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
Q864T8 UniProt NPD GO	B2MG_MONDO	Beta-2-microglobulin precursor	0.07	-	exc	0	Secreted protein				123
P83187 UniProt NPD GO	BRB_BASAL	Beta-basrubin (Fragment)	0.07	-		0					16
P61263 UniProt NPD GO	BD01_PONPY	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.07	-	exc	0	Secreted protein (Potential)				68
P60023 UniProt NPD GO	BD01_PANTR	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1) (cBD1)	0.07	-	exc	0	Secreted protein				68
P60022 UniProt NPD GO	BD01_HUMAN	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1) (hBD-1)	0.07	-	exc	0	Secreted protein		602056	1KJ5	68
P00723 UniProt NPD GO	BGAL_KLULA	Beta-galactosidase (EC 3.2.1.23) (Lactase)	0.07	-	nuc	0					1025
P16278 UniProt NPD GO	BGAL_HUMAN	Beta-galactosidase precursor (EC 3.2.1.23) (Lactase) (Acid beta-galactosidase)	0.07	-	exc	0	Lysosome		253010		677
P48981 UniProt NPD GO	BGAL_MALDO	Beta-galactosidase precursor (EC 3.2.1.23) (Lactase) (Acid beta-galactosidase) (Exo-(1-->4)-beta-D-g ...	0.07	-	end	0					731
P82349 UniProt NPD GO	SGCB_MOUSE	Beta-sarcoglycan (Beta-SG) (43 kDa dystrophin-associated glycoprotein) (43DAG)	0.07	-	cyt	1	Sarcolemma; sarcolemmal membrane; single-pass type II membrane protein	integral to plasma membrane [TAS]			320
Q1KLR6 UniProt NPD GO	BACE1_CAVPO	Beta-secretase 1 precursor (EC 3.4.23.46) (Beta-site APP cleaving enzyme 1) (Beta-site amyloid precu ...	0.07	-	cyt	1	Membrane; single-pass type I membrane protein				473
Q9Y223 UniProt NPD GO	GLCNE_HUMAN	Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (UDP-GlcNAc-2-epimerase/ ...	0.07	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS]	605820		722
O46377 UniProt NPD GO	PGS1_RABIT	Biglycan (Bone/cartilage proteoglycan I) (PG-S1) (Fragment)	0.07	-	cyt	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				135
O02678 UniProt NPD GO	PGS1_CANFA	Biglycan precursor (Bone/cartilage proteoglycan I) (PG-S1)	0.07	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				369
Q64285 UniProt NPD GO	CEL_MOUSE	Bile salt-activated lipase precursor (EC 3.1.1.3) (EC 3.1.1.13) (BAL) (Bile salt-stimulated lipase) ...	0.07	-	mit	0		cytoplasm [ISS]			599
P15411 UniProt NPD GO	BXA2_BOMMO	Bombyxin A-2 precursor (BBX-A2) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin A-2 B ...	0.07	-	exc	0	Secreted protein			1BON	89
P26731 UniProt NPD GO	BXA8_BOMMO	Bombyxin A-8 precursor (BBX-A8) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin A-8 B ...	0.07	-	exc	0	Secreted protein				89
P26735 UniProt NPD GO	BXC2_BOMMO	Bombyxin C-2 precursor (BBX-C2) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin C-2 B ...	0.07	-	end	1 *	Secreted protein				95
P21808 UniProt NPD GO	BXE1_BOMMO	Bombyxin E-1 precursor (BBX-E1) (Bombyxin IV) (4K-prothoracicotropic hormone IV) (4K-PTTH-IV) [Conta ...	0.07	-	exc	0	Secreted protein				98
Q7LZ53 UniProt NPD GO	BRK3_RANNI	Bradykinin-like peptide 3	0.07	-		0	Secreted protein				14
Q9FYA6 UniProt NPD GO	BCAT5_ARATH	Branched-chain-amino-acid aminotransferase 5, chloroplast precursor (EC 2.6.1.42) (Atbcat-5)	0.07	-	mit	0	Plastid; chloroplast				415
Q566B1 UniProt NPD GO	BURS_BOMMO	Bursicon precursor (Bursicon subunit alpha) (Cuticle-tanning hormone)	0.07	-	mit	0	Secreted protein (By similarity)				160
Q9VD83 UniProt NPD GO	BURS_DROME	Bursicon precursor (Bursicon subunit alpha) (Cuticle-tanning hormone)	0.07	-	nuc	1 *	Secreted protein	extracellular region [IDA]			173
P41597 UniProt NPD GO	CCR2_HUMAN	C-C chemokine receptor type 2 (C-C CKR-2) (CC-CKR-2) (CCR-2) (CCR2) (Monocyte chemoattractant protei ...	0.07	-	end	6 *	Membrane; multi-pass membrane protein	cytoplasm [IDA] integral to plasma membrane [TAS] plasma membrane [IDA] soluble fraction [TAS]	601267	1KP1	374
P32248 UniProt NPD GO	CCR7_HUMAN	C-C chemokine receptor type 7 precursor (C-C CKR-7) (CC-CKR-7) (CCR-7) (MIP-3 beta receptor) (EBV-in ...	0.07	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	600242		378
Q9EQS3 UniProt NPD GO	MYCBP_MOUSE	C-Myc-binding protein (Associate of Myc 1) (AMY-1)	0.07	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocates into the nucleus in the S phase of ...				102
