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
Q5YCW1 UniProt NPD GO	TAU_PANTR	Microtubule-associated protein tau	0.41	-	nuc	0	Cytoplasm; cytosol (By similarity). Cell membrane (By similarity). Mostly found in the axons of neur ...	axon [ISS] cytosol [ISS] growth cone [ISS] microtubule associated complex [ISS] plasma membrane [ISS] tubulin [ISS]			775
P79404 UniProt NPD GO	MCR_PIG	Mineralocorticoid receptor (MR) (Fragment)	0.41	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity). Endoplasmic reticulum; endoplasmic reticulum mem ...				164
Q9CY16 UniProt NPD GO	RT28_MOUSE	Mitochondrial 28S ribosomal protein S28 (S28mt) (MRP-S28)	0.41	-	mit	0	Mitochondrion				186
P82932 UniProt NPD GO	RT06_HUMAN	Mitochondrial 28S ribosomal protein S6 (S6mt) (MRP-S6)	0.41	+	mit	0	Mitochondrion	small ribosomal subunit [NAS]			124
P46801 UniProt NPD GO	RM16_ORYSA	Mitochondrial 60S ribosomal protein L16	0.41	-	mit	0	Mitochondrion				185
Q3SZW4 UniProt NPD GO	TIM9B_BOVIN	Mitochondrial import inner membrane translocase subunit Tim9 B (TIMM10B) (Tim10b)	0.41	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				118
P24391 UniProt NPD GO	TOM40_NEUCR	Mitochondrial import receptor subunit tom-40 (Translocase of outer membrane 40 kDa subunit) (Protein ...	0.41	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				349
Q63344 UniProt NPD GO	MOT2_RAT	Monocarboxylate transporter 2 (MCT 2)	0.41	+	end	11 *	Cell membrane; multi-pass membrane protein (By similarity)	membrane fraction [IDA]			489
Q6AYU1 UniProt NPD GO	MO4L1_RAT	Mortality factor 4-like protein 1 (MORF-related gene 15 protein) (Transcription factor-like protein ...	0.41	-	cyt	0	Nucleus (By similarity)				323
P58925 UniProt NPD GO	CXM3A_CONPU	Mu-conotoxin PIIIA precursor (Conotoxin P3.7)	0.41	-	exc	0	Secreted protein			1R9I	73
Q9Z2L6 UniProt NPD GO	MINP1_MOUSE	Multiple inositol polyphosphate phosphatase 1 precursor (EC 3.1.3.62) (Inositol (1,3,4,5)-tetrakisph ...	0.41	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity). Cell membrane (Probable). Also a ...				481
P17200 UniProt NPD GO	ACM4_CHICK	Muscarinic acetylcholine receptor M4	0.41	+	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]			490
Q8R003 UniProt NPD GO	MBN3_MOUSE	Muscleblind-like X-linked protein (Muscleblind-like protein 3) (Cys3His CCG1-required protein) (Prot ...	0.41	-	nuc	0	Nucleus. Mostly nuclear (By similarity)				342
P06906 UniProt NPD GO	MBP_PANTR	Myelin basic protein (MBP)	0.41	-	nuc	0	Myelin membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of myelin				171
Q9UBC5 UniProt NPD GO	MYO1A_HUMAN	Myosin Ia (Brush border myosin I) (BBM-I) (BBMI) (Myosin I heavy chain) (MIHC)	0.41	-	cyt	0		brush border [TAS] muscle myosin [TAS]	607841		1043
Q14324 UniProt NPD GO	MYPC2_HUMAN	Myosin-binding protein C, fast-type (Fast MyBP-C) (C-protein, skeletal muscle fast-isoform)	0.41	+	cyt	0			160793		1142
O24474 UniProt NPD GO	TPSD2_ABIGR	Myrcene synthase, chloroplast precursor (EC 4.2.3.15) (Aggmyr)	0.41	-	cyt	0	Plastid; chloroplast				627
Q3TX08 UniProt NPD GO	TRM1_MOUSE	N(2),N(2)-dimethylguanosine tRNA methyltransferase (EC 2.1.1.32) (tRNA(guanine-26,N(2)-N(2)) methylt ...	0.41	-	mit	0					663
P41227 UniProt NPD GO	ARD1H_HUMAN	N-terminal acetyltransferase complex ARD1 subunit homolog A (EC 2.3.1.88) (EC 2.3.1.-)	0.41	-	nuc	0	Cytoplasm. According to Ref.4. Cytoplasm. Nuclear. According to Ref.2. Also present in the free cyto ...	cytoplasm [IDA] nucleus [IDA]	300013		235
Q5R6P3 UniProt NPD GO	NDUB4_PONPY	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.41	-	nuc	1	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				128
Q9UT93 UniProt NPD GO	ULA1_SCHPO	NEDD8-activating enzyme E1 regulatory subunit (Ubiquitin-like activation protein 1) (Ubiquitin-activ ...	0.41	-	nuc	0					500
P52491 UniProt NPD GO	UBC12_YEAST	NEDD8-conjugating enzyme UBC12 (EC 6.3.2.-) (RUB1-conjugating enzyme) (RUB1-protein ligase) (Ubiquit ...	0.41	-	nuc	0					188
Q9MZJ3 UniProt NPD GO	NKG2A_MACMU	NKG2-A/NKG2-B type II integral membrane protein (NKG2-A/B-activating NK receptor) (NK cell receptor ...	0.41	-	nuc	1	Membrane; single-pass type II membrane protein				233
