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
P27214 UniProt NPD GO	ANX11_BOVIN	Annexin A11 (Annexin XI) (Calcyclin-associated annexin-50) (CAP-50)	0.32	-	nuc	0	Nucleus; nucleoplasm. Found throughout the nucleoplasm at interphase and at the mitotic phase is con ...	nuclear envelope [ISS] nucleoplasm [ISS]			503
P32447 UniProt NPD GO	ASF1_YEAST	Anti-silencing protein 1	0.32	+	nuc	0		chromatin assembly complex [IDA]		1WG3	279
P56425 UniProt NPD GO	BMA34_BOVIN	Antibacterial peptide BMAP-34 precursor	0.32	-	nuc	0	Secreted protein				165
P15497 UniProt NPD GO	APOA1_BOVIN	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.32	-	exc	0	Secreted protein				265
P02648 UniProt NPD GO	APOA1_CANFA	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.32	-	exc	0	Secreted protein				266
Q9CPT0 UniProt NPD GO	B2L14_MOUSE	Apoptosis facilitator Bcl-2-like protein 14	0.32	-	nuc	0	Cytoplasm (By similarity)				328
P18824 UniProt NPD GO	ARM_DROME	Armadillo segment polarity protein	0.32	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein; cytoplasmic side. Inner surface of cell membr ...	adherens junction [IDA] apicolateral plasma membrane [TAS] cytoplasm [TAS] zonula adherens [IDA]			843
Q95MN9 UniProt NPD GO	AIPL1_PANPA	Aryl-hydrocarbon-interacting protein-like 1	0.32	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				384
O46540 UniProt NPD GO	ANF_SHEEP	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin)	0.32	-	exc	0	Secreted protein				152
Q6BU30 UniProt NPD GO	ATG12_DEBHA	Autophagy-related protein 12 (Autophagy-related ubiquitin-like modifier ATG12)	0.32	-	nuc	0	Cytoplasm (By similarity)				153
Q5ABQ7 UniProt NPD GO	ATG3_CANAL	Autophagy-related protein 3 (Autophagy-related E2-like conjugation enzyme ATG3)	0.32	-	nuc	0	Cytoplasm (By similarity)				333
P80356 UniProt NPD GO	AVE3_AVESA	Avenin-3 precursor (Prolamin)	0.32	-	exc	0	Vacuole. Protein bodies inside vacuoles				220
P40259 UniProt NPD GO	CD79B_HUMAN	B-cell antigen receptor complex-associated protein beta-chain precursor (B-cell-specific glycoprotei ...	0.32	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	147245		229
Q13145 UniProt NPD GO	BAMBI_HUMAN	BMP and activin membrane-bound inhibitor homolog precursor (Putative transmembrane protein NMA) (Non ...	0.32	-	mit	1	Membrane; single-pass type I membrane protein (Potential)	cytoplasm [IDA] integral to membrane [TAS]	604444		260
Q94F62 UniProt NPD GO	BAK1_ARATH	BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor (EC 2.7.11.1) (BRI1-associated ...	0.32	-	end	1	Cell membrane; single-pass type I membrane protein. Endosome; endosomal membrane; single-pass type I ...				615
Q2HJ48 UniProt NPD GO	KCTD1_BOVIN	BTB/POZ domain-containing protein KCTD1	0.32	-	mit	0					257
Q719H9 UniProt NPD GO	KCTD1_HUMAN	BTB/POZ domain-containing protein KCTD1	0.32	-	mit	0					257
Q5M956 UniProt NPD GO	KCTD1_MOUSE	BTB/POZ domain-containing protein KCTD1	0.32	-	mit	0					257
P82018 UniProt NPD GO	BCTN5_CAPHI	Bactenecin-5 precursor (Bac5) (ChBac5) (Cathelicidin-2)	0.32	-	nuc	1 *	Secreted protein				176
Q60989 UniProt NPD GO	BIRC4_MOUSE	Baculoviral IAP repeat-containing protein 4 (Inhibitor of apoptosis protein 3) (X-linked inhibitor o ...	0.32	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [IDA]			496
Q9R0I6 UniProt NPD GO	BIRC4_RAT	Baculoviral IAP repeat-containing protein 4 (Inhibitor of apoptosis protein 3) (X-linked inhibitor o ...	0.32	-	nuc	0	Cytoplasm (By similarity)				496
Q8NFJ9 UniProt NPD GO	BBS1_HUMAN	Bardet-Biedl syndrome 1 protein (BBS2-like protein 2)	0.32	-	cyt	0			209901		593
Q8L9S0 UniProt NPD GO	BETL2_ARATH	Bet1-like protein At1g29060	0.32	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				134
P16126 UniProt NPD GO	DRTS_LEIAM	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.32	-	cyt	0					520
Q5U5M8 UniProt NPD GO	BL1S3_MOUSE	Biogenesis of lysosome-related organelles complex-1 subunit 3 (Reduced pigmentation protein) (BLOC s ...	0.32	-	mit	0	Cytoplasm	cytosol [IDA]			195
P18075 UniProt NPD GO	BMP7_HUMAN	Bone morphogenetic protein 7 precursor (BMP-7) (Osteogenic protein 1) (OP-1) (Eptotermin alfa)	0.32	-	exc	0	Secreted protein		112267	1M4U	431
