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
Q2TQ20 UniProt NPD GO	NU2M_SYLJO	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.10	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q04050 UniProt NPD GO	NU4M_BRACM	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.10	-	end	11 *					495
O03727 UniProt NPD GO	NU4M_AGKIN	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.10	-	end	6 *					231
P92503 UniProt NPD GO	NU4M_AGKPI	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.10	-	end	6 *					231
Q34076 UniProt NPD GO	NU4M_CAICR	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.10	-	nuc	1 *					111
P92794 UniProt NPD GO	NU4M_TRIFL	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.10	-	end	6 *					231
P50365 UniProt NPD GO	NU5M_ALLMA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.10	-	end	17 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				641
O79437 UniProt NPD GO	NU5M_RABIT	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.10	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				603
Q01561 UniProt NPD GO	NU5M_TRIRU	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.10	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				653
Q37680 UniProt NPD GO	NU5M_WHEAT	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.10	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				670
Q02500 UniProt NPD GO	NU6M_WHEAT	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.10	-	end	5 *					247
P12628 UniProt NPD GO	MAOX_PHAVU	NADP-dependent malic enzyme (EC 1.1.1.40) (NADP-ME)	0.10	-	nuc	0	Cytoplasm (Potential)				589
P43279 UniProt NPD GO	MAOC_ORYSA	NADP-dependent malic enzyme, chloroplast precursor (EC 1.1.1.40) (NADP-ME)	0.10	-	cyt	0	Plastid; chloroplast				639
Q8BMF3 UniProt NPD GO	MAON_MOUSE	NADP-dependent malic enzyme, mitochondrial precursor (EC 1.1.1.40) (NADP-ME) (Malic enzyme 3)	0.10	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [ISS]			604
Q71UE8 UniProt NPD GO	NEDD8_RAT	NEDD8 precursor (Ubiquitin-like protein NEDD8) (Neddylin)	0.10	-	cyt	0	Nucleus. Mainly (By similarity)				81
Q9VJ33 UniProt NPD GO	NEDD8_DROME	NEDD8 precursor (Ubiquitin-like protein Nedd8) (Neddylin)	0.10	-	nuc	0	Nucleus. Mainly (By similarity)	nucleus [ISS]			84
P29595 UniProt NPD GO	NEDD8_MOUSE	NEDD8 precursor (Ubiquitin-like protein Nedd8) (Neddylin) (Neural precursor cell expressed developme ...	0.10	-	cyt	0	Nucleus. Mainly	nucleus [IDA]			81
Q99344 UniProt NPD GO	UBA3_YEAST	NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-) (Ubiquitin-activating enzyme E1 3) (RUB1-a ...	0.10	-	cyt	0		cytoplasm [IDA]			299
Q9BZM6 UniProt NPD GO	N2DL1_HUMAN	NKG2D ligand 1 precursor (UL16-binding protein 1) (NKG2DL1) (N2DL-1) (ALCAN-beta) (Retinoic acid ear ...	0.10	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor. Detected intracellularly in the endoplasmic reticulum of CM ...	membrane [NAS]	605697		244
Q9BZM5 UniProt NPD GO	N2DL2_HUMAN	NKG2D ligand 2 precursor (UL16-binding protein 2) (NKG2DL2) (N2DL-2) (ALCAN-alpha) (Retinoic acid ea ...	0.10	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor. Secreted protein	membrane [NAS]	605698		246
Q8TD07 UniProt NPD GO	N2DL4_HUMAN	NKG2D ligand 4 precursor (NKG2D ligand 4) (NKG2DL4) (N2DL-4) (Retinoic acid early transcript 1E) (Ly ...	0.10	-	end	2 *	Membrane; single-pass type I membrane protein	plasma membrane [NAS]			263
Q922L6 UniProt NPD GO	NELFD_MOUSE	Negative elongation factor D (NELF-D) (TH1-like protein)	0.10	-	cyt	0	Nucleus (By similarity)				591
P84851 UniProt NPD GO	TX115_PHYSE	Nephrotoxin PsTX-115 (Fragments)	0.10	-	nuc	0	Secreted protein. Found in nematocyst				23
Q9NPG2 UniProt NPD GO	NGB_HUMAN	Neuroglobin	0.10	-	cyt	0		hemoglobin complex [NAS]	605304	1OJ6	151
