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
P79766 UniProt NPD GO	NDFM_CHICK	Neurogenic differentiation factor NeuroM	0.64	-	nuc	0	Nucleus (Potential)				330
P70447 UniProt NPD GO	NGN2_MOUSE	Neurogenin 2 (Atonal protein homolog 4) (Helix-loop-helix protein mATH-4A) (MATH4A)	0.64	-	nuc	0	Nucleus (Potential)				263
O19132 UniProt NPD GO	NOS1_RABIT	Nitric-oxide synthase, brain (EC 1.14.13.39) (NOS type I) (Neuronal NOS) (N-NOS) (nNOS) (Constitutiv ...	0.64	-	nuc	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein (By similarity). In skeletal muscle, i ...				1435
Q12374 UniProt NPD GO	NCA2_YEAST	Nuclear control of ATPase protein 2	0.64	-	nuc	1	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrial outer membrane [IDA] mitochondrion [IDA]			616
Q28147 UniProt NPD GO	PP1R8_BOVIN	Nuclear inhibitor of protein phosphatase 1 (NIPP-1) (Protein phosphatase 1, regulatory inhibitor sub ...	0.64	+	nuc	0	Nucleus (By similarity). Mainly, but not exclusively, nuclear. Nucleus; nucleoplasm; nuclear speckle ...				351
P57740 UniProt NPD GO	NU107_HUMAN	Nuclear pore complex protein Nup107 (Nucleoporin Nup107) (107 kDa nucleoporin)	0.64	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex. Located on both the cytoplasmic and nuclear sides o ...	nuclear pore [IDA]	607617		925
P51448 UniProt NPD GO	RORA_MOUSE	Nuclear receptor ROR-alpha (Nuclear receptor RZR-alpha)	0.64	-	nuc	0	Nucleus (Probable)				523
Q9WUB5 UniProt NPD GO	NCOR1_RAT	Nuclear receptor corepressor 1 (N-CoR1) (N-CoR) (Fragment)	0.64	-	nuc	0	Nucleus (By similarity)				533
Q9LXV5 UniProt NPD GO	NFYA1_ARATH	Nuclear transcription factor Y subunit A-1 (AtNF-YA-1) (Transcriptional activator HAP2A)	0.64	+	nuc	0	Nucleus (Probable)				272
Q13952 UniProt NPD GO	NFYC_HUMAN	Nuclear transcription factor Y subunit gamma (Nuclear transcription factor Y subunit C) (NF-YC) (CAA ...	0.64	+	nuc	0	Nucleus	CCAAT-binding factor complex [IDA] nucleus [IEP]	605344	1N1J	458
Q86WB0 UniProt NPD GO	NIPA_HUMAN	Nuclear-interacting partner of ALK (Nuclear-interacting partner of anaplastic lymphoma kinase) (hNIP ...	0.64	-	nuc	0	Nucleus				502
Q9ZPV5 UniProt NPD GO	NOC2L_ARATH	Nucleolar complex protein 2 homolog (Protein NOC2 homolog)	0.64	+	nuc	0	Nucleus (By similarity)				779
Q8TAK6 UniProt NPD GO	OLIG1_HUMAN	Oligodendrocyte transcription factor 1 (Oligo1)	0.64	-	nuc	0	Nucleus (By similarity)		606385		271
P53347 UniProt NPD GO	ONCM_MOUSE	Oncostatin M precursor (OSM)	0.64	-	exc	0	Secreted protein				263
Q02201 UniProt NPD GO	OSH6_YEAST	Oxysterol-binding protein homolog 6	0.64	-	nuc	0					448
Q9Z1M0 UniProt NPD GO	P2RX7_MOUSE	P2X purinoceptor 7 (ATP receptor) (P2X7) (Purinergic receptor) (P2Z receptor)	0.64	-	cyt	0	Membrane; multi-pass membrane protein	integral to plasma membrane [IMP]			595
Q29087 UniProt NPD GO	PO3F3_PIG	POU domain, class 3, transcription factor 3 (Brain-specific homeobox/POU domain protein 1) (Brain-1) ...	0.64	+	nuc	0	Nucleus (By similarity)				131
Q90435 UniProt NPD GO	PO4F3_BRARE	POU domain, class 4, transcription factor 3 (Brain-specific homeobox/POU domain protein 3.1) (Brn-3. ...	0.64	-	nuc	0	Nucleus				116