P01058 UniProt NPD GO	IBB1_PHAAN	Bowman-Birk type proteinase inhibitor	0.32	-	nuc	0				1TAB	82
P24781 UniProt NPD GO	BRAC_XENLA	Brachyury protein (T protein) (xBRA)	0.32	-	nuc	0	Nucleus			1XBR	432
Q17134 UniProt NPD GO	BRAC1_BRAFL	Brachyury protein homolog 1 (AmBra-1)	0.32	-	nuc	0	Nucleus (Potential)				448
Q9UUG1 UniProt NPD GO	BXDC1_SCHPO	Brix domain-containing protein 1 homolog	0.32	-	nuc	0	Nucleus; nucleolus				317
O00481 UniProt NPD GO	BT3A1_HUMAN	Butyrophilin subfamily 3 member A1 precursor (CD277 antigen)	0.32	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				513
P06472 UniProt NPD GO	HOR7_HORVU	C-hordein (PCP387) (Fragment)	0.32	-	nuc	0					105
Q8BRU4 UniProt NPD GO	CLC9A_MOUSE	C-type lectin domain family 9 member A	0.32	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				238
Q9BDN3 UniProt NPD GO	CD40L_CALJA	CD40 ligand (CD40-L) (Tumor necrosis factor ligand superfamily member 5) (CD154 antigen) [Contains: ...	0.32	-	nuc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	integral to membrane [ISS]			261
P63305 UniProt NPD GO	CD40L_CERTO	CD40 ligand (CD40-L) (Tumor necrosis factor ligand superfamily member 5) (CD154 antigen) [Contains: ...	0.32	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	integral to membrane [ISS]			261
P63304 UniProt NPD GO	CD40L_MACMU	CD40 ligand (CD40-L) (Tumor necrosis factor ligand superfamily member 5) (CD154 antigen) [Contains: ...	0.32	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	integral to membrane [ISS]			261
Q92187 UniProt NPD GO	SIA8D_HUMAN	CMP-N-acetylneuraminate-poly-alpha-2,8-sialyltransferase (EC 2.4.99.-) (Alpha-2,8-sialyltransferase ...	0.32	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)		602547		359
Q64692 UniProt NPD GO	SIA8D_MOUSE	CMP-N-acetylneuraminate-poly-alpha-2,8-sialyltransferase (EC 2.4.99.-) (Alpha-2,8-sialyltransferase ...	0.32	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				359
P61645 UniProt NPD GO	SIA8D_PANTR	CMP-N-acetylneuraminate-poly-alpha-2,8-sialyltransferase (EC 2.4.99.-) (Alpha-2,8-sialyltransferase ...	0.32	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				359
Q86X83 UniProt NPD GO	COMD2_HUMAN	COMM domain-containing protein 2	0.32	-	cyt	0					199
P68356 UniProt NPD GO	CSN6A_BRAOL	COP9 signalosome complex subunit 6a (Signalosome subunit 6a) (Fragments)	0.32	-	nuc	0	Cytoplasm. Nucleus				66
Q6P637 UniProt NPD GO	CSN8_XENTR	COP9 signalosome complex subunit 8 (Signalosome subunit 8)	0.32	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				193
Q9Z0D9 UniProt NPD GO	CX3C1_MOUSE	CX3C chemokine receptor 1 (C-X3-C CKR-1) (CX3CR1) (Fractalkine receptor)	0.32	-	end	7 *	Membrane; multi-pass membrane protein				354
Q9R010 UniProt NPD GO	KIP1_RAT	Calcium and integrin-binding protein 1 (Calmyrin) (DNA-PKcs-interacting protein) (Kinase-interacting ...	0.32	-	nuc	0	Membrane; lipid-anchor (By similarity)	cytoplasm [ISS] endoplasmic reticulum [ISS] membrane [ISS] nucleoplasm [ISS]			190
Q99828 UniProt NPD GO	KIP1_HUMAN	Calcium and integrin-binding protein 1 (Calmyrin) (DNA-PKcs-interacting protein) (Kinase-interacting ...	0.32	-	nuc	0	Membrane; lipid-anchor	cytoplasm [IMP] endoplasmic reticulum [IMP] membrane [IDA] nucleoplasm [IMP]	602293	1XO5	190
Q8LBL1 UniProt NPD GO	KCO1_ARATH	Calcium-activated outward-rectifying potassium channel 1 (AtKCO1)	0.32	-	end	5	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				363
O59868 UniProt NPD GO	ATC1_SCHPO	Calcium-transporting ATPase 1 (EC 3.6.3.8) (Golgi Ca(2+)-ATPase)	0.32	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			899
Q8N5S9 UniProt NPD GO	KKCC1_HUMAN	Calcium/calmodulin-dependent protein kinase kinase 1 (EC 2.7.11.17) (Calcium/calmodulin-dependent pr ...	0.32	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				505
Q9HB71 UniProt NPD GO	CYBP_HUMAN	Calcyclin-binding protein (CacyBP) (hCacyBP) (Siah-interacting protein) (S100A6-binding protein)	0.32	-	nuc	0	Nucleus. Cytoplasm. Cytoplasmic at low calcium concentrations. In neuroblastoma cells, after a retin ...		606186	2A26	228
O82709 UniProt NPD GO	CALX_PEA	Calnexin homolog precursor	0.32	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				551

You are viewing entries 38301 to 38350 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.