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
Q07353 UniProt NPD GO	FL3H_PETHY	Naringenin,2-oxoglutarate 3-dioxygenase (EC 1.14.11.9) (Flavonone-3-hydroxylase) (F3H) (FHT) (Fragme ...	0.22	-	cyt	0					369
Q8MHY9 UniProt NPD GO	KLRD1_PONPY	Natural killer cells antigen CD94 (NK cell receptor) (Killer cell lectin-like receptor subfamily D m ...	0.22	-	exc	1 *	Membrane; single-pass type II membrane protein				179
Q9QZS7 UniProt NPD GO	NPHN_MOUSE	Nephrin precursor (Renal glomerulus-specific cell adhesion receptor)	0.22	-	end	1	Cell membrane; single-pass type I membrane protein (Potential). Located at podocyte slit diaphragm b ...	integral to plasma membrane [TAS]			1242
P13594 UniProt NPD GO	NCA12_MOUSE	Neural cell adhesion molecule 1, 120 kDa isoform precursor (N-CAM 120) (NCAM-120)	0.22	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor			3NCM	725
P13590 UniProt NPD GO	NCAM1_CHICK	Neural cell adhesion molecule 1, 180 kDa isoform precursor (N-CAM 180)	0.22	-	exc	1				1IE5	1091
P62758 UniProt NPD GO	NCALD_CHICK	Neurocalcin delta	0.22	-	cyt	0					192
P62759 UniProt NPD GO	NCALD_POEGU	Neurocalcin delta	0.22	-	cyt	0					192
P18844 UniProt NPD GO	7B2_XENLA	Neuroendocrine protein 7B2 (Secretogranin V) [Contains: N-terminal peptide; C-terminal peptide] (Fra ...	0.22	-	nuc	0	Neuroendocrine and endocrine secretory granules	secretory granule [ISS]			161
Q04940 UniProt NPD GO	NEUG_RAT	Neurogranin (Ng) (Protein kinase C substrate 7.5 kDa protein) (RC3)	0.22	-	nuc	0					78
P60761 UniProt NPD GO	NEUG_MOUSE	Neurogranin (Ng) (RC3)	0.22	-	nuc	0					78
P08858 UniProt NPD GO	TKNK_BOVIN	Neurokinin-B precursor (NKB) (Neuromedin-K)	0.22	-	exc	0	Secreted protein				126
Q9ESQ4 UniProt NPD GO	NMUR2_RAT	Neuromedin U receptor 2 (NMU-R2) (G-protein coupled receptor TGR-1) (G-protein-coupled receptor FM-4 ...	0.22	-	end	7 *	Membrane; multi-pass membrane protein				395
Q99742 UniProt NPD GO	NPAS1_HUMAN	Neuronal PAS domain-containing protein 1 (Neuronal PAS1) (Member of PAS protein 5) (MOP5)	0.22	-	cyt	0	Nucleus (Potential)		603346		590
Q9GZZ6 UniProt NPD GO	ACH10_HUMAN	Neuronal acetylcholine receptor protein subunit alpha-10 precursor (Nicotinic acetylcholine receptor ...	0.22	-	end	4	Membrane; multi-pass membrane protein (Probable)	membrane [TAS]	606372		450
O70174 UniProt NPD GO	ACHA4_MOUSE	Neuronal acetylcholine receptor protein subunit alpha-4 precursor	0.22	-	end	4	Membrane; multi-pass membrane protein	membrane fraction [IDA]			629
P21916 UniProt NPD GO	NEU2_STRCA	Neurophysin 2 (MSEL-neurophysin)	0.22	-	nuc	0	Secreted protein				132
P84471 UniProt NPD GO	TX11B_BUNCA	Neurotoxin T1-1 B chain (Fragment)	0.22	-		0	Secreted protein				15
Q07837 UniProt NPD GO	SLC31_HUMAN	Neutral and basic amino acid transport protein rBAT (B(0,+)-type amino acid transport protein) (NBAT ...	0.22	-	mit	1	Membrane; single-pass type II membrane protein (Potential)	integral to plasma membrane [TAS] membrane fraction [TAS]	220100		685
P80188 UniProt NPD GO	NGAL_HUMAN	Neutrophil gelatinase-associated lipocalin precursor (NGAL) (p25) (25 kDa alpha-2-microglobulin-rela ...	0.22	-	mit	0	Secreted protein		600181	1X8U	198
P17569 UniProt NPD GO	NIA_CUCMA	Nitrate reductase [NADH] (EC 1.7.1.1) (NR)	0.22	-	cyt	0					918
P10322 UniProt NPD GO	NO25_MEDSA	Nodulin 25 precursor (N-25)	0.22	-	nuc	1 *	Peribacteroid space				246
P02315 UniProt NPD GO	H6_ONCMY	Nonhistone chromosomal protein H6 (Histone T) [Contains: Oncorhyncin III]	0.22	-	nuc	0	Nucleus (By similarity). Oncorhyncin III may be secreted				69
P02313 UniProt NPD GO	HMGN2_BOVIN	Nonhistone chromosomal protein HMG-17 (High-mobility group nucleosome-binding domain-containing prot ...	0.22	+	nuc	0	Nucleus				89
Q8SPY5 UniProt NPD GO	RNAS2_MACNE	Nonsecretory ribonuclease precursor (EC 3.1.27.5) (Ribonuclease US) (Eosinophil-derived neurotoxin) ...	0.22	-	exc	0	Lysosome (Probable). Matrix of eosinophil's large specific granule (By similarity)				160
P47786 UniProt NPD GO	RNAS2_SAGOE	Nonsecretory ribonuclease precursor (EC 3.1.27.5) (Ribonuclease US) (Eosinophil-derived neurotoxin) ...	0.22	-	exc	0	Lysosome (Probable). Matrix of eosinophil's large specific granule				158
