Protein YOR111W	0.04	-	cyt	0	Cytoplasm (Potential)				232
Q3E834 UniProt NPD GO	YOS1_YEAST	Protein YOS1 (YIP one suppressor protein 1)	0.04	-	exc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential). Golg ...	endoplasmic reticulum membrane [IDA] ER to Golgi transport vesicle [IDA] integral to Golgi membrane [IDA]			85
P55345 UniProt NPD GO	ANM2_HUMAN	Protein arginine N-methyltransferase 2 (EC 2.1.1.-)	0.04	-	nuc	0		nucleus [TAS]	601961	1X2P	433
P38660 UniProt NPD GO	PDIA6_MESAU	Protein disulfide-isomerase A6 precursor (EC 5.3.4.1) (Protein disulfide isomerase P5)	0.04	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				439
Q2HWU2 UniProt NPD GO	PDIA1_MACFU	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI) (Prolyl 4-hydroxylase subunit beta)	0.04	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Highly abundant. In some cell types, seems to be ...				510
P09103 UniProt NPD GO	PDIA1_MOUSE	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI) (Prolyl 4-hydroxylase subunit beta) (Cellul ...	0.04	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Highly abundant. In some cell types, seems to be ...	endoplasmic reticulum [IDA] microsome [IDA]			509
P17967 UniProt NPD GO	PDI_YEAST	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI) (Thioredoxin-related glycoprotein 1)	0.04	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)	endoplasmic reticulum lumen [TAS]		2B5E	522
O43003 UniProt NPD GO	MMF1_SCHPO	Protein mmf1, mitochondrial precursor (Maintenance of mitochondrial function 1) (Isoleucine biosynth ...	0.04	-	mit	0	Mitochondrion. Cytoplasm	cytoplasm [IDA] mitochondrial matrix [IDA]			162

You are viewing entries 78151 to 78200 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.