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
O42859 UniProt NPD GO	RT02_SCHPO	Probable mitochondrial 40S ribosomal protein mrp2	0.29	-	mit	0	Mitochondrion (By similarity)				105
Q9VUR3 UniProt NPD GO	MCA2_DROME	Probable multisynthetase complex auxiliary component p38	0.29	-	cyt	0					334
Q09510 UniProt NPD GO	MLRH_CAEEL	Probable myosin regulatory light chain	0.29	-	mit	0					172
Q8IYP9 UniProt NPD GO	ZDH23_HUMAN	Probable palmitoyltransferase ZDHHC23 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 23) ( ...	0.29	-	end	6	Membrane; multi-pass membrane protein (Potential)				409
Q9Y2G3 UniProt NPD GO	AT11B_HUMAN	Probable phospholipid-transporting ATPase IF (EC 3.6.3.1) (ATPase class I type 11B) (ATPase IR)	0.29	-	end	8	Membrane; multi-pass membrane protein	nuclear inner membrane [NAS]	605869		1177
Q8GU92 UniProt NPD GO	PDR2_ORYSA	Probable pleiotropic drug resistance protein 2	0.29	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1464
O45228 UniProt NPD GO	PROD_CAEEL	Probable proline oxidase, mitochondrial precursor (EC 1.5.3.-) (Proline dehydrogenase)	0.29	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				616
P83110 UniProt NPD GO	HTRA3_HUMAN	Probable serine protease HTRA3 precursor (EC 3.4.21.-) (High-temperature requirement factor A3) (Pre ...	0.29	-	exc	0	Secreted protein (By similarity)		608785		453
P28257 UniProt NPD GO	YCF27_GALSU	Probable transcriptional regulator ycf27 (OmpR-like protein)	0.29	-	cyt	0	Plastid; chloroplast				255
Q9UT38 UniProt NPD GO	VPS16_SCHPO	Probable vacuolar protein sorting 16	0.29	-	cyt	0					835
Q9WUL5 UniProt NPD GO	PDL2_MOUSE	Programmed cell death 1 ligand 2 precursor (Programmed death ligand 2) (PD-L2) (PD-1-ligand 2) (PDCD ...	0.29	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity)				247
P10765 UniProt NPD GO	PRL_LOXAF	Prolactin (PRL)	0.29	-	mit	0	Secreted protein				199
P49683 UniProt NPD GO	PRLHR_HUMAN	Prolactin-releasing peptide receptor (PrRP receptor) (PrRPR) (G-protein coupled receptor 10) (hGR3)	0.29	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600895		370
O43272 UniProt NPD GO	PROD_HUMAN	Proline oxidase, mitochondrial precursor (EC 1.5.3.-) (Proline dehydrogenase)	0.29	-	nuc	0	Mitochondrion; mitochondrial matrix		606810		516
Q6UW60 UniProt NPD GO	PCSK4_HUMAN	Proprotein convertase subtilisin/kexin type 4 precursor (EC 3.4.21.-) (Proprotein convertase PC4)	0.29	+	end	0	Membrane; single-pass membrane protein (Potential)		600487		755
P34980 UniProt NPD GO	PE2R3_RAT	Prostaglandin E2 receptor, EP3 subtype (Prostanoid EP3 receptor) (PGE receptor, EP3 subtype)	0.29	+	end	6 *	Membrane; multi-pass membrane protein				365
Q63921 UniProt NPD GO	PGH1_RAT	Prostaglandin G/H synthase 1 precursor (EC 1.14.99.1) (Cyclooxygenase-1) (COX-1) (Prostaglandin-endo ...	0.29	-	mit	0	Microsome; microsomal membrane; peripheral membrane protein	cytoplasm [ISS] microsome [ISS] nucleus [ISS]			602
P22141 UniProt NPD GO	PSB2_YEAST	Proteasome component C11 (EC 3.4.25.1) (Macropain subunit C11) (Proteinase YSCE subunit 11) (Multica ...	0.29	-	cyt	0	Cytoplasm. Nucleus	nucleus [IDA] proteasome core complex, beta-subunit compl... [IPI]		2FNY	198
Q3SZV5 UniProt NPD GO	POMP_BOVIN	Proteasome maturation protein (Proteassemblin)	0.29	-	nuc	0	Cytoplasm; cytosol (By similarity). Nucleus (By similarity)				141
Q27575 UniProt NPD GO	PSA73_DROME	Proteasome subunit alpha type 7-1B (EC 3.4.25.1) (Testis-specific proteasome 28 kDa subunit 1B) (Tes ...	0.29	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				252
Q5KB23 UniProt NPD GO	AF9_CRYNE	Protein AF-9 homolog	0.29	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				392
