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
Q9BZW8 UniProt NPD GO	CD244_HUMAN	Natural killer cell receptor 2B4 precursor (NKR2B4) (NK cell type I receptor protein 2B4) (h2B4) (CD ...	0.94	+	exc	1	Membrane; single-pass type I membrane protein (Potential)		605554		370
Q8BG30 UniProt NPD GO	NELFA_MOUSE	Negative elongation factor A (NELF-A) (Wolf-Hirschhorn syndrome candidate 2 homolog) (mWHSC2)	0.94	+	nuc	0	Nucleus (By similarity)				530
P20156 UniProt NPD GO	VGF_RAT	Neurosecretory protein VGF precursor (VGF8a protein)	0.94	+	exc	0	Stored in secretory vesicles and then secreted				617
P28348 UniProt NPD GO	NIRA_EMENI	Nitrogen assimilation transcription factor nirA	0.94	+	nuc	0	Nucleus				892
O13412 UniProt NPD GO	AREA_ASPNG	Nitrogen regulatory protein areA	0.94	-	nuc	0	Nucleus				882
Q8K3Z9 UniProt NPD GO	PO121_MOUSE	Nuclear envelope pore membrane protein POM 121 (Pore membrane protein of 121 kDa)	0.94	+	nuc	1 *	Nucleus; nuclear envelope; nuclear pore complex; single-pass type II membrane protein (By similarity ...				1200
Q60795 UniProt NPD GO	NF2L2_MOUSE	Nuclear factor erythroid 2-related factor 2 (NF-E2-related factor 2) (NFE2-related factor 2) (Nuclea ...	0.94	+	nuc	0	Cytoplasm; cytosol. Nucleus. Cytosolic under unstressed conditions, translocates into the nucleus up ...	nucleus [IDA]		1X2R	597
Q16236 UniProt NPD GO	NF2L2_HUMAN	Nuclear factor erythroid 2-related factor 2 (NF-E2-related factor 2) (NFE2-related factor 2) (Nuclea ...	0.94	+	nuc	0	Cytoplasm; cytosol. Nucleus. Cytosolic under unstressed conditions, translocates into the nucleus up ...		600492		605
Q17370 UniProt NPD GO	NHR47_CAEEL	Nuclear hormone receptor family member nhr-47	0.94	-	nuc	0	Nucleus (Probable)				579
P70365 UniProt NPD GO	NCOA1_MOUSE	Nuclear receptor coactivator 1 (EC 2.3.1.48) (NCoA-1) (Steroid receptor coactivator 1) (SRC-1) (Nucl ...	0.94	+	nuc	0	Nucleus			1OJ5	1447
Q15788 UniProt NPD GO	NCOA1_HUMAN	Nuclear receptor coactivator 1 (EC 2.3.1.48) (NCoA-1) (Steroid receptor coactivator 1) (SRC-1) (RIP1 ...	0.94	+	nuc	0	Nucleus (By similarity)	nucleus [TAS]	602691	2C52	1441
Q9Y6Q9 UniProt NPD GO	NCOA3_HUMAN	Nuclear receptor coactivator 3 (EC 2.3.1.48) (NCoA-3) (Thyroid hormone receptor activator molecule 1 ...	0.94	+	nuc	0	Cytoplasm. Nucleus. Mainly cytoplasmic and weakly nuclear. Upon TNF activation and subsequent phosph ...	nucleus [NAS]	601937	1KBH	1424
Q9JL19 UniProt NPD GO	NCOA6_MOUSE	Nuclear receptor coactivator 6 (Amplified in breast cancer protein 3) (Cancer-amplified transcriptio ...	0.94	-	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			2067
P91136 UniProt NPD GO	NOC3L_CAEEL	Nucleolar complex protein 3 homolog (NOC3 protein homolog) (NOC3-like protein) (Nucleolar complex-as ...	0.94	+	nuc	0	Nucleus; nucleolus (By similarity)				778
