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
P07357 UniProt NPD GO	CO8A_HUMAN	Complement component C8 alpha chain precursor (Complement component 8 subunit alpha)	0.55	-	nuc	0	Secreted protein	extracellular space [TAS] membrane [TAS] membrane attack complex [IDA]	120950		584
P48747 UniProt NPD GO	CO9_RABIT	Complement component C9 precursor	0.55	-	nuc	0	Secreted protein				557
Q8IPM8 UniProt NPD GO	CPLX_DROME	Complexin	0.55	+	nuc	0	Membrane; lipid-anchor (Potential)				142
Q9VF78 UniProt NPD GO	COG2_DROME	Conserved oligomeric Golgi complex component 2 (LdlCp-related protein)	0.55	-	nuc	0	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity)	Golgi transport complex [ISS]			710
P06850 UniProt NPD GO	CRF_HUMAN	Corticoliberin precursor (Corticotropin-releasing factor) (CRF) (Corticotropin-releasing hormone)	0.55	-	exc	0	Secreted protein	soluble fraction [TAS]	122560		196
P01201 UniProt NPD GO	COLI_MACNE	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: NPP; Melanotropin gamma ...	0.55	-	nuc	0					264
Q17391 UniProt NPD GO	CUL3_CAEEL	Cullin-3	0.55	-	cyt	0	Cytoplasm. Nucleus				777
Q00532 UniProt NPD GO	CDKL1_HUMAN	Cyclin-dependent kinase-like 1 (EC 2.7.11.22) (Serine/threonine-protein kinase KKIALRE) (Protein kin ...	0.55	-	cyt	0	Cytoplasm. Nucleus		603441		357
P42666 UniProt NPD GO	CYSP_PLAVS	Cysteine proteinase precursor (EC 3.4.22.-)	0.55	-	nuc	1 *					583
Q92087 UniProt NPD GO	CP19A_ORYLA	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.55	-	end	0	Membrane; peripheral membrane protein				518
P51542 UniProt NPD GO	CP7A1_RABIT	Cytochrome P450 7A1 (EC 1.14.13.17) (Cholesterol 7-alpha-monooxygenase) (CYPVII) (Cholesterol 7-alph ...	0.55	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				501
Q04935 UniProt NPD GO	COX20_YEAST	Cytochrome c oxidase protein 20, mitochondrial precursor	0.55	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrial inner membrane [IDA]			205
Q9WVK8 UniProt NPD GO	CP46A_MOUSE	Cytochrome p450 46A1 (EC 1.14.13.98) (Cholesterol 24-hydroxylase) (CH24H)	0.55	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				500
O14576 UniProt NPD GO	DC1I1_HUMAN	Cytoplasmic dynein 1 intermediate chain 1 (Dynein intermediate chain 1, cytosolic) (DH IC-1) (Cytopl ...	0.55	+	cyt	0		cytoplasmic dynein complex [TAS]	603772		645
P49147 UniProt NPD GO	PA24A_CHICK	Cytosolic phospholipase A2 (cPLA2) (Phospholipase A2 group IVA) [Includes: Phospholipase A2 (EC 3.1. ...	0.55	-	cyt	0	Cytoplasm (By similarity). Cytoplasmic vesicle (By similarity). Translocates to membrane vesicles in ...				748
O77793 UniProt NPD GO	PA24A_HORSE	Cytosolic phospholipase A2 (cPLA2) (Phospholipase A2 group IVA) [Includes: Phospholipase A2 (EC 3.1. ...	0.55	-	cyt	0	Cytoplasm (By similarity). Cytoplasmic vesicle (By similarity). Translocates to membrane vesicles in ...				749
P50393 UniProt NPD GO	PA24A_RAT	Cytosolic phospholipase A2 (cPLA2) (Phospholipase A2 group IVA) [Includes: Phospholipase A2 (EC 3.1. ...	0.55	-	cyt	0	Cytoplasm (By similarity). Cytoplasmic vesicle (By similarity). Translocates to membrane vesicles in ...				752
Q60925 UniProt NPD GO	DBP_MOUSE	D site-binding protein (Albumin D box-binding protein) (Albumin D-element-binding protein)	0.55	+	nuc	0	Nucleus				325
P52702 UniProt NPD GO	DRD2_CERAE	D(2) dopamine receptor (Dopamine D2 receptor)	0.55	-	end	7 *	Membrane; multi-pass membrane protein				443
P14416 UniProt NPD GO	DRD2_HUMAN	D(2) dopamine receptor (Dopamine D2 receptor)	0.55	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] intermediate filament [TAS] plasma membrane [TAS]	126450	1I15	443
P60026 UniProt NPD GO	DRD2_PANTR	D(2) dopamine receptor (Dopamine D2 receptor)	0.55	-	end	7 *	Membrane; multi-pass membrane protein				443
Q6C070 UniProt NPD GO	SPC19_YARLI	DASH complex subunit SPC19 (Outer kinetochore protein SPC19)	0.55	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				166
Q7L5Y6 UniProt NPD GO	DET1_HUMAN	DET1 homolog (De-etiolated-1 homolog)	0.55	-	nuc	0	Nucleus (Probable)		608727		550
