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
P03891 UniProt NPD GO	NU2M_HUMAN	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.20	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	respiratory chain complex I (sensu Eukaryota) [NAS]	535000		347
O03166 UniProt NPD GO	NU2M_LATCH	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.20	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				348
Q9TA28 UniProt NPD GO	NU2M_LOXAF	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.20	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
O79428 UniProt NPD GO	NU2M_RABIT	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.20	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q94VJ9 UniProt NPD GO	NU2M_VARBA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.20	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				345
Q2I3F2 UniProt NPD GO	NU4M_LOXAF	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.20	-	end	13 *					459
P92668 UniProt NPD GO	NU4M_MACRO	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.20	-	end	14 *					459
O03707 UniProt NPD GO	NU4M_CAURH	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.20	-	nuc	6 *					231
P41309 UniProt NPD GO	NU5M_DIDMA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.20	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				602
P03917 UniProt NPD GO	NU5M_GORGO	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.20	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				603
Q34879 UniProt NPD GO	NU5M_LEMCA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.20	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				603
P15552 UniProt NPD GO	NU5M_STRPU	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.20	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				637
Q13564 UniProt NPD GO	ULA1_HUMAN	NEDD8-activating enzyme E1 regulatory subunit (Amyloid protein-binding protein 1) (Amyloid beta prec ...	0.20	-	nuc	0	Cell membrane. Colocalizes with APP in lipid rafts	cytoplasm [TAS] insoluble fraction [IDA]	603385	1YOV	534
P55770 UniProt NPD GO	NHPX_RAT	NHP2-like protein 1 (High mobility group-like nuclear protein 2 homolog 1) (U4/U6.U5 tri-snRNP 15.5 ...	0.20	-	nuc	0	Nucleus; nucleolus (By similarity)				127
P55769 UniProt NPD GO	NHPX_HUMAN	NHP2-like protein 1 (High mobility group-like nuclear protein 2 homolog 1) (U4/U6.U5 tri-snRNP 15.5 ...	0.20	-	nuc	0	Nucleus; nucleolus. Concentrated in the dense fibrillar component of the nucleolus	nucleolus [TAS] nucleus [TAS]	601304	1E7K	127
Q9D0T1 UniProt NPD GO	NHPX_MOUSE	NHP2-like protein 1 (High mobility group-like nuclear protein 2 homolog 1) (U4/U6.U5 tri-snRNP 15.5 ...	0.20	-	nuc	0	Nucleus; nucleolus (By similarity)				127
Q03351 UniProt NPD GO	NTRK3_RAT	NT-3 growth factor receptor precursor (EC 2.7.10.1) (Neurotrophic tyrosine kinase receptor type 3) ( ...	0.20	-	nuc	2 *	Membrane; single-pass type I membrane protein				864
Q8AWF2 UniProt NPD GO	NACA_ORENI	Nascent polypeptide-associated complex subunit alpha (NAC-alpha) (Alpha-NAC)	0.20	-	nuc	0					215
P13204 UniProt NPD GO	ANFB_BOVIN	Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; Aldosterone secretion i ...	0.20	-	nuc	0	Secreted protein				103
Q751E8 UniProt NPD GO	PHO85_ASHGO	Negative regulator of the PHO system (EC 2.7.11.22) (Serine/threonine-protein kinase PHO85)	0.20	-	cyt	0					303
O60500 UniProt NPD GO	NPHN_HUMAN	Nephrin precursor (Renal glomerulus-specific cell adhesion receptor)	0.20	-	end	1	Membrane; single-pass type I membrane protein (Potential). Predominantly located at podocyte slit di ...	integral to plasma membrane [TAS]	602716		1241
Q5RB89 UniProt NPD GO	NET4_PONPY	Netrin-4 precursor	0.20	-	nuc	1 *	Secreted protein; extracellular space (By similarity)				628
O35136 UniProt NPD GO	NCAM2_MOUSE	Neural cell adhesion molecule 2 precursor (N-CAM 2) (RB-8 neural cell adhesion molecule) (R4B12)	0.20	-	end	1	Isoform Long: Cell membrane; single-pass type I membrane protein. Isoform Short: Cell membrane; lipi ...				837
Q9BR09 UniProt NPD GO	NEUL2_HUMAN	Neuralized-like protein 2	0.20	-	cyt	0	Cytoplasm (By similarity)		608597		285
