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
P48986 UniProt NPD GO	NDF6_MOUSE	Neurogenic differentiation factor 6 (NeuroD6) (Atonal protein homolog 2) (Helix-loop-helix protein m ...	0.82	-	nuc	0	Nucleus (Probable)				337
Q04721 UniProt NPD GO	NOTC2_HUMAN	Neurogenic locus notch homolog protein 2 precursor (Notch 2) (hN2) [Contains: Notch 2 extracellular ...	0.82	-	exc	2	Cell membrane; single-pass type I membrane protein. NICD: Nucleus. Following proteolytical processin ...	cell surface [IDA] integral to plasma membrane [IDA] nucleus [IDA]	600275		2471
P21783 UniProt NPD GO	NOTCH_XENLA	Neurogenic locus notch protein homolog precursor (xOTCH)	0.82	+	exc	2	Membrane; single-pass type I membrane protein				2524
P20181 UniProt NPD GO	NT3_MOUSE	Neurotrophin-3 precursor (NT-3) (Neurotrophic factor) (HDNF) (Nerve growth factor 2) (NGF-2)	0.82	-	nuc	0	Secreted protein	cytoplasmic membrane-bound vesicle [IDA] extracellular region [TAS]			258
P18280 UniProt NPD GO	NT3_RAT	Neurotrophin-3 precursor (NT-3) (Neurotrophic factor) (HDNF) (Nerve growth factor 2) (NGF-2)	0.82	-	nuc	0	Secreted protein	plasma membrane [IMP]			258
Q96TA1 UniProt NPD GO	NIBL_HUMAN	Niban-like protein (Meg-3)	0.82	-	cyt	0					733
P38798 UniProt NPD GO	NMD2_YEAST	Nonsense-mediated mRNA decay protein 2 (Up-frameshift suppressor 2)	0.82	-	nuc	0	Cytoplasm (Potential)	cytoplasm [TAS] polysome [IDA]			1089
Q05192 UniProt NPD GO	FTF1B_DROME	Nuclear hormone receptor FTZ-F1 beta (dHR39)	0.82	-	nuc	0	Nucleus	nucleus [IDA]			808
P52948 UniProt NPD GO	NUP98_HUMAN	Nuclear pore complex protein Nup98-Nup96 precursor [Contains: Nuclear pore complex protein Nup98 (Nu ...	0.82	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; nucleoplasmic side. Nup96 is localized to the nucle ...	nuclear pore [IDA] nucleoplasm [TAS]	601021	1KO6	1729
P51449 UniProt NPD GO	RORG_HUMAN	Nuclear receptor ROR-gamma (Nuclear receptor RZR-gamma)	0.82	-	nuc	0	Nucleus (Probable)		602943		518
Q9DBY8 UniProt NPD GO	NVL_MOUSE	Nuclear valosin-containing protein-like (Nuclear VCP-like protein) (NVLp)	0.82	+	nuc	0	Nucleus; nucleolus (By similarity)				855
Q75DA4 UniProt NPD GO	NOG2_ASHGO	Nucleolar GTP-binding protein 2	0.82	-	nuc	0	Nucleus; nucleolus (By similarity)				502
Q8K2H2 UniProt NPD GO	OTU6B_MOUSE	OTU domain-containing protein 6B	0.82	+	nuc	0					294
P54784 UniProt NPD GO	ORC1_YEAST	Origin recognition complex subunit 1 (Origin recognition complex 120 kDa subunit)	0.82	-	nuc	0	Nucleus	nuclear origin of replication recognition c... [TAS] pre-replicative complex [TAS]		1ZHI	914
Q13416 UniProt NPD GO	ORC2_HUMAN	Origin recognition complex subunit 2	0.82	-	nuc	0	Nucleus	nucleus [TAS]	601182		577
P54790 UniProt NPD GO	ORC3_YEAST	Origin recognition complex subunit 3 (Origin recognition complex 62 kDa subunit)	0.82	-	nuc	0	Nucleus	nuclear origin of replication recognition c... [TAS] pre-replicative complex [TAS]			616
Q92570 UniProt NPD GO	NR4A3_HUMAN	Orphan nuclear receptor NR4A3 (Nuclear hormone receptor NOR-1) (Neuron-derived orphan receptor 1) (M ...	0.82	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	600542		626
Q9NQC1 UniProt NPD GO	PHF15_HUMAN	PHD finger protein 15	0.82	-	nuc	0					576
Q6PJE2 UniProt NPD GO	POZP3_HUMAN	POM121 and ZP3 fusion protein (POM-ZP3)	0.82	-	nuc	0			600587		329
P23759 UniProt NPD GO	PAX7_HUMAN	Paired box protein Pax-7 (HUP1)	0.82	+	nuc	0	Nucleus		268220		520
P54821 UniProt NPD GO	PRRX1_HUMAN	Paired mesoderm homeobox protein 1 (PRX-1) (Paired-related homeobox protein 1) (Homeobox protein PHO ...	0.82	+	nuc	0	Nucleus		167420		245
Q9BMM8 UniProt NPD GO	MYSP_SARSC	Paramyosin	0.82	-	nuc	0	Thick filaments of the myofibrils				876
Q9UUE4 UniProt NPD GO	PPIL4_SCHPO	Peptidyl-prolyl cis-trans isomerase cyp6 (EC 5.2.1.8) (PPIase cyp6) (Rotamase cyp8)	0.82	-	nuc	0	Nucleus				432
Q2U256 UniProt NPD GO	PPIL4_ASPOR	Peptidyl-prolyl cis-trans isomerase-like 4 (EC 5.2.1.8) (PPIase) (Rotamase)	0.82	-	nuc	0	Nucleus (By similarity)				461
P12348 UniProt NPD GO	PER_DROPS	Period circadian protein	0.82	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				1241