Q8VI84 UniProt NPD GO	NOC3L_MOUSE	Nucleolar complex protein 3 homolog (NOC3 protein homolog) (NOC3-like protein) (Nucleolar complex-as ...	0.94	+	nuc	0	Nucleus; nucleolus. Nucleus; nucleoplasm; nuclear speckle				807
O94288 UniProt NPD GO	NOC3_SCHPO	Nucleolar complex-associated protein 3	0.94	+	nuc	0	Nucleus; nucleolus				747
Q802W4 UniProt NPD GO	NOL10_BRARE	Nucleolar protein 10	0.94	+	nuc	0	Nucleus; nucleolus (By similarity)				722
Q6DRB1 UniProt NPD GO	GLE1_BRARE	Nucleoporin GLE1 (GLE1-like protein)	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				695
Q12315 UniProt NPD GO	GLE1_YEAST	Nucleoporin GLE1 (Nuclear pore protein GLE1) (RNA export factor GLE1)	0.94	+	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Biased toward ...	mitochondrion [IDA] nuclear pore [IDA]			538
P20676 UniProt NPD GO	NUP1_YEAST	Nucleoporin NUP1 (Nuclear pore protein NUP1)	0.94	+	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; nucleoplasmic side	nuclear pore [IDA]		2BPT	1076
Q09904 UniProt NPD GO	NU124_SCHPO	Nucleoporin nup124 (Nuclear pore protein nup124)	0.94	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex	nuclear pore [TAS]			1159
P12270 UniProt NPD GO	TPR_HUMAN	Nucleoprotein TPR	0.94	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. The assembly of the NPC is a step ...	cytoplasm [TAS] nuclear pore [TAS]	189940		2349
O60890 UniProt NPD GO	OPHN1_HUMAN	Oligophrenin 1	0.94	+	nuc	0			300486		802
Q9QXY4 UniProt NPD GO	OGFR_RAT	Opioid growth factor receptor (OGFr) (Zeta-type opioid receptor)	0.94	-	nuc	0	Cytoplasm; perinuclear region. Nucleus. The OGF/OGFR complex is probably translocated to the nucleus ...				580
O13944 UniProt NPD GO	YEH1_SCHPO	Oxysterol-binding protein homolog C23H4.01c	0.94	+	nuc	0	Cytoplasm				945
Q8BXR9 UniProt NPD GO	OSBL6_MOUSE	Oxysterol-binding protein-related protein 6 (OSBP-related protein 6) (ORP-6)	0.94	-	nuc	0					959
P25066 UniProt NPD GO	P43_XENBO	P43 5S RNA-binding protein (42S P43) (Thesaurin-B)	0.94	-	nuc	0					365
Q9WTU0 UniProt NPD GO	PHF2_MOUSE	PHD finger protein 2 (GRC5)	0.94	+	nuc	0	Nucleus (Potential)				1096
Q80TJ7 UniProt NPD GO	PHF8_MOUSE	PHD finger protein 8	0.94	-	nuc	0				1WEP	1023
Q24705 UniProt NPD GO	PDM2_DROVI	POU domain protein 2 (didymous protein) (Pdm-2) (dPOU-28) (dOct2) (miti-mere) (Fragment)	0.94	+	nuc	0	Nucleus				471
P14859 UniProt NPD GO	PO2F1_HUMAN	POU domain, class 2, transcription factor 1 (Octamer-binding transcription factor 1) (Oct-1) (OTF-1) ...	0.94	+	nuc	0	Nucleus	nucleus [IDA]	164175	1POU	743
P31503 UniProt NPD GO	PO2F1_RAT	POU domain, class 2, transcription factor 1 (Octamer-binding transcription factor 1) (Oct-1) (OTF-1) ...	0.94	+	nuc	0	Nucleus				632
P09086 UniProt NPD GO	PO2F2_HUMAN	POU domain, class 2, transcription factor 2 (Octamer-binding transcription factor 2) (Oct-2) (OTF-2) ...	0.94	+	nuc	0	Nucleus		164176	1HDP	478
