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
Q6CQB5 UniProt NPD GO	ERFB_KLULA	Palmitoyltransferase ERF2 (EC 2.3.1.-) (DHHC cysteine-rich domain-containing protein ERF2) (Ras prot ...	0.60	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				355
Q94G00 UniProt NPD GO	PIN1_MALDO	Peptidyl-prolyl cis-trans isomerase 1 (EC 5.2.1.8) (Rotamase Pin1) (PPIase Pin1) (MdPin1)	0.60	-	nuc	0					121
Q6CGK4 UniProt NPD GO	CWC27_YARLI	Peptidyl-prolyl isomerase CWC27 (EC 5.2.1.8)	0.60	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				356
Q01497 UniProt NPD GO	PEX3_PICAN	Peroxisomal biogenesis factor 3 (Peroxin-3) (Peroxisomal membrane protein PER9)	0.60	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein				457
Q6BS73 UniProt NPD GO	PEX6_DEBHA	Peroxisomal biogenesis factor 6 (Peroxin-6)	0.60	-	nuc	0					1198
P81062 UniProt NPD GO	PITX3_RAT	Pituitary homeobox 3 (Homeobox protein PTX3)	0.60	+	nuc	0	Nucleus				302
P46308 UniProt NPD GO	RR12_ASTLO	Plastid 30S ribosomal protein S12	0.60	+	nuc	0	Plastid				125
P30056 UniProt NPD GO	RR4_EPIVI	Plastid 30S ribosomal protein S4	0.60	-	nuc	0	Plastid				202
P30069 UniProt NPD GO	RK36_EPIVI	Plastid 50S ribosomal protein L36	0.60	-	mit	0	Plastid				37
Q8BZ20 UniProt NPD GO	PRP12_MOUSE	Poly [ADP-ribose] polymerase 12 (EC 2.4.2.30) (PARP-12) (Zinc finger CCCH domain-containing protein ...	0.60	+	nuc	0	Nucleus (Probable)				711
Q05196 UniProt NPD GO	PABP5_ARATH	Polyadenylate-binding protein 5 (Poly(A)-binding protein 5) (PABP 5)	0.60	-	nuc	0					668
Q52PG9 UniProt NPD GO	KCND1_BOVIN	Potassium voltage-gated channel subfamily D member 1	0.60	-	end	5	Membrane; multi-pass membrane protein				648
O60741 UniProt NPD GO	HCN1_HUMAN	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1 (Brain cyclic nucleot ...	0.60	-	nuc	2	Membrane; multi-pass membrane protein	integral to membrane [NAS]	602780		890
Q6FJ55 UniProt NPD GO	FIP1_CANGA	Pre-mRNA polyadenylation factor FIP1	0.60	-	nuc	0	Nucleus (By similarity)				327
Q5A7S5 UniProt NPD GO	RSE1_CANAL	Pre-mRNA-splicing factor RSE1	0.60	-	nuc	0	Nucleus (By similarity)				1219
Q7SEE1 UniProt NPD GO	PAM17_NEUCR	Presequence translocated-associated motor subunit pam-17, mitochondrial precursor	0.60	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				267
P56975 UniProt NPD GO	NRG3_HUMAN	Pro-neuregulin-3, membrane-bound isoform precursor (Pro-NRG3) [Contains: Neuregulin-3 (NRG-3)]	0.60	-	nuc	2	Pro-neuregulin-3, membrane-bound isoform: Cell membrane; single-pass type I membrane protein (By sim ...	extracellular region [NAS] integral to plasma membrane [NAS]	605533		720
Q9U5Z8 UniProt NPD GO	PSD3_ANOST	Probable 26S proteasome non-ATPase regulatory subunit 3 (26S proteasome subunit S3) (Diphenol oxidas ...	0.60	-	cyt	0					500
P33540 UniProt NPD GO	RPOP_NEUCR	Probable DNA-directed RNA polymerase (EC 2.7.7.6)	0.60	-	mit	0					896
Q3UVY1 UniProt NPD GO	GP149_MOUSE	Probable G-protein coupled receptor 149 (G-protein coupled receptor PGR10)	0.60	-	end	4 *	Membrane; multi-pass membrane protein				732
Q11082 UniProt NPD GO	YT66_CAEEL	Probable G-protein coupled receptor B0563.6	0.60	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				434
Q9VXY0 UniProt NPD GO	CP4S3_DROME	Probable cytochrome P450 4s3 (EC 1.14.-.-) (CYPIVS3)	0.60	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				495
Q8VZC7 UniProt NPD GO	DRL36_ARATH	Probable disease resistance protein At5g45510	0.60	+	nuc	0					1202
