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
Q99755 UniProt NPD GO	PI51A_HUMAN	Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha (EC 2.7.1.68) (Phosphatidylinositol-4-phospha ...	0.54	-	nuc	0	Cell membrane. Intracytoplasmic membrane. Associated with the plasma membrane and with internal memb ...		603275		562
O70161 UniProt NPD GO	PI51C_MOUSE	Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma (EC 2.7.1.68) (Phosphatidylinositol-4-phospha ...	0.54	-	nuc	0	Intracytoplasmic membrane. Associated with membranes. Cell membrane; cell-matrix junction; focal adh ...			1Y19	661
Q01647 UniProt NPD GO	CAPP1_FLAPR	Phosphoenolpyruvate carboxylase (EC 4.1.1.31) (PEPCase) (PEPC)	0.54	-	nuc	0	Cytoplasm				967
Q8UVX0 UniProt NPD GO	PIWI_BRARE	Piwi-like protein 1	0.54	+	mit	0	Nucleus (Potential)	nucleoplasm [IDA]			858
P30058 UniProt NPD GO	RR8_EPIVI	Plastid 30S ribosomal protein S8	0.54	-	nuc	0	Plastid				134
O08969 UniProt NPD GO	PHLA2_MOUSE	Pleckstrin homology-like domain family A member 2 (Imprinted in placenta and liver protein) (50C15 p ...	0.54	-	mit	0	Cytoplasm (Probable)	cytoplasm [TAS]			144
Q28645 UniProt NPD GO	PODXL_RABIT	Podocalyxin-like protein 1 precursor	0.54	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				551
P18493 UniProt NPD GO	PARP1_BOVIN	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) (PARP-1) (ADPRT) (NAD(+) ADP-ribosyltransferase 1) (Pol ...	0.54	+	nuc	0	Nucleus				1015
P11103 UniProt NPD GO	PARP1_MOUSE	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) (PARP-1) (ADPRT) (NAD(+) ADP-ribosyltransferase 1) (Pol ...	0.54	+	nuc	0	Nucleus	nucleus [TAS]			1012
Q2EMV9 UniProt NPD GO	PRP14_MOUSE	Poly [ADP-ribose] polymerase 14 (EC 2.4.2.30) (PARP-14) (Collaborator of STAT6) (CoaSt6)	0.54	-	cyt	0	Nucleus. Cytoplasm. In steady state cells the protein is mostly nuclear. A minor proportion is detec ...			1X4R	1817
Q38849 UniProt NPD GO	KAT2_ARATH	Potassium channel KAT2	0.54	-	mit	5	Membrane; multi-pass membrane protein				708
Q6C007 UniProt NPD GO	CWC2_YARLI	Pre-mRNA-splicing factor CWC2	0.54	-	nuc	0	Nucleus (By similarity)				382
Q4W9V0 UniProt NPD GO	SLT11_ASPFU	Pre-mRNA-splicing factor slt11	0.54	-	nuc	0	Nucleus (By similarity)				383
P32452 UniProt NPD GO	PHA2_YEAST	Prephenate dehydratase (EC 4.2.1.51) (PDT)	0.54	-	nuc	0		cytoplasm [IDA]			368
Q95ND4 UniProt NPD GO	EGF_FELCA	Pro-epidermal growth factor precursor (EGF) [Contains: Epidermal growth factor]	0.54	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1210
O95786 UniProt NPD GO	DDX58_HUMAN	Probable ATP-dependent RNA helicase DDX58 (EC 3.6.1.-) (DEAD-box protein 58) (Retinoic acid-inducibl ...	0.54	-	cyt	0	Cytoplasm		609631		925
Q91ZV8 UniProt NPD GO	GP124_MOUSE	Probable G-protein coupled receptor 124 precursor (Tumor endothelial marker 5)	0.54	-	end	6	Membrane; multi-pass membrane protein				1329
O82486 UniProt NPD GO	MTA70_ARATH	Probable N6-adenosine-methyltransferase MT-A70-like protein (EC 2.1.1.62)	0.54	-	nuc	0	Nucleus (Probable)	nucleus [ISS]			685
Q9US07 UniProt NPD GO	ARP8_SCHPO	Probable actin-related protein 8	0.54	-	nuc	0	Nucleus	nucleus [IDA]			620
Q9TVL3 UniProt NPD GO	CDK9_CAEEL	Probable cell division protein kinase 9 (EC 2.7.11.22) (EC 2.7.11.23) (Cyclin-dependent kinase 9)	0.54	-	nuc	0	Nucleus				478
P34574 UniProt NPD GO	CLH_CAEEL	Probable clathrin heavy chain protein 1	0.54	-	cyt	0	Cytoplasmic face of coated pits and vesicles (By similarity)				1681
Q9VMS9 UniProt NPD GO	C4AC1_DROME	Probable cytochrome P450 4ac1 (EC 1.14.-.-) (CYPIVAC1)	0.54	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				509
Q9FJ62 UniProt NPD GO	GLPQ1_ARATH	Probable glycerophosphoryl diester phosphodiesterase 1 precursor (EC 3.1.4.46)	0.54	-	end	1 *	Cell membrane; lipid-anchor; GPI-anchor				766
Q21993 UniProt NPD GO	PFD5_CAEEL	Probable prefoldin subunit 5	0.54	+	nuc	0					152