Q5TYX0 UniProt NPD GO	PRAM5_HUMAN	PRAME family member 5	0.64	-	mit	0					476
Q5VXH4 UniProt NPD GO	PRAM6_HUMAN	PRAME family member 6	0.64	-	mit	0					476
P0C1J0 UniProt NPD GO	CYP15_RHIOR	Peptidyl-prolyl cis-trans isomerase cyp15 (EC 5.2.1.8) (PPIase cyp15) (Rotamase cyp15) (Cyclophilin ...	0.64	-	cyt	0					630
Q25637 UniProt NPD GO	PER_PERAM	Period circadian protein	0.64	-	nuc	0	Nucleus. Nuclear at specific periods of the day. Interaction with TIM is required for nuclear locali ...				893
Q13515 UniProt NPD GO	BFSP2_HUMAN	Phakinin (Beaded filament structural protein 2) (Lens fiber cell beaded filament protein CP 49) (CP4 ...	0.64	-	nuc	0	Membrane. Cytoplasm. Membrane- and cytoskeleton-associated	intermediate filament [TAS]	604219		415
Q8L796 UniProt NPD GO	PI5K2_ARATH	Phosphatidylinositol-4-phosphate 5-kinase 2 (EC 2.7.1.68) (AtPIP5K2) (1-phosphatidylinositol-4-phosp ...	0.64	-	mit	0					754
P37216 UniProt NPD GO	AROG_LYCES	Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplast precursor (EC 2.5.1.54) (Phospho-2-keto-3 ...	0.64	-	mit	0	Plastid; chloroplast				541
Q02735 UniProt NPD GO	CAPP_MEDSA	Phosphoenolpyruvate carboxylase (EC 4.1.1.31) (PEPCase) (PEPC)	0.64	-	cyt	0	Cytoplasm				966
Q5ZIB8 UniProt NPD GO	PIRK5_CHICK	Phosphoinositide 3-kinase regulatory subunit 5 (PI3-kinase regulatory subunit 5)	0.64	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Membrane; peripheral membrane protein (By simila ...				881
Q8BWJ3 UniProt NPD GO	KPB2_MOUSE	Phosphorylase b kinase regulatory subunit alpha, liver isoform (Phosphorylase kinase alpha L subunit ...	0.64	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				1235
Q91VY6 UniProt NPD GO	PSCBP_MOUSE	Pleckstrin homology Sec7 and coiled-coil domains-binding protein (Cytohesin-binding protein HE) (Cbp ...	0.64	-	nuc	0	Cytoplasm (By similarity). Membrane (By similarity). May also be membrane-associated (By similarity) ...				359
Q3ZBA3 UniProt NPD GO	PKHA2_BOVIN	Pleckstrin homology domain-containing family A member 2	0.64	-	nuc	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein (By similarity). Nucleus (By s ...				425
P21246 UniProt NPD GO	PTN_HUMAN	Pleiotrophin precursor (PTN) (Heparin-binding growth-associated molecule) (HB-GAM) (Heparin-binding ...	0.64	-	nuc	1 *	Secreted protein	extracellular space [TAS]	162095		168
Q03220 UniProt NPD GO	CTL1_YEAST	Polynucleotide 5'-triphosphatase (EC 3.1.3.33) (mRNA 5'-triphosphatase) (TPase)	0.64	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			320
Q921L8 UniProt NPD GO	GLT11_MOUSE	Polypeptide N-acetylgalactosaminyltransferase 11 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltran ...	0.64	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				608
Q96FL9 UniProt NPD GO	GLT14_HUMAN	Polypeptide N-acetylgalactosaminyltransferase 14 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltran ...	0.64	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)		608225		552
