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
P50368 UniProt NPD GO	NU5M_SCHCO	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.02	-	end	17 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				686
P19047 UniProt NPD GO	NU5M_ARTSA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5) (Fragment)	0.02	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				59
Q37712 UniProt NPD GO	NU6M_ARTSF	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.02	-	end	4 *					155
P69232 UniProt NPD GO	NU6M_BRAFL	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.02	-	end	4 *					167
P69233 UniProt NPD GO	NU6M_BRALA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.02	-	end	4 *					167
O21336 UniProt NPD GO	NU6M_DASNO	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.02	-	end	5 *					175
P92670 UniProt NPD GO	NU6M_MACRO	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.02	-	end	5 *					167
O79679 UniProt NPD GO	NU6M_PELSU	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.02	-	end	4 *					173
Q9G6M4 UniProt NPD GO	NU6M_PTEDA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.02	-	end	5 *					175
Q9G3S5 UniProt NPD GO	NU6M_PTESA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.02	-	end	5 *					175
O79438 UniProt NPD GO	NU6M_RABIT	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.02	-	end	5 *					174
O63849 UniProt NPD GO	NU6M_SARGL	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.02	-	end	5 *					185
O57380 UniProt NPD GO	ADH8_RANPE	NADP-dependent alcohol dehydrogenase (EC 1.1.1.2)	0.02	-	nuc	0				1P0F	372
O93868 UniProt NPD GO	MTDH_AGABI	NADP-dependent mannitol dehydrogenase (EC 1.1.1.138) (MtDH) (Mannitol 2-dehydrogenase [NADP+])	0.02	-	cyt	0				1H5Q	261
P54387 UniProt NPD GO	DHE4_AGABI	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (NADP-dependent glutamate dehydrogenas ...	0.02	-	cyt	0					457
P54388 UniProt NPD GO	DHE4_LACBI	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (NADP-dependent glutamate dehydrogenas ...	0.02	-	cyt	0					450
P00369 UniProt NPD GO	DHE4_NEUCR	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (NADP-dependent glutamate dehydrogenas ...	0.02	-	cyt	0					453
Q9HGU3 UniProt NPD GO	DHE4_NEUSI	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (NADP-dependent glutamate dehydrogenas ...	0.02	-	cyt	0					453
P07262 UniProt NPD GO	DHE4_YEAST	NADP-specific glutamate dehydrogenase 1 (EC 1.4.1.4) (NADP-GDH 1) (NADP-dependent glutamate dehydrog ...	0.02	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			454
Q9VXB0 UniProt NPD GO	NECAP_DROME	NECAP-like protein CG9132	0.02	-	cyt	0		clathrin vesicle coat [ISS] coated pit [ISS]			246
Q8R0W6 UniProt NPD GO	NFIP1_MOUSE	NEDD4 family-interacting protein 1 (NEDD4 WW domain-binding protein 5)	0.02	-	end	3	Golgi apparatus; Golgi membrane; multi-pass membrane protein	integral to membrane [TAS]			221
Q03919 UniProt NPD GO	RUB1_YEAST	NEDD8-like protein RUB1 precursor (Ubiquitin-like protein RUB1)	0.02	-	cyt	0		cytoplasm [IDA]			77
Q8BR37 UniProt NPD GO	NHLC1_MOUSE	NHL repeat-containing protein 1 (Malin)	0.02	-	mit	0	Endoplasmic reticulum (By similarity). Nucleus (By similarity). Localizes at the endoplasmic reticul ...				401
Q6IMG5 UniProt NPD GO	NHLC1_RAT	NHL repeat-containing protein 1 (Malin)	0.02	-	mit	0	Endoplasmic reticulum (By similarity). Nucleus (By similarity). Localizes at the endoplasmic reticul ...				396
Q6P499 UniProt NPD GO	NPAL3_HUMAN	NIPA-like protein 3	0.02	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				406
O96009 UniProt NPD GO	NAPSA_HUMAN	Napsin-A precursor (EC 3.4.23.-) (Napsin-1) (NAPA) (TA01/TA02) (Aspartyl protease 4) (Asp 4) (ASP4)	0.02	-	mit	0			605631		420
