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
P13542 UniProt NPD GO	MYH8_MOUSE	Myosin-8 (Myosin heavy chain, skeletal muscle, perinatal) (MyHC-perinatal)	0.95	+	nuc	0	Thick filaments of the myofibrils				1937
Q9UR39 UniProt NPD GO	HST4_SCHPO	NAD-dependent deacetylase hst4 (EC 3.5.1.-) (Homologous to SIR2 protein 4)	0.95	-	nuc	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA]			415
Q9GZU8 UniProt NPD GO	NIP30_HUMAN	NEFA-interacting nuclear protein NIP30	0.95	+	nuc	0	Nucleus (Potential)				254
Q6X4W1 UniProt NPD GO	NELF_HUMAN	Nasal embryonic luteinizing hormone-releasing hormone factor (Nasal embryonic LHRH factor)	0.95	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Found on the outside of the LHRH cell me ...		608137		530
Q99NF2 UniProt NPD GO	NELF_MOUSE	Nasal embryonic luteinizing hormone-releasing hormone factor (Nasal embryonic LHRH factor) (Juxtasyn ...	0.95	-	nuc	0	Cell membrane; peripheral membrane protein. Found on the outside of the LHRH cell membrane and axons ...				532
P53094 UniProt NPD GO	MDS3_YEAST	Negative regulator of sporulation MDS3 (MCK1 dosage suppressor 3)	0.95	-	nuc	0	Cytoplasm	cytoplasm [IDA] mitochondrion [IDA]			1487
Q8NF91 UniProt NPD GO	SYNE1_HUMAN	Nesprin-1 (Nuclear envelope spectrin repeat protein 1) (Synaptic nuclear envelope protein 1) (Syne-1 ...	0.95	-	nuc	0	Nucleus; nuclear membrane; single-pass type IV membrane protein (Potential). The largest part of the ...	Golgi apparatus [IDA] integral to membrane [IDA] nuclear envelope [IDA] postsynaptic membrane [IDA]	608441		8797
Q9QZQ0 UniProt NPD GO	NPAS3_MOUSE	Neuronal PAS domain-containing protein 3 (Neuronal PAS3) (Member of PAS protein 6) (MOP6)	0.95	+	nuc	0	Nucleus	nucleus [IDA]			925
P18494 UniProt NPD GO	GLN3_YEAST	Nitrogen regulatory protein GLN3	0.95	-	nuc	0	Nucleus	cytosol [IDA] nucleus [IDA]			730
Q01168 UniProt NPD GO	NUT1_MAGGR	Nitrogen regulatory protein NUT1	0.95	-	nuc	0	Nucleus				956
Q92269 UniProt NPD GO	NRFA_PENUR	Nitrogen regulatory protein nrfA	0.95	-	nuc	0	Nucleus				865
O35893 UniProt NPD GO	SP100_MUSCR	Nuclear autoantigen Sp-100 (Speckled 100 kDa) (Nuclear dot-associated Sp100 protein)	0.95	+	nuc	0	Nucleus (By similarity). Found in the nuclear body, also known as nuclear domain 10 (ND10), PML onco ...				482
Q9Y2N3 UniProt NPD GO	PO121_HUMAN	Nuclear envelope pore membrane protein POM 121 (Pore membrane protein of 121 kDa) (P145)	0.95	+	nuc	1 *	Nucleus; nuclear envelope; nuclear pore complex; single-pass type II membrane protein (By similarity ...				1229
P17924 UniProt NPD GO	NFIB_CHICK	Nuclear factor 1 B-type (Nuclear factor 1/B) (NF1-B) (NFI-B) (NF-I/B) (CCAAT-box-binding transcripti ...	0.95	-	nuc	0	Nucleus				560
P13622 UniProt NPD GO	NFIB_MESAU	Nuclear factor 1 B-type (Nuclear factor 1/B) (NF1-B) (NFI-B) (NF-I/B) (CCAAT-box-binding transcripti ...	0.95	-	nuc	0	Nucleus				561
