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
Q91VR7 UniProt NPD GO	MLP3A_MOUSE	Microtubule-associated proteins 1A/1B light chain 3A precursor (MAP1A/MAP1B LC3 A) (MAP1A/1B light c ...	0.43	-	nuc	0	LC3-I: Cytoplasm. LC3-II: Intracytoplasmic membrane; lipid-anchor. LC3-II binds to the autophagic me ...	autophagic vacuole [ISS] cytoplasm [ISS] organelle membrane [ISS]			121
Q6XVN8 UniProt NPD GO	MLP3A_RAT	Microtubule-associated proteins 1A/1B light chain 3A precursor (MAP1A/MAP1B LC3 A) (MAP1A/1B light c ...	0.43	-	nuc	0	LC3-I: Cytoplasm. LC3-II: Intracytoplasmic membrane; lipid-anchor. LC3-II binds to the autophagic me ...	autophagic vacuole [IDA] cytoplasm [IDA] organelle membrane [IDA]			121
O35972 UniProt NPD GO	RM23_MOUSE	Mitochondrial 39S ribosomal protein L23 (L23mt) (MRP-L23) (L23 mitochondrial-related protein)	0.43	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IDA]			146
P10662 UniProt NPD GO	RT01_YEAST	Mitochondrial 40S ribosomal protein MRP1	0.43	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			321
P10850 UniProt NPD GO	RM14_TETPY	Mitochondrial 60S ribosomal protein L14	0.43	+	nuc	0	Mitochondrion				119
O59781 UniProt NPD GO	GEM1_SCHPO	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (GTPase EF-hand protein of mitochondria 1)	0.43	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				630
Q19766 UniProt NPD GO	TOM20_CAEEL	Mitochondrial import receptor subunit TOM20 homolog (Mitochondrial 20 kDa outer membrane protein) (O ...	0.43	-	nuc	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (Potential)				188
P48941 UniProt NPD GO	RT11_CHOCR	Mitochondrial ribosomal protein S11	0.43	-	nuc	0	Mitochondrion				116
Q9CXT8 UniProt NPD GO	MPPB_MOUSE	Mitochondrial-processing peptidase subunit beta, mitochondrial precursor (EC 3.4.24.64) (Beta-MPP) ( ...	0.43	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrial inner membrane [IDA]			489
Q9C9U4 UniProt NPD GO	MPK15_ARATH	Mitogen-activated protein kinase 15 (EC 2.7.11.24) (MAP kinase 15) (AtMPK15)	0.43	-	cyt	0					431
Q92398 UniProt NPD GO	SPM1_SCHPO	Mitogen-activated protein kinase spm1 (EC 2.7.11.24) (MAP kinase spm1) (MAP kinase pmk1)	0.43	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			422
Q95KI4 UniProt NPD GO	MOAP1_MACFA	Modulator of apoptosis 1 (MAP-1)	0.43	+	nuc	0					351
Q96BY2 UniProt NPD GO	MOAP1_HUMAN	Modulator of apoptosis 1 (MAP-1) (MAP1) (Paraneoplastic antigen MA4)	0.43	+	nuc	0			609485		351
O70436 UniProt NPD GO	SMAD2_RAT	Mothers against decapentaplegic homolog 2 (SMAD 2) (Mothers against DPP homolog 2) (Mad-related prot ...	0.43	-	nuc	0	Cytoplasm. In the cytoplasm in the absence of ligand. Nucleus. Migration to the nucleus when complex ...	nucleus [ISS] transcription factor complex [ISS]			467
Q62432 UniProt NPD GO	SMAD2_MOUSE	Mothers against decapentaplegic homolog 2 (SMAD 2) (Mothers against DPP homolog 2) (Mad-related prot ...	0.43	-	nuc	0	Cytoplasm. In the cytoplasm in the absence of ligand. Nucleus. Migration to the nucleus when complex ...	nucleus [IDA] transcription factor complex [IDA]			467