Q8WMJ4 UniProt NPD GO	NXPH3_MACMU	Neurexophilin-3 (Fragment)	0.20	-	nuc	0	Secreted protein (Potential)				95
O95158 UniProt NPD GO	NXPH4_HUMAN	Neurexophilin-4 precursor	0.20	-	mit	0	Secreted protein (Potential)	extracellular region [NAS]	604637		308
Q09666 UniProt NPD GO	AHNK_HUMAN	Neuroblast differentiation-associated protein AHNAK (Desmoyokin) (Fragments)	0.20	-	nuc	0	Nucleus	nucleus [NAS]	103390		2960
P20241 UniProt NPD GO	NRG_DROME	Neuroglian precursor	0.20	-	end	1	Membrane; single-pass type I membrane protein	lateral plasma membrane [TAS] plasma membrane [IEP] pleated septate junction [IDA]		1CFB	1302
Q92686 UniProt NPD GO	NEUG_HUMAN	Neurogranin (Ng) (RC3)	0.20	-	nuc	0			602350		78
Q5IS77 UniProt NPD GO	ACHA4_PANTR	Neuronal acetylcholine receptor protein subunit alpha-4 precursor	0.20	-	end	4	Membrane; multi-pass membrane protein (By similarity)				627
Q16612 UniProt NPD GO	NP311_HUMAN	Neuronal protein 3.1 (p311 protein)	0.20	-	nuc	0			607332		68
P48097 UniProt NPD GO	NEUY_LAMFL	Neuropeptide Y precursor (NPY)	0.20	-	nuc	1 *	Secreted protein				104
Q9I8P3 UniProt NPD GO	NEUY_BRARE	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.20	-	exc	1 *	Secreted protein				96
Q04573 UniProt NPD GO	NPY1R_MOUSE	Neuropeptide Y receptor type 1 (NPY1-R)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				382
P28824 UniProt NPD GO	NRP1_XENLA	Neuropilin-1 precursor (A5 protein) (A5 antigen)	0.20	-	end	1	Membrane; single-pass type I membrane protein				928
Q8QFX6 UniProt NPD GO	NRP1A_BRARE	Neuropilin-1a precursor (znrp1)	0.20	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]			923
O04796 UniProt NPD GO	PERN_IPOBA	Neutral peroxidase precursor (EC 1.11.1.7) (SwPN1)	0.20	-	exc	0	Secreted protein (By similarity)				348
P30152 UniProt NPD GO	NGAL_RAT	Neutrophil gelatinase-associated lipocalin precursor (NGAL) (p25) (Alpha-2-microglobulin-related pro ...	0.20	-	mit	0	Secreted protein				198
Q8CGU6 UniProt NPD GO	NICA_RAT	Nicastrin precursor	0.20	-	end	1	Membrane; single-pass type I membrane protein (Potential)	endoplasmic reticulum [ISS] Golgi apparatus [ISS] integral to plasma membrane [ISS] lysosomal membrane [IDA]			708
Q80Z39 UniProt NPD GO	GP109_RAT	Nicotinic acid receptor (G-protein coupled receptor 109) (G-protein coupled receptor HM74) (Protein ...	0.20	-	end	6 *	Membrane; multi-pass membrane protein				360
P27967 UniProt NPD GO	NIA1_HORVU	Nitrate reductase [NADH] (EC 1.7.1.1) (NR)	0.20	-	nuc	0					915
P27969 UniProt NPD GO	NIA2_HORVU	Nitrate reductase [NADH] (EC 1.7.1.1) (NR) (Fragment)	0.20	-	cyt	0					912
P11605 UniProt NPD GO	NIA1_TOBAC	Nitrate reductase [NADH] 1 (EC 1.7.1.1) (NR1)	0.20	-	cyt	0					904
O95897 UniProt NPD GO	NOE2_HUMAN	Noelin-2 precursor (Olfactomedin-2)	0.20	-	exc	0	Secreted protein (Probable)				454
Q6BUA6 UniProt NPD GO	NUDF_DEBHA	Nuclear distribution protein PAC1 (nudF homolog)	0.20	-	nuc	0	Cytoplasm. Localizes to the plus ends of microtubules and the mitotic spindle poles (By similarity)				529
Q5QMG3 UniProt NPD GO	NFYB2_ORYSA	Nuclear transcription factor Y subunit B-2 (OsNF-YB-2) (Transcriptional activator HAP3A)	0.20	-	nuc	0	Nucleus (Probable)				178
Q10100 UniProt NPD GO	NTF2_SCHPO	Nuclear transport factor 2 (NTF-2)	0.20	-	cyt	0	Cytoplasm (By similarity)				123
Q61937 UniProt NPD GO	NPM_MOUSE	Nucleophosmin (NPM) (Nucleolar phosphoprotein B23) (Numatrin) (Nucleolar protein NO38)	0.20	-	nuc	0	Nucleus; nucleolus. Generally nucleolar, but is translocated to the nucleoplasm in case of serum sta ...	centrosome [ISS] cytoplasm [ISS] nucleolus [IDA] nucleus [ISS]			292
P13084 UniProt NPD GO	NPM_RAT	Nucleophosmin (NPM) (Nucleolar phosphoprotein B23) (Numatrin) (Nucleolar protein NO38)	0.20	-	nuc	0	Nucleus; nucleolus. Generally nucleolar, but is translocated to the nucleoplasm in case of serum sta ...	centrosome [ISS] cytoplasm [ISS] nucleus [ISS]			292
Q40646 UniProt NPD GO	OLEO2_ORYSA	Oleosin 18 kDa (OSE721)	0.20	-	end	2 *	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface				172

You are viewing entries 50901 to 50950 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.