P23802 UniProt NPD GO	NLTP_ELECO	Nonspecific lipid-transfer protein (LTP) (Alpha-amylase inhibitor I-2)	0.22	-	nuc	0					95
Q8TAT6 UniProt NPD GO	NPL4_HUMAN	Nuclear protein localization protein 4 homolog (Protein NPL4)	0.22	-	cyt	0	Cytoplasm (By similarity). Endoplasmic reticulum (By similarity). Nucleus (By similarity). Associate ...	endoplasmic reticulum [ISS] nuclear envelope-endoplasmic reticulum network [ISS]	606590		607
O82248 UniProt NPD GO	NFYB5_ARATH	Nuclear transcription factor Y subunit B-5 (AtNF-YB-5)	0.22	-	nuc	0	Nucleus (Probable)				160
P83503 UniProt NPD GO	NYX_MOUSE	Nyctalopin precursor	0.22	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				476
Q8NGE8 UniProt NPD GO	OR4D9_HUMAN	Olfactory receptor 4D9 (Olfactory receptor OR11-253)	0.22	-	end	6 *	Membrane; multi-pass membrane protein				314
Q9NZP0 UniProt NPD GO	OR6C3_HUMAN	Olfactory receptor 6C3 (HSA8)	0.22	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			311
O94302 UniProt NPD GO	RFT1_SCHPO	Oligosaccharide translocation protein rft1	0.22	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				527
P83859 UniProt NPD GO	OX26_HUMAN	Orexigenic neuropeptide QRFP precursor (P518) [Contains: QRF-amide (Pyroglutamylated arginine-phenyl ...	0.22	-	mit	0	Secreted protein		609795		136
O43613 UniProt NPD GO	OX1R_HUMAN	Orexin receptor type 1 (Ox1r) (Hypocretin receptor type 1)	0.22	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602392		425
P58307 UniProt NPD GO	OX1R_MOUSE	Orexin receptor type 1 (Ox1r) (Hypocretin receptor type 1)	0.22	-	end	7 *	Membrane; multi-pass membrane protein				416
P56718 UniProt NPD GO	OX1R_RAT	Orexin receptor type 1 (Ox1r) (Hypocretin receptor type 1)	0.22	-	end	7 *	Membrane; multi-pass membrane protein				416
P12852 UniProt NPD GO	PSBQ_CHLRE	Oxygen-evolving enhancer protein 3, chloroplast precursor (OEE3)	0.22	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				199
Q9H1P3 UniProt NPD GO	OSBL2_HUMAN	Oxysterol-binding protein-related protein 2 (OSBP-related protein 2) (ORP-2)	0.22	-	cyt	0			606731		480
Q9CPV9 UniProt NPD GO	P2Y12_MOUSE	P2Y purinoceptor 12 (P2Y12)	0.22	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IC]			347
Q9H244 UniProt NPD GO	P2Y12_HUMAN	P2Y purinoceptor 12 (P2Y12) (P2Y12 platelet ADP receptor) (P2Y(ADP)) (ADP-glucose receptor) (ADPG-R) ...	0.22	-	end	7 *	Membrane; multi-pass membrane protein	membrane [NAS]	609821		342
Q63371 UniProt NPD GO	P2RY6_RAT	P2Y purinoceptor 6 (P2Y6)	0.22	-	end	6 *	Membrane; multi-pass membrane protein	apical plasma membrane [IDA] basolateral plasma membrane [IDA]			328
P50479 UniProt NPD GO	PDLI4_HUMAN	PDZ and LIM domain protein 4 (LIM protein RIL) (Reversion-induced LIM protein)	0.22	-	nuc	0			603422		330
Q42384 UniProt NPD GO	PRL1_ARATH	PP1/PP2A phosphatases pleiotropic regulator PRL1	0.22	-	nuc	0					486
Q9UVH3 UniProt NPD GO	AKR1_MORAP	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1) (Fragment)	0.22	-	cyt	5	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				559
P31229 UniProt NPD GO	PAHO_RANTE	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.22	-	nuc	0	Secreted protein				36
Q9R155 UniProt NPD GO	S26A4_MOUSE	Pendrin (Sodium-independent chloride/iodide transporter) (Solute carrier family 26 member 4)	0.22	-	end	11	Membrane; multi-pass membrane protein (Probable)				780
P61408 UniProt NPD GO	AF1_GRASP	Peptide GsAF 1 (GsAF I)	0.22	-	nuc	0	Secreted protein				29
Q9FUZ0 UniProt NPD GO	DEFM_LYCES	Peptide deformylase, mitochondrial precursor (EC 3.5.1.88) (PDF) (Polypeptide deformylase)	0.22	-	mit	0	Mitochondrion (Potential)				277
O75594 UniProt NPD GO	PGRP_HUMAN	Peptidoglycan recognition protein precursor (PGRP-S)	0.22	-	exc	0	Secreted protein; cytoplasmic granule (By similarity)	extracellular region [NAS]	604963	1YCK	196
P38876 UniProt NPD GO	PTH_YEAST	Peptidyl-tRNA hydrolase (EC 3.1.1.29) (PTH)	0.22	-	cyt	0	Mitochondrion	mitochondrion [IDA]			190

You are viewing entries 48701 to 48750 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.