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
Q6H501 UniProt NPD GO	HKT6_ORYSA	Probable cation transporter HKT6 (OsHKT6)	0.22	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				530
Q9LVT4 UniProt NPD GO	DRL37_ARATH	Probable disease resistance protein At5g47250	0.22	-	cyt	0		mitochondrion [IDA]			843
O59855 UniProt NPD GO	HSP72_SCHPO	Probable heat shock protein ssa2	0.22	-	cyt	0	Cytoplasm (Potential)				646
Q2HU65 UniProt NPD GO	H2A2_MEDTR	Probable histone H2A.2	0.22	+	nuc	0	Nucleus (By similarity)				153
Q8VC74 UniProt NPD GO	OXAL2_MOUSE	Probable inner membrane protein OXA1L2, mitochondrial precursor	0.22	-	end	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				331
P87207 UniProt NPD GO	MNT3_CANAL	Probable mannosyltransferase MNT3 (EC 2.4.1.131)	0.22	-	exc	0	Membrane; single-pass type II membrane protein (Potential)				378
Q03862 UniProt NPD GO	ARX1_YEAST	Probable metalloprotease ARX1 (EC 3.-.-.-) (Associated with ribosomal export complex protein 1)	0.22	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleoplasm [IDA]			593
Q8LGI2 UniProt NPD GO	SCPDH_ARATH	Probable mitochondrial saccharopine dehydrogenase At5g39410 (EC 1.5.1.9) (SDH)	0.22	-	cyt	0	Mitochondrion; mitochondrial membrane				454
Q5Y5T1 UniProt NPD GO	ZDH20_MOUSE	Probable palmitoyltransferase ZDHHC20 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 20) ( ...	0.22	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				380
Q9C5M8 UniProt NPD GO	PEL18_ARATH	Probable pectate lyase 18 precursor (EC 4.2.2.2) (Pectate lyase A10)	0.22	-	mit	0					408
P53916 UniProt NPD GO	TEP1_YEAST	Probable phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase TEP1 (EC 3.1.3.67)	0.22	-	cyt	0					434
Q9XUE6 UniProt NPD GO	PMM_CAEEL	Probable phosphomannomutase (EC 5.4.2.8) (PMM)	0.22	-	nuc	1 *	Cytoplasm (By similarity)				245
O82291 UniProt NPD GO	PAP3_ARATH	Probable plastid-lipid-associated protein 3, chloroplast precursor (AtPap3) (Fibrillin-3)	0.22	-	mit	0	Plastid; chloroplast (Potential)	thylakoid membrane (sensu Viridiplantae) [IDA]			376
P57681 UniProt NPD GO	PCYOX_ARATH	Probable prenylcysteine oxidase precursor (EC 1.8.3.5)	0.22	-	exc	0	Lysosome (By similarity)				500
Q09720 UniProt NPD GO	PSB2_SCHPO	Probable proteasome subunit beta type 2 (EC 3.4.25.1)	0.22	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [TAS]			194
P87120 UniProt NPD GO	RNP3_SCHPO	Probable ribonuclease P protein subunit 3 (EC 3.1.26.5)	0.22	-	cyt	0	Nucleus (Potential)				235
Q10013 UniProt NPD GO	SMD1_CAEEL	Probable small nuclear ribonucleoprotein Sm D1 (snRNP core protein D1) (Sm-D1)	0.22	+	nuc	0	Nucleus (By similarity)				126
P15399 UniProt NPD GO	PBAS_RAT	Probasin precursor (PB) (M-40)	0.22	-	exc	0	Nucleus. Secreted protein				177
Q16342 UniProt NPD GO	PDCD2_HUMAN	Programmed cell death protein 2 (Zinc finger protein Rp-8) (Zinc finger MYND domain-containing prote ...	0.22	-	cyt	0	Nucleus (Potential)		600866		344
Q6UC74 UniProt NPD GO	PRL_CEREL	Prolactin precursor (PRL)	0.22	-	nuc	0	Secreted protein				229
P37884 UniProt NPD GO	PRL_MESAU	Prolactin precursor (PRL)	0.22	-	exc	0	Secreted protein				226
Q28235 UniProt NPD GO	PRLR_CEREL	Prolactin receptor precursor (PRL-R)	0.22	-	exc	1 *	Membrane; single-pass type I membrane protein	cell surface [ISS]			581
P05710 UniProt NPD GO	PRLR_RAT	Prolactin receptor precursor (PRL-R) (Lactogen receptor)	0.22	-	exc	1	Membrane; single-pass type I membrane protein	cell surface [ISS]		1F6F	610
