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
Q2TGY3 UniProt NPD GO	NU2M_MARFA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.09	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q2TGY2 UniProt NPD GO	NU2M_MARZI	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.09	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q2TGY1 UniProt NPD GO	NU2M_MUSKA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.09	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q36451 UniProt NPD GO	NU2M_ORNAN	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.09	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
P15578 UniProt NPD GO	NU2M_PODAN	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.09	-	end	11 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				556
Q35924 UniProt NPD GO	NU2M_SALSA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.09	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				349
Q9B6C8 UniProt NPD GO	NU2M_YARLI	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.09	-	end	13 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				469
P19042 UniProt NPD GO	NU2M_ARTSA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2) (Fragments)	0.09	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				136
Q37711 UniProt NPD GO	NU4M_ARTSF	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.09	-	end	11 *					386
P48915 UniProt NPD GO	NU4M_CHOCR	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.09	-	end	15 *					492
Q4JQH8 UniProt NPD GO	NU4M_TETNG	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.09	-	end	13 *					460
O03695 UniProt NPD GO	NU4M_ATRPI	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.09	-	end	6 *					231
O03699 UniProt NPD GO	NU4M_BOTER	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.09	-	end	6 *					231
O03700 UniProt NPD GO	NU4M_BOTLA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.09	-	end	6 *					231
O03701 UniProt NPD GO	NU4M_BOTSC	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.09	-	end	6 *					231
P92649 UniProt NPD GO	NU4M_LACMU	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.09	-	end	6 *					231
O03763 UniProt NPD GO	NU4M_PORHY	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.09	-	end	6 *					231
Q36150 UniProt NPD GO	NU4M_TARSY	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.09	-	mit	3 *					167
P92681 UniProt NPD GO	NU4M_TRIOK	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.09	-	exc	6 *					231
O79409 UniProt NPD GO	NU4LM_SCYCA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.09	-	mit	3 *					98
P10330 UniProt NPD GO	NU5M_OENBE	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.09	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				670
P60497 UniProt NPD GO	NU6M_ARATH	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.09	-	end	4 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				205
P18933 UniProt NPD GO	NU6M_DROME	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.09	-	end	4 *					174
Q672K1 UniProt NPD GO	NOX3_RAT	NADPH oxidase 3 (EC 1.6.3.-)	0.09	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				568
Q00141 UniProt NPD GO	NCPR_ASPNG	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.09	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)	microsome [IDA]			693
Q9AS33 UniProt NPD GO	NPL4_ORYSA	NPL4-like protein	0.09	-	mit	0					415
P31836 UniProt NPD GO	NCAM1_BOVIN	Neural cell adhesion molecule 1, 140 kDa isoform precursor (N-CAM 140) (NCAM-140)	0.09	-	end	1	Membrane; single-pass type I membrane protein				853
P41271 UniProt NPD GO	NBL1_HUMAN	Neuroblastoma suppressor of tumorigenicity 1 precursor (Zinc finger protein DAN) (N03)	0.09	-	exc	0	Secreted protein		600613		180
Q06880 UniProt NPD GO	NBL1_RAT	Neuroblastoma suppressor of tumorigenicity 1 precursor (Zinc finger protein DAN) (N03)	0.09	-	nuc	0	Secreted protein (By similarity)				178
P34965 UniProt NPD GO	NEUU_RABIT	Neuromedin U-25 (NmU-25)	0.09	-	cyt	0	Secreted protein				25
P47759 UniProt NPD GO	NSG2_MOUSE	Neuron-specific protein family member 2 (Protein p19) (8.5 protein)	0.09	-	cyt	1	Intracytoplasmic membrane; single-pass type II membrane protein. Mainly Golgi stack, but also found ...				171
P36544 UniProt NPD GO	ACHA7_HUMAN	Neuronal acetylcholine receptor protein subunit alpha-7 precursor	0.09	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]	118511		502
Q866A2 UniProt NPD GO	ACHA7_MACMU	Neuronal acetylcholine receptor protein subunit alpha-7 precursor	0.09	-	end	4	Membrane; multi-pass membrane protein				502
P49582 UniProt NPD GO	ACHA7_MOUSE	Neuronal acetylcholine receptor protein subunit alpha-7 precursor	0.09	-	end	4	Membrane; multi-pass membrane protein				502
Q05941 UniProt NPD GO	ACHA7_RAT	Neuronal acetylcholine receptor protein subunit alpha-7 precursor	0.09	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]			502
Q8MJV2 UniProt NPD GO	NPBW2_BOVIN	Neuropeptides B/W receptor type 2 (G-protein coupled receptor 8)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				336
P35519 UniProt NPD GO	NEU1_ANSAN	Neurophysin 1 (VLDV-neurophysin)	0.09	-	nuc	0	Secreted protein				93
P81768 UniProt NPD GO	NEU2_LOXAF	Neurophysin 2 (Neurophysin-II) (E-NP)	0.09	-	nuc	0	Secreted protein				92
P01482 UniProt NPD GO	SCX5_ANDMA	Neurotoxin 5 (Neurotoxin V) (Amm V) (AmmV) (Amm5)	0.09	-	nuc	0	Secreted protein				64
P83302 UniProt NPD GO	NXOH9_OPHHA	Neurotoxin Oh9-1	0.09	-	nuc	0	Secreted protein				57
P84014 UniProt NPD GO	TX23_PHORI	Neurotoxin PRTx23C2	0.09	-	nuc	0	Secreted protein				55
Q9DEQ3 UniProt NPD GO	TXL1_NAJAT	Neurotoxin homolog NL1 precursor	0.09	-	mit	0	Secreted protein				86
Q9BLM4 UniProt NPD GO	SCXA_ANDAU	Neurotoxin pcD-1005 precursor	0.09	-	exc	0	Secreted protein				85
P30783 UniProt NPD GO	TXA2_RADMA	Neurotoxin-2 (Toxin RTX-II)	0.09	-	nuc	0	Secreted protein. Found in nematocyst				48
Q5G863 UniProt NPD GO	DEF1_PANTR	Neutrophil defensin 1 precursor (Defensin, alpha 1)	0.09	-	exc	0	Secreted protein				94
Q9JHE8 UniProt NPD GO	NINJ2_RAT	Ninjurin-2 (Nerve injury-induced protein 2)	0.09	-	end	2	Membrane; multi-pass membrane protein				144
P39866 UniProt NPD GO	NIA2_PHAVU	Nitrate reductase [NADH] 2 (EC 1.7.1.1) (NR-2)	0.09	-	cyt	0					890
P32020 UniProt NPD GO	NLTP_MOUSE	Nonspecific lipid-transfer protein (EC 2.3.1.176) (Propanoyl-CoA C-acyltransferase) (NSL-TP) (Sterol ...	0.09	-	pox	0	Cytoplasm. Isoform SCP2: Mitochondrion. Cytoplasmic in the liver and also associated with mitochondr ...	mitochondrion [IDA] peroxisome [TAS]			547
P24296 UniProt NPD GO	NLTP1_WHEAT	Nonspecific lipid-transfer protein precursor (LTP) (Phospholipid transfer protein) (PLTP) (ns-LTP1) ...	0.09	-	exc	0				1GH1	113
Q5RFF8 UniProt NPD GO	NLE1_PONPY	Notchless homolog 1	0.09	-	cyt	0	Nucleus; nucleolus (By similarity)				484

You are viewing entries 66601 to 66650 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.