Q9D0A0 UniProt NPD GO	DET1_MOUSE	DET1 homolog (De-etiolated-1 homolog)	0.55	-	nuc	0	Nucleus (By similarity)				550
Q6BX14 UniProt NPD GO	DPB3_DEBHA	DNA polymerase epsilon subunit C (EC 2.7.7.7) (DNA polymerase II subunit C)	0.55	-	nuc	0	Nucleus (By similarity)				277
Q9Y767 UniProt NPD GO	DPOG_NEUCR	DNA polymerase gamma (EC 2.7.7.7) (Mitochondrial DNA polymerase catalytic subunit)	0.55	-	mit	0	Mitochondrion (By similarity)				1305
Q9HGI2 UniProt NPD GO	RAD52_NEUCR	DNA repair and recombination protein mus-11 (RAD52 homolog)	0.55	-	nuc	0	Nucleus (By similarity)				600
O43502 UniProt NPD GO	RA51C_HUMAN	DNA repair protein RAD51 homolog 3	0.55	-	cyt	0	Nucleus (Probable)	nucleus [TAS]	602774		376
P97311 UniProt NPD GO	MCM6_MOUSE	DNA replication licensing factor MCM6 (Mis5 homolog)	0.55	-	cyt	0	Nucleus (By similarity)	nucleus [IDA]			821
Q9NG98 UniProt NPD GO	TOP3A_DROME	DNA topoisomerase 3-alpha (EC 5.99.1.2) (DNA topoisomerase III alpha)	0.55	-	nuc	0					1250
P48378 UniProt NPD GO	RFX2_HUMAN	DNA-binding protein RFX2	0.55	+	nuc	0	Nucleus (Probable)		142765		723
Q5E9Z7 UniProt NPD GO	RPO3D_BOVIN	DNA-directed RNA polymerase III subunit D (EC 2.7.7.6) (DNA-directed RNA polymerase III 47 kDa polyp ...	0.55	-	nuc	0	Nucleus (By similarity)				398
P93974 UniProt NPD GO	RPOA_EREDI	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.55	-	cyt	0	Plastid; chloroplast				339
Q8HTL7 UniProt NPD GO	RPOB2_CHLRE	DNA-directed RNA polymerase beta chain C-terminal subunit (EC 2.7.7.6) (PEP) (Plastid-encoded RNA po ...	0.55	-	nuc	0	Plastid; chloroplast				626
Q3BAQ1 UniProt NPD GO	RPOC1_PHAAO	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.55	-	cyt	0	Plastid; chloroplast				679
Q17298 UniProt NPD GO	MEC4_CAEBR	Degenerin mec-4 (Mechanosensory protein 4)	0.55	-	vac	1	Membrane; multi-pass membrane protein				768
P61827 UniProt NPD GO	DRE2G_ARATH	Dehydration-responsive element-binding protein 2G (DREB2G protein)	0.55	-	nuc	0	Nucleus (Probable)				307
P36413 UniProt NPD GO	ODP2_DICDI	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochond ...	0.55	-	nuc	0	Mitochondrion; mitochondrial matrix				592
P42658 UniProt NPD GO	DPP6_HUMAN	Dipeptidyl aminopeptidase-like protein 6 (Dipeptidylpeptidase VI) (Dipeptidylpeptidase 6) (Dipeptidy ...	0.55	-	mit	1	Membrane; single-pass type II membrane protein (Probable)		126141	1XFD	865
P97318 UniProt NPD GO	DAB1_MOUSE	Disabled homolog 1	0.55	-	nuc	0		intracellular [TAS]		1OQN	588
Q9QZK7 UniProt NPD GO	DOK3_MOUSE	Docking protein 3 (Downstream of tyrosine kinase 3) (P62(dok)-like protein) (DOK-L)	0.55	-	nuc	0	Cytoplasm	cytoplasm [IDA]			444
P68350 UniProt NPD GO	DOF15_ARATH	Dof zinc finger protein DOF1.5 (AtDOF1.5)	0.55	-	nuc	0	Nucleus				175
Q9QZ59 UniProt NPD GO	DMRT1_MOUSE	Doublesex- and mab-3-related transcription factor 1	0.55	-	nuc	0	Nucleus (Potential)				374
Q6P9N1 UniProt NPD GO	DRC1A_MOUSE	Down-regulated by CTNNB1 protein A	0.55	-	nuc	0	Cytoplasm (By similarity)				521
Q8VID6 UniProt NPD GO	PDE11_RAT	Dual 3',5'-cyclic-AMP and -GMP phosphodiesterase 11A (EC 3.1.4.17) (EC 3.1.4.35) (cAMP and cGMP phos ...	0.55	-	end	0	Cytoplasm; cytosol (By similarity)				935
P46734 UniProt NPD GO	MP2K3_HUMAN	Dual specificity mitogen-activated protein kinase kinase 3 (EC 2.7.12.2) (MAP kinase kinase 3) (MAPK ...	0.55	-	cyt	0			602315		347
Q96S53 UniProt NPD GO	TESK2_HUMAN	Dual specificity testis-specific protein kinase 2 (EC 2.7.12.1) (Testicular protein kinase 2)	0.55	-	mit	0	Nucleus	nucleus [ISS]	604746		571
Q39565 UniProt NPD GO	DYHB_CHLRE	Dynein beta chain, flagellar outer arm	0.55	-	end	0	Flagellum				4568
Q95LG1 UniProt NPD GO	LYAM2_HORSE	E-selectin precursor (Endothelial leukocyte adhesion molecule 1) (ELAM-1) (Leukocyte-endothelial cel ...	0.55	+	nuc	1	Membrane; single-pass type I membrane protein				610
P61559 UniProt NPD GO	ENH1_PANTR	ERV-H1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (Env protein) (ERV-H/env6 ...	0.55	-	nuc	2 *					457

You are viewing entries 21901 to 21950 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.