P60986 UniProt NPD GO	PIP_BOVIN	Prolactin-inducible protein homolog precursor	0.22	-	exc	0	Secreted protein (By similarity)				145
P79393 UniProt NPD GO	PI2R_BOVIN	Prostacyclin receptor (Prostanoid IP receptor) (PGI receptor) (Prostaglandin I2 receptor)	0.22	-	end	7 *	Membrane; multi-pass membrane protein				385
P43118 UniProt NPD GO	PF2R_RAT	Prostaglandin F2-alpha receptor (Prostanoid FP receptor) (PGF receptor) (PGF2 alpha receptor)	0.22	-	end	7 *	Membrane; multi-pass membrane protein				366
Q8BHL8 UniProt NPD GO	PSMF1_MOUSE	Proteasome inhibitor PI31 subunit	0.22	-	nuc	0					271
Q27562 UniProt NPD GO	PSA1_DICDI	Proteasome subunit alpha type 1 (EC 3.4.25.1) (Proteasome subunit C2)	0.22	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				248
Q9XZG5 UniProt NPD GO	PSA5_TRYBB	Proteasome subunit alpha type 5 (EC 3.4.25.1) (20S proteasome subunit alpha-5)	0.22	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				246
Q9D9B4 UniProt NPD GO	CJ011_MOUSE	Protein C10orf11 homolog	0.22	-	nuc	0					229
P59037 UniProt NPD GO	CU084_HUMAN	Protein C21orf84	0.22	-	nuc	0					77
Q8IYB1 UniProt NPD GO	CC059_HUMAN	Protein C3orf59	0.22	-	cyt	0					489
Q6P6G2 UniProt NPD GO	CF089_RAT	Protein C6orf89 homolog	0.22	-	mit	1	Membrane; single-pass membrane protein (Potential)				348
Q5BN46 UniProt NPD GO	CI116_HUMAN	Protein C9orf116 (Pierce 1)	0.22	-	nuc	0					136
Q5TBE3 UniProt NPD GO	CI153_HUMAN	Protein C9orf153	0.22	-	nuc	0					101
Q9UBA6 UniProt NPD GO	G8_HUMAN	Protein G8	0.22	-	nuc	0			605447		126
Q92546 UniProt NPD GO	K0258_HUMAN	Protein KIAA0258	0.22	-	cyt	0					391
Q4R7X9 UniProt NPD GO	LMBRL_MACFA	Protein LMBR1L	0.22	-	end	9 *	Cell membrane; multi-pass membrane protein (By similarity)				489
Q6UX01 UniProt NPD GO	LMBRL_HUMAN	Protein LMBR1L (Lipocalin-1-interacting membrane receptor) (Lipocalin-interacting membrane receptor) ...	0.22	-	end	9 *	Cell membrane; multi-pass membrane protein		610007		489
Q9D1E5 UniProt NPD GO	LMBRL_MOUSE	Protein LMBR1L (Uteroglobin receptor)	0.22	-	end	9 *	Cell membrane; multi-pass membrane protein (By similarity)				489
Q9NQG1 UniProt NPD GO	MANBL_HUMAN	Protein MANBAL	0.22	-	nuc	1 *					85
Q9D8X0 UniProt NPD GO	MANBL_MOUSE	Protein MANBAL	0.22	-	nuc	1 *					85
Q9UGV2 UniProt NPD GO	NDRG3_HUMAN	Protein NDRG3	0.22	-	cyt	0		cytoplasm [IDA]	605273		375
Q8R2R1 UniProt NPD GO	POMT1_MOUSE	Protein O-mannosyl-transferase 1 (EC 2.4.1.109) (Dolichyl-phosphate-mannose--protein mannosyltransfe ...	0.22	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum membrane [ISS]			746
Q6UWI2 UniProt NPD GO	PARM1_HUMAN	Protein PARM-1 precursor	0.22	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				310
Q923D3 UniProt NPD GO	PARM1_MOUSE	Protein PARM-1 precursor	0.22	-	mit	1	Membrane; single-pass type I membrane protein (Potential)				296
Q5RAF8 UniProt NPD GO	PARM1_PONPY	Protein PARM-1 precursor	0.22	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				310
Q8J212 UniProt NPD GO	RHO1_KLULA	Protein Rho1	0.22	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				208
Q8WXG8 UniProt NPD GO	S100Z_HUMAN	Protein S100-Z (S100 calcium-binding protein Z)	0.22	-	nuc	0					98
P21552 UniProt NPD GO	WNT2_MOUSE	Protein Wnt-2 precursor (IRP protein) (INT-1-related protein)	0.22	-	mit	0	Secreted protein; extracellular space; extracellular matrix				360

You are viewing entries 48801 to 48850 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.