Q29013 UniProt NPD GO	PO2F2_PIG	POU domain, class 2, transcription factor 2 (Octamer-binding transcription factor 2) (Oct-2) (OTF-2) ...	0.94	+	nuc	0	Nucleus				478
P12272 UniProt NPD GO	PTHR_HUMAN	Parathyroid hormone-related protein precursor (PTH-rP) (PTHrP) [Contains: PTHrP[1-36]; PTHrP[38-94]; ...	0.94	+	mit	0	Cytoplasm. Nucleus. Secreted protein	cytoplasm [TAS] extracellular space [TAS]	168470	1M5N	177
P0C1I9 UniProt NPD GO	CYP11_RHIOR	Peptidyl-prolyl cis-trans isomerase cyp11 (EC 5.2.1.8) (PPIase cyp11) (Rotamase cyp11) (Cyclophilin ...	0.94	+	nuc	0					338
P55201 UniProt NPD GO	BRPF1_HUMAN	Peregrin (Bromodomain and PHD finger-containing protein 1) (BR140 protein)	0.94	-	nuc	0	Nucleus (Probable)	nucleus [TAS]	602410		1214
Q8NEY8 UniProt NPD GO	PPHLN_HUMAN	Periphilin-1 (Gastric cancer antigen Ga50)	0.94	-	nuc	0	Nucleus. Cytoplasm. In undifferentiated keratinocytes expressed in speckle-type nuclear granules and ...		608150		458
Q86YN6 UniProt NPD GO	PRGC2_HUMAN	Peroxisome proliferator-activated receptor gamma coactivator 1-beta (PPAR gamma coactivator-1beta) ( ...	0.94	+	nuc	0	Nucleus	nucleus [ISS]	608886		1023
Q61194 UniProt NPD GO	P3C2A_MOUSE	Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing alpha polypeptide (EC 2.7.1.154) (Pho ...	0.94	-	nuc	0				2B3R	1686
P28069 UniProt NPD GO	PIT1_HUMAN	Pituitary-specific positive transcription factor 1 (Pit-1) (Growth hormone factor 1) (GHF-1)	0.94	+	nuc	0	Nucleus		173110		291
Q96RN5 UniProt NPD GO	PCQAP_HUMAN	Positive cofactor 2 glutamine/Q-rich-associated protein (PC2 glutamine/Q-rich-associated protein) (T ...	0.94	-	nuc	0	Cytoplasm. Nucleus		607372		788
Q4WZJ6 UniProt NPD GO	RAD18_ASPFU	Postreplication repair ubiquitin-protein ligase E3 rad18 (EC 6.-.-.-)	0.94	-	nuc	0	Nucleus (By similarity)				418
Q92953 UniProt NPD GO	KCNB2_HUMAN	Potassium voltage-gated channel subfamily B member 2 (Voltage-gated potassium channel subunit Kv2.2) ...	0.94	-	nuc	5	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	607738		911
Q6CU65 UniProt NPD GO	CEF1_KLULA	Pre-mRNA-splicing factor CEF1	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				543
P19735 UniProt NPD GO	PRP6_YEAST	Pre-mRNA-splicing factor PRP6	0.94	-	nuc	0	Nucleus	U4/U6 x U5 tri-snRNP complex [IDA]			899
Q4WHG0 UniProt NPD GO	CEF1_ASPFU	Pre-mRNA-splicing factor cef1	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				792
Q5AW35 UniProt NPD GO	CEF1_EMENI	Pre-mRNA-splicing factor cef1	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				791
Q7RWR8 UniProt NPD GO	CWC26_NEUCR	Pre-mRNA-splicing factor cwc-26	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				377
Q4WKB9 UniProt NPD GO	CWC22_ASPFU	Pre-mRNA-splicing factor cwc22	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				881

You are viewing entries 2401 to 2450 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.