P09893 UniProt NPD GO	2SSE_BRANA	Napin embryo-specific precursor (1.7S seed storage protein) [Contains: Napin embryo-specific small c ...	0.41	-	exc	1 *					186
P80208 UniProt NPD GO	2SS3_BRANA	Napin-3 (Napin BnIII) (Napin nIII) (1.7S seed storage protein) [Contains: Napin-3 small chain; Napin ...	0.41	-	nuc	0					125
P47245 UniProt NPD GO	NRDC_RAT	Nardilysin precursor (EC 3.4.24.61) (N-arginine dibasic convertase) (NRD convertase) (NRD-C)	0.41	-	mit	0					1161
Q8C4Y3 UniProt NPD GO	NELFB_MOUSE	Negative elongation factor B (NELF-B)	0.41	-	cyt	0	Nucleus (By similarity)				580
Q03333 UniProt NPD GO	NEC2_PIG	Neuroendocrine convertase 2 precursor (EC 3.4.21.94) (NEC 2) (PC2) (Prohormone convertase 2) (Propro ...	0.41	-	cyt	0	Secretory vesicle. Localized in the secretion granules				638
Q9CR53 UniProt NPD GO	NEUB_MOUSE	Neuromedin B-32 precursor [Contains: Neuromedin B]	0.41	-	nuc	1 *	Secreted protein				121
Q8BZP8 UniProt NPD GO	NPSR1_MOUSE	Neuropeptide S receptor (G-protein coupled receptor 154) (G-protein coupled receptor PGR14)	0.41	-	end	7	Membrane; multi-pass membrane protein (By similarity)				371
Q9VC27 UniProt NPD GO	NICA_DROME	Nicastrin homolog precursor	0.41	-	exc	1 *	Membrane; single-pass type I membrane protein (By similarity)				695
Q92091 UniProt NPD GO	NOS2_ONCMY	Nitric oxide synthase, inducible (EC 1.14.13.39) (NOS type II) (Inducible NO synthase) (Inducible NO ...	0.41	-	nuc	0					470
P38681 UniProt NPD GO	NIR_NEUCR	Nitrite reductase [NAD(P)H] (EC 1.7.1.4)	0.41	-	mit	0					1176
P46950 UniProt NPD GO	SNG1_YEAST	Nitrosoguanidine resistance protein SNG1	0.41	-	end	6	Membrane; multi-pass membrane protein (Potential)				547
P49321 UniProt NPD GO	NASP_HUMAN	Nuclear autoantigenic sperm protein (NASP)	0.41	-	nuc	0	Nucleus	nucleus [TAS]	603185		788
O16604 UniProt NPD GO	NHR75_CAEEL	Nuclear hormone receptor family member nhr-75	0.41	-	cyt	0	Nucleus (Potential)				347
Q12769 UniProt NPD GO	NU160_HUMAN	Nuclear pore complex protein Nup160 (Nucleoporin Nup160) (160 kDa nucleoporin)	0.41	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex	nuclear pore [IDA]	607614		1316
Q9Z0W3 UniProt NPD GO	NU160_MOUSE	Nuclear pore complex protein Nup160 (Nucleoporin Nup160) (160 kDa nucleoporin) (Gene trap locus 1-13 ...	0.41	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex	nuclear pore [IDA]			1402
Q8VCB1 UniProt NPD GO	NDC1_MOUSE	Nucleoporin NDC1 (Transmembrane protein 48)	0.41	-	end	5 *	Nucleus; nuclear envelope; nuclear pore complex; central core structure; multi-pass membrane protein ...				673
Q9BTX1 UniProt NPD GO	NDC1_HUMAN	Nucleoporin NDC1 (hNDC1) (Transmembrane protein 48)	0.41	-	end	5 *	Nucleus; nuclear envelope; nuclear pore complex; central core structure; multi-pass membrane protein ...	nuclear pore [IDA]			674
Q5RB98 UniProt NPD GO	NUPL2_PONPY	Nucleoporin-like 2	0.41	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side (By similarity). Excluded from the ...				423
Q9EPK6 UniProt NPD GO	SIL1_MOUSE	Nucleotide exchange factor SIL1 precursor	0.41	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen				465
P81914 UniProt NPD GO	OR33A_DROME	Odorant receptor 33a	0.41	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			378
P47874 UniProt NPD GO	OMP_HUMAN	Olfactory marker protein (Olfactory neuronal-specific protein)	0.41	-	cyt	0	Cytoplasm		164340		162
Q90XB3 UniProt NPD GO	OLIG2_CHICK	Oligodendrocyte transcription factor 2 (Oligo2)	0.41	-	nuc	0	Nucleus (Potential)				298
P70112 UniProt NPD GO	OAZ1_MESAU	Ornithine decarboxylase antizyme (ODC-Az)	0.41	-	nuc	0					221
P54369 UniProt NPD GO	OAZ1_MOUSE	Ornithine decarboxylase antizyme (ODC-Az)	0.41	-	nuc	0					226
P54370 UniProt NPD GO	OAZ1_RAT	Ornithine decarboxylase antizyme (ODC-Az)	0.41	-	nuc	0				1ZO0	226
O22591 UniProt NPD GO	PSBQ_ONOVI	Oxygen-evolving enhancer protein 3, chloroplast precursor (OEE3) (16 kDa subunit of oxygen evolving ...	0.41	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				231
O04886 UniProt NPD GO	PME1_CITSI	Pectinesterase-1 precursor (EC 3.1.1.11) (Pectin methylesterase) (PE)	0.41	+	mit	1 *					584

You are viewing entries 31251 to 31300 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.