Q9MAG3 UniProt NPD GO	WBC25_ARATH	Probable white-brown complex homolog protein 25	0.54	-	end	5 *	Membrane; multi-pass membrane protein (By similarity)				1096
Q9JK53 UniProt NPD GO	PRELP_MOUSE	Prolargin precursor (Proline-arginine-rich end leucine-rich repeat protein)	0.54	-	mit	0	Secreted protein; extracellular space; extracellular matrix				378
P29122 UniProt NPD GO	PCSK6_HUMAN	Proprotein convertase subtilisin/kexin type 6 precursor (EC 3.4.21.-) (Paired basic amino acid cleav ...	0.54	-	nuc	0	PACE4A-I and PACE4-AII are secreted. PACE4C and PACE4CS are not secreted and remain probably in zymo ...		167405		969
Q28691 UniProt NPD GO	PE2R4_RABIT	Prostaglandin E2 receptor, EP4 subtype (Prostanoid EP4 receptor) (PGE receptor, subtype EP4)	0.54	-	end	6 *	Membrane; multi-pass membrane protein				488
Q9FYL3 UniProt NPD GO	ARTE_ARATH	Protein ARTEMIS, chloroplast precursor (Arabidopsis thaliana envelope membrane integrase) (Ath4) (AL ...	0.54	-	end	4	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein				1013
Q9FKZ3 UniProt NPD GO	ASL2_ARATH	Protein ASYMMETRIC LEAVES2 (LOB domain-containing protein 36)	0.54	-	nuc	0					313
Q9GKS9 UniProt NPD GO	CT012_MACFA	Protein C20orf12 homolog	0.54	-	nuc	0					606
Q8N7X0 UniProt NPD GO	CF103_HUMAN	Protein C6orf103	0.54	-	cyt	0					754
Q9D3P8 UniProt NPD GO	CI046_MOUSE	Protein C9orf46 homolog	0.54	-	nuc	2	Membrane; multi-pass membrane protein (Potential)				147
P35621 UniProt NPD GO	DVR1_BRARE	Protein DVR-1 precursor	0.54	-	exc	0	Secreted protein (By similarity)				355
Q9SQI2 UniProt NPD GO	GIGAN_ARATH	Protein GIGANTEA	0.54	-	nuc	0	Nucleus				1173
P38300 UniProt NPD GO	MBA1_YEAST	Protein MBA1, mitochondrial precursor	0.54	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA]			278
Q84VT7 UniProt NPD GO	WUS_LYCES	Protein WUSCHEL (LeWUS)	0.54	-	nuc	0	Nucleus (By similarity)				272
P70701 UniProt NPD GO	WN10A_MOUSE	Protein Wnt-10a precursor	0.54	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				417
Q9UBV4 UniProt NPD GO	WNT16_HUMAN	Protein Wnt-16 precursor	0.54	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix	extracellular region [NAS]	606267		365
Q61010 UniProt NPD GO	DTX1_MOUSE	Protein deltex-1 (Deltex-1) (Deltex1) (mDTX1) (FXI-T1)	0.54	+	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Partially (By similarity)				627
P34807 UniProt NPD GO	DPY20_CAEEL	Protein dpy-20 (Protein dumpy-20)	0.54	-	nuc	0					359
P83733 UniProt NPD GO	MTRM_DROYA	Protein matrimony (Cell cycle arrest protein D52)	0.54	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			219
O14156 UniProt NPD GO	PP2C4_SCHPO	Protein phosphatase 2C homolog 4 (EC 3.1.3.16) (PP2C-4)	0.54	-	mit	0	Vacuole; vacuolar membrane; peripheral membrane protein	vacuolar membrane [IDA]			383
Q5XIS1 UniProt NPD GO	SSH3_RAT	Protein phosphatase Slingshot homolog 3 (EC 3.1.3.48) (EC 3.1.3.16) (SSH-3L)	0.54	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				652
Q5BEE5 UniProt NPD GO	SEY1_EMENI	Protein sey1	0.54	-	cyt	2	Membrane; multi-pass membrane protein (Potential)				858
P25991 UniProt NPD GO	SUF_DROME	Protein suppressor of forked	0.54	-	cyt	0	Nucleus (Probable)				733
Q24155 UniProt NPD GO	TRUNK_DROME	Protein trunk precursor	0.54	-	exc	0	Secreted protein (Potential)				226
Q9QVP9 UniProt NPD GO	FAK2_MOUSE	Protein tyrosine kinase 2 beta (EC 2.7.10.2) (Focal adhesion kinase 2) (FADK 2) (Proline-rich tyrosi ...	0.54	-	nuc	0	Cytoplasm. Cell membrane. Interaction with Nephrocystin induces the membrane-association of the kina ...				1009
Q9UKW4 UniProt NPD GO	VAV3_HUMAN	Protein vav-3	0.54	-	mit	0			605541		847
P35546 UniProt NPD GO	RET_MOUSE	Proto-oncogene tyrosine-protein kinase receptor ret precursor (EC 2.7.10.1) (C-ret)	0.54	-	end	0	Membrane; single-pass type I membrane protein			1UEF	1115

You are viewing entries 22701 to 22750 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.