Q70IA8 UniProt NPD GO	MOL2C_HUMAN	Mps one binder kinase activator-like 2C (Mob1 homolog 2C) (Protein Mob3C)	0.43	-	nuc	0					216
P01523 UniProt NPD GO	CXM3A_CONGE	Mu-conotoxin GIIIA precursor (Myotoxin I) (Geographutoxin I) (GTx-I) (Conotoxin G3.9)	0.43	-	exc	0	Secreted protein			1TCK	74
P15941 UniProt NPD GO	MUC1_HUMAN	Mucin-1 precursor (MUC-1) (Polymorphic epithelial mucin) (PEM) (PEMT) (Episialin) (Tumor-associated ...	0.43	-	exc	1 *	Cell membrane; single-pass type I membrane protein. Isoform 5, isoform 9: Secreted protein. Two secr ...	integral to plasma membrane [TAS]	113720	2ACM	1255
Q8K595 UniProt NPD GO	MCLN2_MOUSE	Mucolipin-2	0.43	-	end	5	Membrane; multi-pass membrane protein (Potential)				566
Q5R890 UniProt NPD GO	MINP1_PONPY	Multiple inositol polyphosphate phosphatase 1 precursor (EC 3.1.3.62) (Inositol (1,3,4,5)-tetrakisph ...	0.43	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				487
Q91439 UniProt NPD GO	MBP_SQUAC	Myelin basic protein (MBP)	0.43	-	nuc	0	Myelin membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of myelin				154
P87346 UniProt NPD GO	MBP_XENLA	Myelin basic protein (MBP) (Myelin A1 protein)	0.43	-	nuc	0	Myelin membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of myelin				175
P02687 UniProt NPD GO	MBP_BOVIN	Myelin basic protein (MBP) (Myelin A1 protein) (20 kDa microtubule-stabilizing protein)	0.43	-	nuc	0	Myelin membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of myelin				169
P02688 UniProt NPD GO	MBP_RAT	Myelin basic protein S (MBP S)	0.43	-	nuc	0	Myelin membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of myelin	compact myelin [IDA]			194
P20138 UniProt NPD GO	CD33_HUMAN	Myeloid cell surface antigen CD33 precursor (Siglec-3) (gp67)	0.43	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	159590		364
P13541 UniProt NPD GO	MYH3_MOUSE	Myosin heavy chain, fast skeletal muscle, embryonic (Fragment)	0.43	-	nuc	0	Thick filaments of the myofibrils				159
P20689 UniProt NPD GO	MYLK2_RAT	Myosin light chain kinase 2, skeletal/cardiac muscle (EC 2.7.11.18) (MLCK2)	0.43	-	nuc	0	Cytoplasm (By similarity). Colocalizes with phosphorylated myosin light chain (RLCP) at filaments of ...				609
O70468 UniProt NPD GO	MYPC3_MOUSE	Myosin-binding protein C, cardiac-type (Cardiac MyBP-C) (C-protein, cardiac muscle isoform)	0.43	-	cyt	0		cytoskeleton [TAS]			1270
P16419 UniProt NPD GO	MYPC2_CHICK	Myosin-binding protein C, fast-type (Fast MyBP-C) (C-protein, skeletal muscle fast-isoform)	0.43	-	nuc	0					1131
P29966 UniProt NPD GO	MARCS_HUMAN	Myristoylated alanine-rich C-kinase substrate (MARCKS) (Protein kinase C substrate, 80 kDa protein, ...	0.43	+	nuc	0		actin cytoskeleton [TAS]	177061		331
Q6CW60 UniProt NPD GO	ECO1_KLULA	N-acetyltransferase ECO1 (EC 2.3.1.-) (Establishment of cohesion protein 1)	0.43	-	mit	0	Nucleus (By similarity)				271
O49255 UniProt NPD GO	NAC29_ARATH	NAC domain-containing protein 29 (ANAC029) (NAC2) (NAC-LIKE, ACTIVATED BY AP3/PI protein) (NAP)	0.43	-	cyt	0	Nucleus (Potential)	nucleus [IDA]			268