O74539 UniProt NPD GO	MAK3_SCHPO	Peroxide stress-activated histidine kinase mak3 (EC 2.7.13.3) (Mcs4-associated kinase 3) (His-Asp ph ...	0.82	-	nuc	0	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA]			2344
P62025 UniProt NPD GO	PHAR2_RAT	Phosphatase and actin regulator 2	0.82	-	nuc	0					569
Q15735 UniProt NPD GO	PI5PA_HUMAN	Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A (EC 3.1.3.56)	0.82	-	nuc	0	Cytoplasm (By similarity). Predominantly localized to membrane ruffles (By similarity)	cytoplasm [IDA] ruffle [IDA]	606481		1006
P10490 UniProt NPD GO	CAPP1_MESCR	Phosphoenolpyruvate carboxylase 1 (EC 4.1.1.31) (PEPCase 1) (PEPC 1)	0.82	-	nuc	0	Cytoplasm				966
O02696 UniProt NPD GO	PI3R5_PIG	Phosphoinositide 3-kinase regulatory subunit 5 (PI3-kinase regulatory subunit 5) (PI3-kinase p101 su ...	0.82	-	nuc	0	Nucleus. Cytoplasm. Membrane; peripheral membrane protein				877
Q8WYR1 UniProt NPD GO	PI3R5_HUMAN	Phosphoinositide 3-kinase regulatory subunit 5 (PI3-kinase regulatory subunit 5) (PI3-kinase p101 su ...	0.82	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Membrane; peripheral membrane protein (By simila ...				880
Q9SWI1 UniProt NPD GO	PKS1_ARATH	Phytochrome kinase substrate 1	0.82	-	nuc	0	Cytoplasm				439
P51004 UniProt NPD GO	PAPO1_XENLA	Poly(A) polymerase alpha-A (EC 2.7.7.19) (PAP) (Polynucleotide adenylyltransferase) (Fragment)	0.82	+	nuc	0	Nucleus				715
Q8S4P4 UniProt NPD GO	EZ3_MAIZE	Polycomb protein EZ3 (Enhancer of zeste protein 3)	0.82	-	nuc	0	Nucleus (Probable)				895
Q96GD3 UniProt NPD GO	SCMH1_HUMAN	Polycomb protein SCMH1 (Sex comb on midleg homolog 1)	0.82	-	nuc	0	Nucleus (Probable)	nucleus [IC]			660
Q8QHL5 UniProt NPD GO	PHC2_BRARE	Polyhomeotic-like protein 2	0.82	+	nuc	0	Nucleus (Probable)				827
Q9QWH1 UniProt NPD GO	PHC2_MOUSE	Polyhomeotic-like protein 2 (mPH2) (Early development regulatory protein 2) (p36)	0.82	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			850
P10862 UniProt NPD GO	RAD18_YEAST	Postreplication repair ubiquitin-protein ligase E3 RAD18 (EC 6.-.-.-) (Radiation sensitivity protein ...	0.82	-	nuc	0	Nucleus	nuclear chromatin [IDA]			487
Q9NR82 UniProt NPD GO	KCNQ5_HUMAN	Potassium voltage-gated channel subfamily KQT member 5 (Voltage-gated potassium channel subunit Kv7. ...	0.82	-	end	5	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	607357		897
Q6CKI1 UniProt NPD GO	PRP5_KLULA	Pre-mRNA-processing ATP-dependent RNA helicase PRP5 (EC 3.6.1.-)	0.82	-	nuc	0	Nucleus (By similarity)				812
Q9P7C7 UniProt NPD GO	PRP11_SCHPO	Pre-mRNA-processing ATP-dependent RNA helicase prp11 (EC 3.6.1.-)	0.82	-	nuc	0	Nucleus (By similarity)				1014
Q6C024 UniProt NPD GO	PRP28_YARLI	Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 (EC 3.6.1.-)	0.82	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				575
O42904 UniProt NPD GO	PRP31_SCHPO	Pre-mRNA-splicing factor 31	0.82	+	nuc	0	Nucleus (Potential)				518
Q5K9L1 UniProt NPD GO	CEF1_CRYNE	Pre-mRNA-splicing factor CEF1	0.82	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				838
Q5K654 UniProt NPD GO	CLF1_PARBR	Pre-mRNA-splicing factor CLF1	0.82	+	cyt	0	Nucleus (By similarity)				677
Q4PB95 UniProt NPD GO	PRP45_USTMA	Pre-mRNA-splicing factor PRP45 (Pre-mRNA-processing protein 45)	0.82	-	nuc	0	Nucleus (By similarity)				638
Q753K4 UniProt NPD GO	SYF2_ASHGO	Pre-mRNA-splicing factor SYF2	0.82	-	nuc	0	Nucleus (By similarity)				192
Q4WUA0 UniProt NPD GO	CWC24_ASPFU	Pre-mRNA-splicing factor cwc24	0.82	-	nuc	0	Nucleus (By similarity)				339
O35569 UniProt NPD GO	NRG2_RAT	Pro-neuregulin-2, membrane-bound isoform precursor (Pro-NRG2) [Contains: Neuregulin-2 (NRG-2) (Neura ...	0.82	-	nuc	1	Pro-neuregulin-2, membrane-bound isoform: Cell membrane; single-pass type I membrane protein (By sim ...				868
Q9Y4C8 UniProt NPD GO	RBM19_HUMAN	Probable RNA-binding protein 19 (RNA-binding motif protein 19)	0.82	+	nuc	0	Nucleus; nucleolus				960

You are viewing entries 7951 to 8000 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.