P97863 UniProt NPD GO	NFIB_MOUSE	Nuclear factor 1 B-type (Nuclear factor 1/B) (NF1-B) (NFI-B) (NF-I/B) (CCAAT-box-binding transcripti ...	0.95	-	nuc	0	Nucleus				570
O54968 UniProt NPD GO	NF2L2_RAT	Nuclear factor erythroid 2-related factor 2 (NF-E2-related factor 2) (NFE2-related factor 2) (Nuclea ...	0.95	+	nuc	0	Cytoplasm; cytosol (By similarity). Nucleus (By similarity). Cytosolic under unstressed conditions, ...				597
O77245 UniProt NPD GO	E75_METEN	Nuclear hormone receptor E75	0.95	-	nuc	0	Nucleus (Potential)				606
Q24143 UniProt NPD GO	HR96_DROME	Nuclear hormone receptor HR96 (dHR96)	0.95	-	nuc	0	Nucleus				723
Q9WUI9 UniProt NPD GO	NCOA2_RAT	Nuclear receptor coactivator 2 (NCoA-2) (Transcriptional intermediary factor 2)	0.95	-	nuc	0	Nucleus				1465
Q9W705 UniProt NPD GO	NCOA2_XENLA	Nuclear receptor coactivator 2 (NCoA-2) (Transcriptional intermediary factor 2) (xTIF2)	0.95	-	nuc	0	Nucleus				1516
O09000 UniProt NPD GO	NCOA3_MOUSE	Nuclear receptor coactivator 3 (EC 2.3.1.48) (NCoA-3) (Thyroid hormone receptor activator molecule 1 ...	0.95	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Mainly cytoplasmic and weakly nuclear. Upon TNF ...	nucleus [IDA]			1398
P26377 UniProt NPD GO	STP2_BOVIN	Nuclear transition protein 2 (TP-2) (TP2)	0.95	+	mit	0	Nucleus				132
Q8WTT2 UniProt NPD GO	NOC3L_HUMAN	Nucleolar complex protein 3 homolog (NOC3 protein homolog) (NOC3-like protein) (Nucleolar complex-as ...	0.95	+	nuc	0	Nucleus; nucleolus. Nucleus; nucleoplasm; nuclear speckle				800
Q7T0Q5 UniProt NPD GO	NOL10_XENLA	Nucleolar protein 10	0.95	-	nuc	0	Nucleus; nucleolus (By similarity)				689
Q6NVM6 UniProt NPD GO	NOL10_XENTR	Nucleolar protein 10	0.95	-	nuc	0	Nucleus; nucleolus (By similarity)				686
Q5M8L0 UniProt NPD GO	OTU6B_XENTR	OTU domain-containing protein 6B	0.95	+	nuc	0					294
Q99J31 UniProt NPD GO	OPHN1_MOUSE	Oligophrenin 1	0.95	+	nuc	0		actin cytoskeleton [IDA]			802
Q7YQL6 UniProt NPD GO	OPHN1_PANTR	Oligophrenin 1	0.95	+	nuc	0					802
Q7YQL5 UniProt NPD GO	OPHN1_PONPY	Oligophrenin 1	0.95	+	nuc	0					802
Q12451 UniProt NPD GO	OSH2_YEAST	Oxysterol-binding protein homolog 2	0.95	+	nuc	0	Cell membrane; peripheral membrane protein. Cell periphery, enriched in small buds of G1 phase cells ...	bud neck [IDA] plasma membrane [IDA]			1283
Q62755 UniProt NPD GO	NR1H2_RAT	Oxysterols receptor LXR-beta (Liver X receptor beta) (Nuclear orphan receptor LXR-beta) (Ubiquitousl ...	0.95	+	nuc	0	Nucleus (Potential)				446
Q812D1 UniProt NPD GO	PSIP1_RAT	PC4 and SFRS1-interacting protein (Lens epithelium-derived growth factor)	0.95	+	nuc	0	Nucleus (By similarity)				528
P68907 UniProt NPD GO	PZRN3_RAT	PDZ domain-containing RING finger protein 3 (Semaphorin cytoplasmic domain-associated protein 3) (SE ...	0.95	+	nuc	0					1062
