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
Q37375 UniProt NPD GO	NU4M_ACACA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.08	-	end	14 *					497
O03173 UniProt NPD GO	NU4M_LATCH	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.08	-	end	12 *					461
P15582 UniProt NPD GO	NU4M_PODAN	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.08	-	end	14 *					519
Q9ZZ45 UniProt NPD GO	NU4M_SQUAC	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.08	-	end	13 *					460
O03703 UniProt NPD GO	NU4M_CERGO	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.08	-	end	6 *					231
O03778 UniProt NPD GO	NU4M_SISMI	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.08	-	end	6 *					231
Q34948 UniProt NPD GO	NU4LM_LUMTE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.08	-	end	3 *					98
Q95916 UniProt NPD GO	NU4LM_POLOR	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.08	-	end	3 *					98
P29388 UniProt NPD GO	NU5M_ARATH	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.08	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				669
P26849 UniProt NPD GO	NU5M_MARPO	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.08	-	end	17 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				669
Q9ZZM3 UniProt NPD GO	NU5M_SALSA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.08	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				612
P48924 UniProt NPD GO	NU6M_CHOCR	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.08	-	end	5 *					204
Q34944 UniProt NPD GO	NU6M_LUMTE	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.08	-	end	4 *					156
Q9CQ54 UniProt NPD GO	N4BM_MOUSE	NADH-ubiquinone oxidoreductase subunit B14.5b (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-B14.5b) (CI-B14. ...	0.08	-	cyt	1	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)	mitochondrial inner membrane [IDA]			120
P93338 UniProt NPD GO	GAPN_NICPL	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.9) (Non-phosphorylating glyceralde ...	0.08	-	cyt	0	Cytoplasm				496
P51615 UniProt NPD GO	MAOX_VITVI	NADP-dependent malic enzyme (EC 1.1.1.40) (NADP-ME)	0.08	-	nuc	0	Cytoplasm (Potential)				591
Q29558 UniProt NPD GO	MAOX_PIG	NADP-dependent malic enzyme (EC 1.1.1.40) (NADP-ME) (Malic enzyme 1) (Fragment)	0.08	-	cyt	0	Cytoplasm	cytosol [ISS]			557
Q9HFR6 UniProt NPD GO	DHE4_TUBBO	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (NADP-dependent glutamate dehydrogenas ...	0.08	-	cyt	0					457
Q672J9 UniProt NPD GO	NOX3_MOUSE	NADPH oxidase 3 (EC 1.6.3.-)	0.08	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				568
Q05001 UniProt NPD GO	NCPR_CATRO	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.08	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Anchored to the ...				714
Q9HDG2 UniProt NPD GO	NCPR_PHACH	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.08	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				736
Q6GLN5 UniProt NPD GO	NFIP1_XENLA	NEDD4 family-interacting protein 1	0.08	-	vac	3	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				212
Q19360 UniProt NPD GO	UBA3_CAEEL	NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-) (Ubiquitin-activating enzyme 3 homolog) (E ...	0.08	-	cyt	0					430
P42744 UniProt NPD GO	ULA1_ARATH	NEDD8-activating enzyme E1 regulatory subunit (Auxin-resistance protein AXR1)	0.08	-	mit	0	Nucleus				540
Q6CSW8 UniProt NPD GO	UBC12_KLULA	NEDD8-conjugating enzyme UBC12 (EC 6.3.2.-) (RUB1-conjugating enzyme) (RUB1-protein ligase) (Ubiquit ...	0.08	-	nuc	0					184