Q9XI78 UniProt NPD GO	FUT8_ARATH	Probable fucosyltransferase 8 (EC 2.4.1.-) (AtFUT8)	0.60	-	cyt	0	Golgi apparatus (Potential)				500
P33893 UniProt NPD GO	GATB_YEAST	Probable glutamyl-tRNA(Gln) amidotransferase subunit B, mitochondrial precursor (EC 6.3.5.-) (GLU-AD ...	0.60	-	mit	0	Mitochondrion (Probable)	mitochondrion [IDA]			541
Q75A41 UniProt NPD GO	CRR1_ASHGO	Probable glycosidase CRR1 precursor (EC 3.2.-.-) (CRH-related protein 1)	0.60	-	exc	0	Spore wall envelope (By similarity)				450
Q9VGP6 UniProt NPD GO	PFD3_DROME	Probable prefoldin subunit 3	0.60	-	cyt	0					185
Q22431 UniProt NPD GO	ARI2_CAEEL	Probable protein ariadne-2 (Ari-2)	0.60	-	nuc	0	Nucleus (By similarity)				482
P43078 UniProt NPD GO	PTPX_CANAL	Probable tyrosine-protein phosphatase (EC 3.1.3.48)	0.60	-	nuc	0					597
Q9JJR5 UniProt NPD GO	BCA3_MOUSE	Proline-rich protein BCA3 (Breast cancer-associated gene 3 protein) (PKA-interacting protein) (AKIP1 ...	0.60	+	nuc	0	Nucleus (By similarity). Locates to punctate spots (By similarity)				212
Q8CG70 UniProt NPD GO	P3H3_MOUSE	Prolyl 3-hydroxylase 3 precursor (EC 1.14.11.7) (Leprecan-like protein 2) (Protein B)	0.60	-	exc	0	Endoplasmic reticulum (By similarity)				732
O22621 UniProt NPD GO	ALF_PETHY	Protein ALF (Aberrant leaf and flower protein)	0.60	-	cyt	0	Nucleus (Probable)				412
Q04005 UniProt NPD GO	LIC4_YEAST	Protein ATC1/LIC4 (AIP3 complex protein 1) (Lithium comvertas protein 4)	0.60	-	nuc	0	Cytoplasm. Nucleus. The nuclear location is modulated by calcineurin	nucleus [IDA]			294
Q5JTZ5 UniProt NPD GO	CI152_HUMAN	Protein C9orf152	0.60	-	nuc	0					218
Q69YI7 UniProt NPD GO	CI090_HUMAN	Protein C9orf90	0.60	-	nuc	0					327
Q99234 UniProt NPD GO	DFG16_YEAST	Protein DFG16 (Extracellular matrix protein 41) (Zinc-regulated gene 11 protein)	0.60	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				619
Q3TJZ6 UniProt NPD GO	FA98A_MOUSE	Protein FAM98A	0.60	+	nuc	0					515
Q5FWT1 UniProt NPD GO	FA98A_RAT	Protein FAM98A	0.60	+	nuc	0					515
P33418 UniProt NPD GO	LOS1_YEAST	Protein LOS1	0.60	-	cyt	0	Nucleus	mitochondrion [IDA] nuclear matrix [IDA]			1100
Q9Y2L5 UniProt NPD GO	TRS85_HUMAN	Protein TRS85 homolog	0.60	-	nuc	0	Golgi apparatus; cis-Golgi network (By similarity)	Golgi cis-face [NAS]			1435
P51028 UniProt NPD GO	WNT8A_BRARE	Protein Wnt-8a precursor	0.60	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				359
P17885 UniProt NPD GO	BIMA_EMENI	Protein bimA	0.60	-	nuc	0	Nucleus (Potential)				806
P18756 UniProt NPD GO	ETS1B_XENLA	Protein c-ets-1-B (C-ets-1B) (XE1-B) (Fragment)	0.60	+	nuc	0	Nucleus				268
Q7PN68 UniProt NPD GO	DRM_ANOGA	Protein drumstick	0.60	-	nuc	0	Nucleus (By similarity)				81
P38094 UniProt NPD GO	FLUG_EMENI	Protein fluG	0.60	-	nuc	0	Cytoplasm				865
Q8NFP9 UniProt NPD GO	NBEA_HUMAN	Protein neurobeachin (Lysosomal-trafficking regulator 2) (Protein BCL8B)	0.60	-	end	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	cytosol [ISS] endomembrane system [ISS] Golgi trans face [ISS] plasma membrane [ISS] postsynaptic membrane [ISS]	604889	1MI1	2946
Q8K330 UniProt NPD GO	SSH3_MOUSE	Protein phosphatase Slingshot homolog 3 (EC 3.1.3.48) (EC 3.1.3.16) (SSH-3L) (mSSH-3L)	0.60	-	mit	0	Cytoplasm. Nucleus				649
O59671 UniProt NPD GO	POF4_SCHPO	Protein pof4	0.60	+	nuc	0					199
O13795 UniProt NPD GO	POF8_SCHPO	Protein pof8	0.60	-	nuc	0					402
P18102 UniProt NPD GO	TLL_DROME	Protein tailless	0.60	-	nuc	0	Nucleus (Potential)				452

You are viewing entries 19201 to 19250 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.