Q3KN66 UniProt NPD GO	NGB_PANTR	Neuroglobin	0.10	-	cyt	0					151
P34963 UniProt NPD GO	NEUU_CHICK	Neuromedin U-25 (NmU-25) [Contains: Neuromedin U-9 (NmU-9)]	0.10	-	cyt	0	Secreted protein				25
P54131 UniProt NPD GO	ACHA7_BOVIN	Neuronal acetylcholine receptor protein subunit alpha-7 precursor	0.10	-	end	4	Membrane; multi-pass membrane protein				499
P22770 UniProt NPD GO	ACHA7_CHICK	Neuronal acetylcholine receptor protein subunit alpha-7 precursor	0.10	-	end	4	Membrane; multi-pass membrane protein			1KL8	502
P36608 UniProt NPD GO	NCS1_CAEEL	Neuronal calcium sensor 1 (NCS-1)	0.10	-	cyt	0	Membrane; lipid-anchor (By similarity)				190
Q09711 UniProt NPD GO	NCS1_SCHPO	Neuronal calcium sensor 1 (NCS-1)	0.10	-	cyt	0	Membrane; peripheral membrane protein	cytoplasm [IDA] plasma membrane [IDA]			189
Q5R412 UniProt NPD GO	NEGR1_PONPY	Neuronal growth regulator 1 precursor	0.10	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				354
Q80Z24 UniProt NPD GO	NEGR1_MOUSE	Neuronal growth regulator 1 precursor (Kilon protein) (Kindred of IgLON) (Neurotractin)	0.10	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				348
P47972 UniProt NPD GO	NPTX2_HUMAN	Neuronal pentraxin-2 precursor (NP2) (Neuronal pentraxin II) (NP-II)	0.10	-	nuc	0	Secreted protein (By similarity)		600750		431
Q16517 UniProt NPD GO	NNAT_HUMAN	Neuronatin	0.10	-	mit	1 *			603106		81
Q61979 UniProt NPD GO	NNAT_MOUSE	Neuronatin	0.10	-	mit	1 *					81
Q924H0 UniProt NPD GO	NPFF2_MOUSE	Neuropeptide FF receptor 2 (Neuropeptide NPFF receptor) (G-protein coupled receptor 74)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				417
P28672 UniProt NPD GO	NEUY_CARAU	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.10	-	vac	1 *	Secreted protein				96
Q9DGK7 UniProt NPD GO	NEUY_CYPCA	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.10	-	exc	1 *	Secreted protein				96
Q9DDN6 UniProt NPD GO	NPY2R_CHICK	Neuropeptide Y receptor type 2 (NPY2-R) (NPY-Y2 receptor)	0.10	-	end	7	Membrane; multi-pass membrane protein				385
P60772 UniProt NPD GO	NXS5_NAJSP	Neurotoxin 5 (Toxin 5)	0.10	-	nuc	0	Secreted protein				61
P83915 UniProt NPD GO	TX21_PHOKE	Neurotoxin PKTx21C2	0.10	-	nuc	0	Secreted protein				32
P84018 UniProt NPD GO	T244_PHONI	Neurotoxin PNTx24A0C4	0.10	-	cyt	0	Secreted protein				33
P25434 UniProt NPD GO	NT3_RAJCL	Neurotrophin-3 (NT-3) (Neurotrophic factor) (HDNF) (Nerve growth factor 2) (NGF-2) (Fragment)	0.10	-	nuc	0	Secreted protein				43
Q54BK2 UniProt NPD GO	NCSEA_DICDI	Neutral ceramidase A precursor (EC 3.5.1.23) (NCDase A) (N-CDase A) (Acylsphingosine deacylase 2A) ( ...	0.10	-	end	1 *	Secreted protein (Potential)				714
Q62714 UniProt NPD GO	DEF4_RAT	Neutrophil antibiotic peptide NP-4 precursor (Neutrophil defensin 4) (RatNP-4)	0.10	-	exc	0	Secreted protein				93
Q9BZQ4 UniProt NPD GO	NMNA2_HUMAN	Nicotinamide mononucleotide adenylyltransferase 2 (EC 2.7.7.1) (NMN adenylyltransferase 2)	0.10	-	cyt	0	Cytoplasm		608701		307
Q8BNJ3 UniProt NPD GO	NMNA2_MOUSE	Nicotinamide mononucleotide adenylyltransferase 2 (EC 2.7.7.1) (NMN adenylyltransferase 2)	0.10	-	cyt	0	Cytoplasm (By similarity)				307
P43490 UniProt NPD GO	NAMPT_HUMAN	Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) (NAmPRTase) (Nampt) (Pre-B cell-enhancing facto ...	0.10	-	cyt	0	Cytoplasm (By similarity)		608764	2GVJ	491
Q99KQ4 UniProt NPD GO	NAMPT_MOUSE	Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) (NAmPRTase) (Nampt) (Pre-B-cell colony-enhancin ...	0.10	-	cyt	0	Cytoplasm	cytoplasm [IDA]		2H3B	491
Q52I78 UniProt NPD GO	NAMPT_PIG	Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) (NAmPRTase) (Nampt) (Pre-B-cell colony-enhancin ...	0.10	-	cyt	0	Cytoplasm (By similarity)				491

You are viewing entries 64801 to 64850 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.