Q02373 UniProt NPD GO	NDUBA_BOVIN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.43	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side				175
Q18217 UniProt NPD GO	ULA1_CAEEL	NEDD8-activating enzyme E1 regulatory subunit (Ubiquitin-like activation protein 1)	0.43	-	cyt	0					541
Q09969 UniProt NPD GO	BNIP3_CAEEL	NIP3 homolog (CeBNIP3)	0.43	-	nuc	1					210
O43908 UniProt NPD GO	NKG2F_HUMAN	NKG2-F type II integral membrane protein (NKG2-F-activating NK receptor) (NK cell receptor F)	0.43	-	nuc	1	Membrane; single-pass type II membrane protein		602893		158
P63239 UniProt NPD GO	NEC1_MOUSE	Neuroendocrine convertase 1 precursor (EC 3.4.21.93) (NEC 1) (PC1) (Prohormone convertase 1) (Propro ...	0.43	+	nuc	0	Secretory vesicle. Localized in the secretion granules			1KN6	753
P63240 UniProt NPD GO	NEC1_MUSCO	Neuroendocrine convertase 1 precursor (EC 3.4.21.93) (NEC 1) (PC1) (Prohormone convertase 1) (Propro ...	0.43	+	exc	0	Secretory vesicle. Localized in the secretion granules				753
P43443 UniProt NPD GO	NEUB_XENLA	Neuromedin B precursor	0.43	-	nuc	1 *	Secreted protein				120
P29371 UniProt NPD GO	NK3R_HUMAN	Neuromedin K receptor (NKR) (Neurokinin B receptor) (NK-3 receptor) (NK-3R) (Tachykinin receptor 3)	0.43	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	162332		465
P05480 UniProt NPD GO	SRC_MOUSE	Neuronal proto-oncogene tyrosine-protein kinase Src (EC 2.7.10.2) (p60-Src) (c-Src) (pp60c-src)	0.43	-	nuc	0					540
Q11088 UniProt NPD GO	NLP1_CAEEL	Neuropeptide-like protein 1 precursor	0.43	-	exc	1 *					176
P97333 UniProt NPD GO	NRP1_MOUSE	Neuropilin-1 precursor (A5 protein)	0.43	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [IC]			923
O14786 UniProt NPD GO	NRP1_HUMAN	Neuropilin-1 precursor (Vascular endothelial cell growth factor 165 receptor) (CD304 antigen)	0.43	-	end	1	Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein		602069	1KEX	923
Q9BE70 UniProt NPD GO	GANC_MACFA	Neutral alpha-glucosidase C (EC 3.2.1.-) (Fragment)	0.43	+	mit	0					769
Q62609 UniProt NPD GO	NOE1_RAT	Noelin precursor (Neuronal olfactomedin-related ER localized protein) (Olfactomedin-1) (Pancortin) ( ...	0.43	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				485
P63056 UniProt NPD GO	NOE3_MOUSE	Noelin-3 precursor (Olfactomedin-3) (Optimedin)	0.43	-	mit	0	Secreted protein. Isoform 2 is secreted more efficiently than isoform 1	extracellular space [IDA] Golgi apparatus [IDA]			478
P63057 UniProt NPD GO	NOE3_RAT	Noelin-3 precursor (Olfactomedin-3) (Optimedin)	0.43	-	mit	0	Secreted protein. Isoform 2 is secreted more efficiently than isoform 1				478
Q27976 UniProt NPD GO	CALD1_BOVIN	Non-muscle caldesmon (CDM) (L-caldesmon) (Fragment)	0.43	-	nuc	0	On thin filaments in smooth muscle and on stress fibers in fibroblasts (nonmuscle) (By similarity)				83
Q9Z2D3 UniProt NPD GO	DFNA5_MOUSE	Non-syndromic hearing impairment protein 5 homolog	0.43	+	nuc	0					512

You are viewing entries 29801 to 29850 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.