Q8BVG5 UniProt NPD GO	GLT14_MOUSE	Polypeptide N-acetylgalactosaminyltransferase 14 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltran ...	0.64	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				550
Q8MVS5 UniProt NPD GO	GLT35_DROME	Polypeptide N-acetylgalactosaminyltransferase 35A (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltra ...	0.64	-	vac	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi stack [NAS]			632
Q8C7U7 UniProt NPD GO	GALT6_MOUSE	Polypeptide N-acetylgalactosaminyltransferase 6 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.64	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				622
Q9NZV8 UniProt NPD GO	KCND2_HUMAN	Potassium voltage-gated channel subfamily D member 2 (Voltage-gated potassium channel subunit Kv4.2) ...	0.64	-	end	6 *	Membrane; multi-pass membrane protein. Detected in dendrites in cultured hippocampal neurons. Associ ...	cell surface [IEP] dendritic spine [NAS]	605410		630
Q9Z0V2 UniProt NPD GO	KCND2_MOUSE	Potassium voltage-gated channel subfamily D member 2 (Voltage-gated potassium channel subunit Kv4.2) ...	0.64	-	end	6 *	Membrane; multi-pass membrane protein				630
Q8HYZ1 UniProt NPD GO	KCND2_MUSPF	Potassium voltage-gated channel subfamily D member 2 (Voltage-gated potassium channel subunit Kv4.2) ...	0.64	-	end	6 *	Membrane; multi-pass membrane protein				630
P59995 UniProt NPD GO	KCND2_RABIT	Potassium voltage-gated channel subfamily D member 2 (Voltage-gated potassium channel subunit Kv4.2) ...	0.64	-	end	6 *	Membrane; multi-pass membrane protein				630
Q9JK97 UniProt NPD GO	KCNQ4_MOUSE	Potassium voltage-gated channel subfamily KQT member 4 (Voltage-gated potassium channel subunit Kv7. ...	0.64	-	nuc	0	Cell membrane; basal cell membrane; multi-pass membrane protein. Situated at the basal membrane of c ...				276
Q59W52 UniProt NPD GO	PRP28_CANAL	Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 (EC 3.6.1.-)	0.64	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				581
Q6T412 UniProt NPD GO	CWC2_LEPMC	Pre-mRNA-splicing factor CWC2	0.64	+	nuc	0	Nucleus (By similarity)				421
Q6CXH8 UniProt NPD GO	RSE1_KLULA	Pre-mRNA-splicing factor RSE1	0.64	-	nuc	0	Nucleus (By similarity)				1269
P01132 UniProt NPD GO	EGF_MOUSE	Pro-epidermal growth factor precursor (EGF) [Contains: Epidermal growth factor]	0.64	+	exc	2 *	Membrane; single-pass type I membrane protein	extracellular space [IDA]		3EGF	1217
P25161 UniProt NPD GO	PSD3_DROME	Probable 26S proteasome non-ATPase regulatory subunit 3 (26S proteasome subunit S3) (Diphenol oxidas ...	0.64	-	cyt	0		proteasome regulatory particle (sensu Eukar... [IDA]			494
Q64060 UniProt NPD GO	DDX4_RAT	Probable ATP-dependent RNA helicase DDX4 (EC 3.6.1.-) (DEAD box protein 4) (VASA homolog) (rVLG)	0.64	-	nuc	0					713
Q9FFT9 UniProt NPD GO	RH32_ARATH	Probable DEAD-box ATP-dependent RNA helicase 32 (EC 3.6.1.-)	0.64	+	nuc	0					739
Q9DDD1 UniProt NPD GO	GP149_CHICK	Probable G-protein coupled receptor 149 (G-protein coupled receptor R35)	0.64	-	end	7 *	Membrane; multi-pass membrane protein				723

You are viewing entries 17001 to 17050 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.