Q95102 UniProt NPD GO	NRAM1_BISBI	Natural resistance-associated macrophage protein 1 (NRAMP 1)	0.02	-	end	11	Membrane; multi-pass membrane protein (Probable)				548
Q27981 UniProt NPD GO	NRAM1_BOVIN	Natural resistance-associated macrophage protein 1 (NRAMP 1)	0.02	-	end	11	Membrane; multi-pass membrane protein (Probable)				548
Q27946 UniProt NPD GO	NRAM1_BUBBU	Natural resistance-associated macrophage protein 1 (NRAMP 1)	0.02	-	end	11	Membrane; multi-pass membrane protein (Probable)				548
P56436 UniProt NPD GO	NRAM1_CEREL	Natural resistance-associated macrophage protein 1 (NRAMP 1)	0.02	-	end	11	Membrane; multi-pass membrane protein (Probable)				548
O77741 UniProt NPD GO	NRAM1_PIG	Natural resistance-associated macrophage protein 1 (NRAMP 1)	0.02	-	end	10	Membrane; multi-pass membrane protein (Probable)				538
P49280 UniProt NPD GO	NRAM1_SHEEP	Natural resistance-associated macrophage protein 1 (NRAMP 1)	0.02	-	end	11	Membrane; multi-pass membrane protein (Probable)				548
Q94EG3 UniProt NPD GO	NEC1_NICLS	Nectarin-1 precursor (EC 1.15.1.1) (Superoxide dismutase [Mn])	0.02	-	mit	0	Secreted protein. Found in the nectar				229
O43402 UniProt NPD GO	CX4NB_HUMAN	Neighbor of COX4	0.02	-	cyt	0		cytoplasm [TAS] mitochondrion [TAS] nucleus [TAS]	604886		210
P41492 UniProt NPD GO	NSK1_SARBU	Neosulfakinin-1 (Neosulfakinin-I) (Neb-SK-I)	0.02	-		0	Secreted protein				9
Q6IUR5 UniProt NPD GO	NENF_RAT	Neudesin precursor (Neuron-derived neurotrophic factor) (Spinal cord injury-related protein 10) (SCI ...	0.02	-	mit	1 *	Secreted protein; extracellular space (By similarity)				171
P19851 UniProt NPD GO	TKNB_CHICK	Neurokinin-A (Substance K) (Neuromedin-L)	0.02	-		0	Secreted protein			1N6T	10
P67934 UniProt NPD GO	TKNK_PIG	Neurokinin-B (NKB) (Neuromedin-K)	0.02	-		0	Secreted protein				10
P67935 UniProt NPD GO	TKNK_RANRI	Neurokinin-B (NKB) (Neuromedin-K)	0.02	-		0	Secreted protein				10
P01297 UniProt NPD GO	NEUB_PIG	Neuromedin B-32 [Contains: Neuromedin B]	0.02	-	cyt	0	Secreted protein				32
P23260 UniProt NPD GO	GRP_RANRI	Neuromedin C	0.02	-		0	Secreted protein				10
Q15822 UniProt NPD GO	ACHA2_HUMAN	Neuronal acetylcholine receptor protein subunit alpha-2 precursor	0.02	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]	118502		529
Q91X60 UniProt NPD GO	ACHA2_MOUSE	Neuronal acetylcholine receptor protein subunit alpha-2 precursor	0.02	-	end	4	Membrane; multi-pass membrane protein (By similarity)				512
Q5IS52 UniProt NPD GO	ACHA2_PANTR	Neuronal acetylcholine receptor protein subunit alpha-2 precursor	0.02	-	end	4	Membrane; multi-pass membrane protein (By similarity)				529
P32297 UniProt NPD GO	ACHA3_HUMAN	Neuronal acetylcholine receptor protein subunit alpha-3 precursor	0.02	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]	118503		503
P18257 UniProt NPD GO	ACHN3_CARAU	Neuronal acetylcholine receptor protein subunit non-alpha-3 precursor (GFN-alpha-3)	0.02	-	end	4	Membrane; multi-pass membrane protein				466
P51674 UniProt NPD GO	GPM6A_HUMAN	Neuronal membrane glycoprotein M6-a (M6a)	0.02	-	end	4 *	Membrane; multi-pass membrane protein	cell surface [IEP]	601275		278
P35802 UniProt NPD GO	GPM6A_MOUSE	Neuronal membrane glycoprotein M6-a (M6a)	0.02	-	end	4 *	Membrane; multi-pass membrane protein				278
Q5R9Q3 UniProt NPD GO	GPM6A_PONPY	Neuronal membrane glycoprotein M6-a (M6a)	0.02	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				278
Q9VU58 UniProt NPD GO	NPLP2_DROME	Neuropeptide-like 2 precursor (NEF peptide)	0.02	-	exc	0	Secreted protein	extracellular region [NAS]			86

You are viewing entries 84551 to 84600 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.