P51378 UniProt NPD GO	PHCA_PORPU	C-phycocyanin alpha chain	0.07	-	cyt	0	Plastid; chloroplast				162
Q36699 UniProt NPD GO	PHCA_RHOVL	C-phycocyanin alpha chain	0.07	-	nuc	0	Plastid; chloroplast				162
O19909 UniProt NPD GO	PHCB_CYACA	C-phycocyanin beta chain	0.07	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen. Phycobilisome rod				172
P51377 UniProt NPD GO	PHCB_PORPU	C-phycocyanin beta chain	0.07	-	cyt	0	Plastid; chloroplast				172
Q9NY25 UniProt NPD GO	CLC5A_HUMAN	C-type lectin domain family 5 member A (C-type lectin superfamily member 5) (Myeloid DAP12-associati ...	0.07	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)	integral to plasma membrane [TAS]	604987		188
O88680 UniProt NPD GO	C3AR_CAVPO	C3a anaphylatoxin chemotactic receptor (C3a-R) (C3AR)	0.07	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			475
P47777 UniProt NPD GO	CD59_SAISC	CD59 glycoprotein precursor (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory prot ...	0.07	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				131
P81509 UniProt NPD GO	CHBBB_CROHO	CHH-B subunit beta	0.07	-	cyt	0	Secreted protein				117
Q5RFC1 UniProt NPD GO	CKLF6_PONPY	CKLF-like MARVEL transmembrane domain-containing protein 6 (Chemokine-like factor superfamily member ...	0.07	-	end	3	Membrane; multi-pass membrane protein (By similarity)				183
Q75IW1 UniProt NPD GO	COBL2_ORYSA	COBRA-like 2 protein precursor (BRITTLE CULM1-like 2 protein)	0.07	-	end	2 *	Membrane; single-pass membrane protein (Potential)				458
Q9BRT8 UniProt NPD GO	CBWD1_HUMAN	COBW domain-containing protein 1 (COBP) (NPC-A-6 COBW domain-containing protein 1) (NPC-A-6)	0.07	-	cyt	0					395
Q9XZ58 UniProt NPD GO	CSN5_DROME	COP9 signalosome complex subunit 5 (EC 3.4.-.-) (Signalosome subunit 5) (Dch5) (JAB1 homolog)	0.07	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)	cytoplasm [IDA] signalosome complex [IMP]			327
O35864 UniProt NPD GO	CSN5_MOUSE	COP9 signalosome complex subunit 5 (EC 3.4.-.-) (Signalosome subunit 5) (SGN5) (Jun activation domai ...	0.07	-	nuc	0	Cytoplasm. Nucleus	signalosome complex [IDA] transcription factor complex [TAS]			333
P43255 UniProt NPD GO	CSN8_ARATH	COP9 signalosome complex subunit 8 (CSN complex subunit 8) (Constitutive photomorphogenesis protein ...	0.07	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)				197
P08521 UniProt NPD GO	LPCP_YEAST	CPA1 leader peptide	0.07	-	nuc	0		cytosol [IC]			25
Q8WSW3 UniProt NPD GO	MTCD_TETTH	Cadmium metallothionein precursor (MT-Cd) (Cd-MT)	0.07	-	nuc	0					162
P81695 UniProt NPD GO	MT_EISFO	Cadmium-metallothionein (MT) (Fragment)	0.07	-	nuc	0	Cytoplasm				75
Q800R2 UniProt NPD GO	CR11_LITCE	Caerin-1.1 precursor [Contains: Caerin-1.1.1; Caerin-1.1.2; Caerin-1.1.4]	0.07	-	exc	0	Secreted protein				75
P48451 UniProt NPD GO	CANB1_DROME	Calcineurin subunit B isoform 1 (Protein phosphatase 2B regulatory subunit)	0.07	-	cyt	0		synaptic vesicle [NAS]			170
Q9VA73 UniProt NPD GO	CMC1_DROME	Calcium-binding mitochondrial carrier Aralar1	0.07	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				695
Q7PPA5 UniProt NPD GO	ATC1_ANOGA	Calcium-transporting ATPase sarcoplasmic/endoplasmic reticulum type (EC 3.6.3.8) (Calcium pump)	0.07	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...				1018
P98194 UniProt NPD GO	AT2C1_HUMAN	Calcium-transporting ATPase type 2C member 1 (EC 3.6.3.8) (ATPase 2C1) (ATP-dependent Ca(2+) pump PM ...	0.07	-	end	8	Golgi apparatus; Golgi membrane; multi-pass membrane protein	integral to membrane [TAS]	604384		919
Q80XR2 UniProt NPD GO	AT2C1_MOUSE	Calcium-transporting ATPase type 2C member 1 (EC 3.6.3.8) (ATPase 2C1) (ATP-dependent Ca(2+) pump PM ...	0.07	-	end	8	Golgi apparatus; Golgi stack; Golgi stack membrane; multi-pass membrane protein (By similarity)				918
P54670 UniProt NPD GO	CAF1_DICDI	Calfumirin-1 (CAF-1)	0.07	-	cyt	0					169
P41839 UniProt NPD GO	ALL1_CALVO	Callatostatin-1 (Leu-callatostatin-1) [Contains: Callatostatin-2 (Leu-callatostatin-2); Callatostati ...	0.07	-		0	Secreted protein				16

You are viewing entries 69601 to 69650 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.