O75420 UniProt NPD GO	PERQ1_HUMAN	PERQ amino acid rich with GYF domain protein 1	0.95	+	nuc	0					817
P31370 UniProt NPD GO	POU1_DUGJA	POU domain protein 1 (DjPOU1)	0.95	+	nuc	0	Nucleus (Probable)				559
P25425 UniProt NPD GO	PO2F1_MOUSE	POU domain, class 2, transcription factor 1 (Octamer-binding transcription factor 1) (Oct-1) (OTF-1) ...	0.95	+	nuc	0	Nucleus	nucleus [IDA]			770
Q00196 UniProt NPD GO	PO2F2_MOUSE	POU domain, class 2, transcription factor 2 (Octamer-binding transcription factor 2) (Oct-2) (OTF-2) ...	0.95	+	nuc	0	Nucleus	nucleus [IDA]			462
Q8BJI4 UniProt NPD GO	PO6F2_MOUSE	POU domain, class 6, transcription factor 2	0.95	+	nuc	0	Nucleus (By similarity)				691
Q06188 UniProt NPD GO	YL455_YEAST	PWWP domain-containing protein YLR455W	0.95	+	nuc	0	Nucleus	nucleus [IDA]			304
Q8TEW0 UniProt NPD GO	PARD3_HUMAN	Partitioning-defective 3 homolog (PARD-3) (PAR-3) (Atypical PKC isotype-specific-interacting protein ...	0.95	-	nuc	0	Intracytoplasmic membrane. Cell membrane; cell-cell junction. Partially localized along the cell-cel ...	tight junction [IDA]	606745		1356
P48725 UniProt NPD GO	PCNT_MOUSE	Pericentrin	0.95	+	nuc	0		centriole [IDA]			1920
P56645 UniProt NPD GO	PER3_HUMAN	Period circadian protein 3 (hPER3)	0.95	-	nuc	0	Nucleus (Potential)		603427		1201
Q811R2 UniProt NPD GO	PRGC2_RAT	Peroxisome proliferator-activated receptor gamma coactivator 1-beta (PPAR gamma coactivator-1beta) ( ...	0.95	+	nuc	0		nucleus [ISS]			1010
Q925J9 UniProt NPD GO	PPRB_MOUSE	Peroxisome proliferator-activated receptor-binding protein (PBP) (PPAR-binding protein) (Thyroid hor ...	0.95	+	nuc	0	Nucleus (By similarity)	mediator complex [IDA]			1575
Q15648 UniProt NPD GO	PPRB_HUMAN	Peroxisome proliferator-activated receptor-binding protein (PBP) (PPAR-binding protein) (Thyroid hor ...	0.95	+	nuc	0	Nucleus	mediator complex [IDA] nucleus [IDA]	604311	1RKH	1581
Q8BKC8 UniProt NPD GO	PI4KB_MOUSE	Phosphatidylinositol 4-kinase beta (EC 2.7.1.67) (PtdIns 4-kinase beta) (PI4Kbeta) (PI4K-beta)	0.95	-	nuc	0	Intracytoplasmic membrane (By similarity). Mitochondrion; mitochondrial outer membrane; peripheral m ...				801
O00443 UniProt NPD GO	P3C2A_HUMAN	Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing alpha polypeptide (EC 2.7.1.154) (Pho ...	0.95	-	nuc	0	Cell membrane. Golgi apparatus. Clathrin-coated vesicles. According to Ref.2, Ref.5. Nuclear. Cytopl ...		603601		1686
Q5RAY1 UniProt NPD GO	P3C2A_PONPY	Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing alpha polypeptide (EC 2.7.1.154) (Pho ...	0.95	-	nuc	0					1685
P47147 UniProt NPD GO	YMR1_YEAST	Phosphoinositide 3-phosphatase (EC 3.1.3.-) (Yeast myotubularin-related protein 1)	0.95	-	nuc	0	Cytoplasm	cytoplasm [IDA]			688

You are viewing entries 1951 to 2000 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.