Q5M971 UniProt NPD GO	AF1Q_RAT	Protein AF1q	0.29	-	nuc	0					90
Q9NXR7 UniProt NPD GO	BRE_HUMAN	Protein BRE (Brain and reproductive organ-expressed protein) (BRCA1/BRCA2-containing complex subunit ...	0.29	-	cyt	0	Cytoplasm. Mainly. Nucleus. Also found in the nucleus	cytoplasm [IDA] nuclear ubiquitin ligase complex [IDA] nucleus [IDA]			415
Q05949 UniProt NPD GO	BUR2_YEAST	Protein BUR2 (Bypass UAS requirement protein 2) (Chromosome stability protein 4)	0.29	+	mit	0	Nucleus	nucleus [IDA]			395
Q9H2I8 UniProt NPD GO	CJ011_HUMAN	Protein C10orf11	0.29	-	nuc	0					198
Q96SZ5 UniProt NPD GO	CJ022_HUMAN	Protein C10orf22	0.29	-	nuc	0					270
Q96M42 UniProt NPD GO	CU129_HUMAN	Protein C21orf129	0.29	-	nuc	0					142
Q6MG12 UniProt NPD GO	CF136_RAT	Protein C6orf136 homolog	0.29	-	cyt	0					172
P21560 UniProt NPD GO	CBP3_YEAST	Protein CBP3, mitochondrial precursor	0.29	-	mit	0	Mitochondrion; mitochondrial membrane	mitochondrial envelope [TAS]			335
P40366 UniProt NPD GO	DLS1_YEAST	Protein DLS1 (DPB3-like subunit of ISW2 complex 1)	0.29	-	nuc	0	Nucleus	chromatin accessibility complex [IPI] nucleus [IDA]			167
P42835 UniProt NPD GO	EGT2_YEAST	Protein EGT2 precursor (Early G1 transcript 2)	0.29	-	exc	0		cell wall (sensu Fungi) [IDA]			1041
Q8IYN6 UniProt NPD GO	F100B_HUMAN	Protein FAM100B	0.29	-	nuc	0					164
Q5VSJ3 UniProt NPD GO	FA23B_HUMAN	Protein FAM23B	0.29	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				274
Q9NZY2 UniProt NPD GO	FM30A_HUMAN	Protein FAM30A	0.29	-	nuc	0					154
P38345 UniProt NPD GO	FMP21_YEAST	Protein FMP21, mitochondrial precursor (Found in mitochondrial proteome protein 21)	0.29	-	mit	0	Mitochondrion	mitochondrion [IDA]			138
P34313 UniProt NPD GO	G10_CAEEL	Protein G10 homolog	0.29	-	nuc	0	Nucleus (Potential)				147
Q5VW38 UniProt NPD GO	GP107_HUMAN	Protein GPR107 precursor (Lung seven transmembrane receptor 1)	0.29	-	end	7	Membrane; multi-pass membrane protein				600
Q43214 UniProt NPD GO	H2A6_WHEAT	Protein H2A.6 (wcH2A-3)	0.29	-	mit	0	Nucleus (By similarity)				147
P28318 UniProt NPD GO	M126_CHICK	Protein MRP-126	0.29	-	nuc	0					119
Q64311 UniProt NPD GO	NTAN1_MOUSE	Protein N-terminal asparagine amidohydrolase (EC 3.5.1.-) (Protein NH2-terminal asparagine deamidase ...	0.29	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [IDA] nucleus [IDA]			309
P53224 UniProt NPD GO	ORM1_YEAST	Protein ORM1	0.29	-	mit	3	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			222
P39937 UniProt NPD GO	PAC2_YEAST	Protein PAC2	0.29	-	nuc	0					518
Q02772 UniProt NPD GO	PT191_YEAST	Protein PET191, mitochondrial precursor	0.29	-	nuc	0	Mitochondrion	mitochondrial inner membrane [TAS]			108
Q03178 UniProt NPD GO	PIR1_YEAST	Protein PIR1 precursor (Covalently-linked cell wall protein 6)	0.29	-	exc	0	Cell wall. Attached to the cell wall	cell wall (sensu Fungi) [IDA]			341
Q9HF54 UniProt NPD GO	RHO1_ASHGO	Protein RHO1	0.29	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				207
Q5FVJ0 UniProt NPD GO	RUFY3_RAT	Protein RUFY3 (Rap2-interacting protein x) (RIPx)	0.29	-	nuc	0					469
P36135 UniProt NPD GO	UTH1_YEAST	Protein UTH1	0.29	-	nuc	0		cell wall (sensu Fungi) [IDA] mitochondrial outer membrane [TAS]			450
Q2QL85 UniProt NPD GO	WNT2_MICMU	Protein Wnt-2 precursor	0.29	-	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
P31284 UniProt NPD GO	WNT3_XENLA	Protein Wnt-3 (XWnt-3) (Fragment)	0.29	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				137
O15978 UniProt NPD GO	WNT5_HALRO	Protein Wnt-5 precursor	0.29	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix				363

You are viewing entries 41651 to 41700 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.