Q6DGQ1 UniProt NPD GO	KBRS1_BRARE	NF-kappa-B inhibitor-interacting Ras-like protein 1 (I-kappa-B-interacting Ras-like protein 1) (Kapp ...	0.08	-	cyt	0	Cytoplasm (By similarity)				192
Q9EQ80 UniProt NPD GO	NF3L_MOUSE	NIF3-like protein 1	0.08	-	mit	0	Cytoplasm (By similarity)	cytoplasm [IDA]			350
P28374 UniProt NPD GO	DNP_DENAN	Natriuretic peptide (DNP)	0.08	-	nuc	0	Secreted protein				38
Q61477 UniProt NPD GO	NBL1_MOUSE	Neuroblastoma suppressor of tumorigenicity 1 precursor (Zinc finger protein DAN) (N03)	0.08	-	nuc	0	Secreted protein (By similarity)				178
Q6WZ17 UniProt NPD GO	NGB_PIG	Neuroglobin	0.08	-	cyt	0					151
P42857 UniProt NPD GO	NSG1_HUMAN	Neuron-specific protein family member 1 (Brain neuron cytoplasmic protein 1) (D4S234)	0.08	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)	cytoplasm [TAS] nucleus [TAS]	607645		185
Q9I8C7 UniProt NPD GO	ACH10_CHICK	Neuronal acetylcholine receptor protein subunit alpha-10 precursor (Nicotinic acetylcholine receptor ...	0.08	-	end	4	Membrane; multi-pass membrane protein (Probable)				452
Q91614 UniProt NPD GO	NCS1_XENLA	Neuronal calcium sensor 1 (NCS-1) (Frequenin)	0.08	-	nuc	0	Membrane; lipid-anchor (By similarity)				189
P0C0P5 UniProt NPD GO	NPS_BOVIN	Neuropeptide S precursor	0.08	-	mit	0	Secreted protein (Potential)				89
Q9I9D3 UniProt NPD GO	NEUY_ICTPU	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.08	-	exc	1 *	Secreted protein				95
P48146 UniProt NPD GO	NPBW2_HUMAN	Neuropeptides B/W receptor type 2 (G-protein coupled receptor 8)	0.08	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]	600731		333
P13724 UniProt NPD GO	NEUT_CHICK	Neurotensin (NT)	0.08	-		0	Secreted protein				13
Q8MUB1 UniProt NPD GO	SCK38_MESMA	Neurotoxin BmK38 precursor	0.08	-	exc	0	Secreted protein				62
P83894 UniProt NPD GO	TX13_PHONI	Neurotoxin PNTx13C3	0.08	-	nuc	0	Secreted protein				32
P83559 UniProt NPD GO	TXMG3_MACGS	Neurotoxin magi-3	0.08	-	nuc	0	Secreted protein				46
P19651 UniProt NPD GO	TXA1_STOHE	Neurotoxin-1 (Toxin SHP-I) (SHNA) (Neurotoxin ShI)	0.08	-	nuc	0	Secreted protein. Found in nematocyst			2SH1	48
P81468 UniProt NPD GO	DEF4_MESAU	Neutrophil defensin 4 (HANP-4)	0.08	-	nuc	0	Secreted protein				33
P39864 UniProt NPD GO	NIA_PHYIN	Nitrate reductase [NADPH] (EC 1.7.1.3) (NR)	0.08	-	mit	0					902
P32962 UniProt NPD GO	NRL2_ARATH	Nitrilase 2 (EC 3.5.5.1)	0.08	-	cyt	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Tightly associated with the plasma mem ...				339
P26204 UniProt NPD GO	BGLS_TRIRP	Non-cyanogenic beta-glucosidase precursor (EC 3.2.1.21)	0.08	-	cyt	0					493
P07597 UniProt NPD GO	NLTP1_HORVU	Nonspecific lipid-transfer protein 1 precursor (LTP 1) (Probable amylase/protease inhibitor)	0.08	-	exc	1 *				1MID	117
P10973 UniProt NPD GO	NLTPA_RICCO	Nonspecific lipid-transfer protein A (NS-LTP A) (Phospholipid transfer protein) (PLTP)	0.08	-	nuc	0					92
Q58D20 UniProt NPD GO	NLE1_BOVIN	Notchless homolog 1	0.08	-	cyt	0	Nucleus; nucleolus (By similarity)				485
P47123 UniProt NPD GO	MOG1_YEAST	Nuclear import protein MOG1 (Multicopy suppressor of GSP1)	0.08	-	cyt	0	Nucleus	nucleus [IDA]		1JHS	218
Q06287 UniProt NPD GO	NEP1_YEAST	Nucleolar essential protein 1 (Essential for mitotic growth 1)	0.08	-	cyt	0	Nucleus; nucleolus	cytoplasm [IDA] nuclear microtubule [IDA] nucleolus [IDA] nucleus [IDA] small nucleolar ribonucleoprotein complex [IPI]			252

You are viewing entries 68501 to 68550 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.