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
Q95708 UniProt NPD GO	NU3M_HYLLA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.06	-	end	3 *					115
Q35262 UniProt NPD GO	NU3M_ONCKE	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.06	-	end	3 *					116
P11629 UniProt NPD GO	NU3M_ONCMY	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.06	-	end	3 *					116
P25707 UniProt NPD GO	NU3M_ONCTS	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.06	-	end	3 *					116
P05506 UniProt NPD GO	NU3M_RAT	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.06	-	end	3 *					115
O99869 UniProt NPD GO	NU3M_SOLTU	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.06	-	mit	2 *					118
P34853 UniProt NPD GO	NU4M_APILI	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.06	-	end	13 *					447
P24892 UniProt NPD GO	NU4M_CAEEL	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.06	-	end	13 *					409
P48917 UniProt NPD GO	NU4M_PICCA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.06	-	end	14 *					511
P92492 UniProt NPD GO	NU4M_AGKCO	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.06	-	end	6 *					231
P51898 UniProt NPD GO	NU4M_ANOAR	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.06	-	nuc	5 *					221
P18934 UniProt NPD GO	NU4LM_DROME	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.06	-	end	3 *					96
P07708 UniProt NPD GO	NU4LM_DROYA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.06	-	end	3 *					96
P12773 UniProt NPD GO	NU4LM_PARLI	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.06	-	end	3 *					97
P25000 UniProt NPD GO	NU4LM_PISOC	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.06	-	end	3 *					98
Q9ZZ46 UniProt NPD GO	NU4LM_SQUAC	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.06	-	cyt	3 *					98
P48918 UniProt NPD GO	NU5M_ALBCO	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.06	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				545
P34855 UniProt NPD GO	NU5M_APILI	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.06	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				554
P48919 UniProt NPD GO	NU5M_CANPA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.06	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				555
P48176 UniProt NPD GO	NU5M_ONCMY	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.06	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				612
P50366 UniProt NPD GO	NU5M_PHYIN	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.06	-	end	17 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				664
Q9ZYM7 UniProt NPD GO	NU5M_RHISA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.06	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				552
Q36151 UniProt NPD GO	NU5M_TARSY	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5) (Fragment)	0.06	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				79
P34856 UniProt NPD GO	NU6M_ANOGA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.06	-	end	4 *					174
O99827 UniProt NPD GO	NU6M_RHISA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.06	-	end	4 *					149
P78804 UniProt NPD GO	DHE4_SCHPO	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (NADP-dependent glutamate dehydrogenas ...	0.06	-	cyt	0					451
Q9HBY0 UniProt NPD GO	NOX3_HUMAN	NADPH oxidase 3 (EC 1.6.3.-) (gp91phox homolog 3) (GP91-3) (Mitogenic oxidase 2)	0.06	-	end	5 *	Membrane; multi-pass membrane protein (Potential)		607105		568
Q93725 UniProt NPD GO	NEDD8_CAEEL	NEDD8 precursor (Ubiquitin-like protein Nedd8) (Neddylin) (Protein NED-8)	0.06	-	nuc	0	Nucleus. Cytoplasm. Mainly nuclear during interphase; also cytoplasmic during interphase and mitosis ...				77
P0C031 UniProt NPD GO	RUB2_ORYSA	NEDD8-like protein RUB2 precursor (Ubiquitin-related protein 2) (OsRUB2)	0.06	-	cyt	0					77
Q32NS2 UniProt NPD GO	KBRS2_XENLA	NF-kappa-B inhibitor-interacting Ras-like protein 2 (I-kappa-B-interacting Ras-like protein 2) (Kapp ...	0.06	-	cyt	0	Cytoplasm (By similarity)				163
Q99LD8 UniProt NPD GO	DDAH2_MOUSE	NG,NG-dimethylarginine dimethylaminohydrolase 2 (EC 3.5.3.18) (Dimethylargininase-2) (Dimethylargini ...	0.06	-	cyt	0					285
Q9H841 UniProt NPD GO	NPAL2_HUMAN	NIPA-like protein 2	0.06	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				368
Q21434 UniProt NPD GO	NRAML_CAEEL	NRAMP-like transporter smf-1	0.06	-	end	10	Membrane; multi-pass membrane protein (Probable)				557
O70378 UniProt NPD GO	CX4NB_MOUSE	Neighbor of COX4	0.06	-	cyt	0		mitochondrion [IDA]			207
P02683 UniProt NPD GO	NSG1_RAT	Neuron-specific protein family member 1 (Brain neuron cytoplasmic protein 1)	0.06	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				185
Q62092 UniProt NPD GO	NSG1_MOUSE	Neuron-specific protein family member 1 (Brain neuron cytoplasmic protein 1) (P21) (M234)	0.06	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				185
Q8BNY6 UniProt NPD GO	NCS1_MOUSE	Neuronal calcium sensor 1 (NCS-1) (Frequenin homolog)	0.06	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein (By similarity). Ass ...	axon [IDA] dendrite [IDA]			189
P62167 UniProt NPD GO	NCS1_CHICK	Neuronal calcium sensor 1 (NCS-1) (Frequenin homolog) (Frequenin-like protein) (Frequenin-like ubiqu ...	0.06	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein (By similarity). Ass ...				189
P62166 UniProt NPD GO	NCS1_HUMAN	Neuronal calcium sensor 1 (NCS-1) (Frequenin homolog) (Frequenin-like protein) (Frequenin-like ubiqu ...	0.06	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein. Associated with Gol ...		603315	1G8I	189
P62168 UniProt NPD GO	NCS1_RAT	Neuronal calcium sensor 1 (NCS-1) (Frequenin homolog) (Frequenin-like protein) (Frequenin-like ubiqu ...	0.06	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein (By similarity). Ass ...				189
P0C0P6 UniProt NPD GO	NPS_HUMAN	Neuropeptide S precursor	0.06	-	nuc	0	Secreted protein (Potential)		609513		89
P29071 UniProt NPD GO	NEUY_ONCMY	Neuropeptide Y (NPY)	0.06	-	nuc	0	Secreted protein				36
P79113 UniProt NPD GO	NPY2R_BOVIN	Neuropeptide Y receptor type 2 (NPY2-R) (NPY-Y2 receptor)	0.06	-	end	7	Membrane; multi-pass membrane protein				384
Q9Z2D5 UniProt NPD GO	NPY2R_CAVPO	Neuropeptide Y receptor type 2 (NPY2-R) (NPY-Y2 receptor)	0.06	-	end	7	Membrane; multi-pass membrane protein				381
O02836 UniProt NPD GO	NPY2R_PIG	Neuropeptide Y receptor type 2 (NPY2-R) (NPY-Y2 receptor)	0.06	-	end	7	Membrane; multi-pass membrane protein				382
P81796 UniProt NPD GO	NEUT_BUFMA	Neurotensin (NT)	0.06	-		0	Secreted protein				13
Q95WD2 UniProt NPD GO	SCE3_CENSC	Neurotoxin E3 precursor (CsE3)	0.06	-	exc	1 *	Secreted protein				87
P83560 UniProt NPD GO	TXMG4_MACGS	Neurotoxin Magi 4 precursor	0.06	-	exc	0	Secreted protein				105
Q9FKT9 UniProt NPD GO	NAS2_ARATH	Nicotianamine synthase 2 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-adenosyl-m ...	0.06	-	mit	0					320
P32860 UniProt NPD GO	NFU1_YEAST	NifU-like protein, mitochondrial precursor	0.06	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			256

You are viewing entries 72601 to 72650 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.