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
P26232 UniProt NPD GO	CTN2_HUMAN	Alpha-2 catenin (Alpha-catenin-related protein) (Alpha N-catenin)	0.41	-	nuc	0		cytoskeleton [NAS]	114025		952
Q8K4T1 UniProt NPD GO	SIA8F_MOUSE	Alpha-2,8-sialyltransferase 8F (EC 2.4.99.-) (ST8Sia VI)	0.41	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				398
O19025 UniProt NPD GO	ADA2B_MACPR	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Fragment)	0.41	-	end	6 *	Membrane; multi-pass membrane protein				387
P04654 UniProt NPD GO	CAS2_SHEEP	Alpha-S2-casein precursor	0.41	-	exc	0	Secreted protein				223
P83960 UniProt NPD GO	BNCA_BENHI	Alpha-benincasin (Fragment)	0.41	-	nuc	0					27
Q9UBT7 UniProt NPD GO	CTNL1_HUMAN	Alpha-catulin (Catenin alpha-like protein 1) (Alpha-catenin-related protein) (ACRP)	0.41	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein		604785		734
Q5RC06 UniProt NPD GO	CTNL1_PONPY	Alpha-catulin (Catenin alpha-like protein 1) (Alpha-catenin-related protein) (ACRP)	0.41	-	nuc	0	Cytoplasm (By similarity). Cytoplasm; cell cortex (By similarity)				734
P63277 UniProt NPD GO	AMELX_MOUSE	Amelogenin, X isoform precursor (Leucine-rich amelogenin peptide) (LRAP)	0.41	-	exc	0	Secreted protein; extracellular space; extracellular matrix				210
P63278 UniProt NPD GO	AMELX_RAT	Amelogenin, X isoform precursor (Leucine-rich amelogenin peptide) (LRAP)	0.41	-	exc	0	Secreted protein; extracellular space; extracellular matrix				210
O73683 UniProt NPD GO	A4_TETFL	Amyloid beta A4 protein precursor (APP) (ABPP) (Alzheimer disease amyloid A4 A4 protein homolog) [Co ...	0.41	-	end	1	Membrane; single-pass type I membrane protein				780
P79307 UniProt NPD GO	A4_PIG	Amyloid beta A4 protein precursor (APP) (ABPP) (Alzheimer disease amyloid protein homolog) [Contains ...	0.41	-	end	1	Membrane; single-pass type I membrane protein (By similarity). Cell surface protein that rapidly bec ...				770
Q8BTZ4 UniProt NPD GO	ANC5_MOUSE	Anaphase-promoting complex subunit 5 (APC5) (Cyclosome subunit 5)	0.41	-	cyt	0					740
Q9WVM3 UniProt NPD GO	APC7_MOUSE	Anaphase-promoting complex subunit 7 (APC7) (Cyclosome subunit 7) (Prediabetic NOD sera-reactive aut ...	0.41	-	nuc	0					565
Q9QZ10 UniProt NPD GO	ANX10_MOUSE	Annexin A10	0.41	-	cyt	0		mitochondrion [IDA]			324
P50994 UniProt NPD GO	ANXA4_CANFA	Annexin A4 (Annexin IV) (Lipocortin IV) (36 kDa zymogen granule membrane-associated protein) (ZAP36) ...	0.41	-	cyt	0					318
P55260 UniProt NPD GO	ANXA4_RAT	Annexin A4 (Annexin IV) (Lipocortin IV) (36 kDa zymogen granule membrane-associated protein) (ZAP36) ...	0.41	-	cyt	0					318
P13214 UniProt NPD GO	ANXA4_BOVIN	Annexin A4 (Annexin IV) (Lipocortin IV) (Endonexin I) (Chromobindin-4) (Protein II) (P32.5) (Placent ...	0.41	-	cyt	0				1I4A	318
P83143 UniProt NPD GO	AFP2L_MALPA	Antifungal protein 2 large subunit (CW-2) (Fragment)	0.41	-		0					20
Q9ULZ1 UniProt NPD GO	APEL_HUMAN	Apelin precursor (APJ endogenous ligand) [Contains: Apelin-36; Apelin-31; Apelin-28; Apelin-13]	0.41	+	exc	1 *	Secreted protein		300297		77
Q61268 UniProt NPD GO	APOC4_MOUSE	Apolipoprotein C-IV precursor (Apo-CIV) (ApoC-IV) (Apolipoprotein C2-linked) (ACL)	0.41	-	exc	0	Secreted protein				124
P18054 UniProt NPD GO	LOX12_HUMAN	Arachidonate 12-lipoxygenase, 12S-type (EC 1.13.11.31) (12-LOX) (Platelet-type lipoxygenase 12)	0.41	-	mit	0	Cytoplasm	cytosol [IDA] sarcolemma [IDA]	152391		662
P54136 UniProt NPD GO	SYR_HUMAN	Arginyl-tRNA synthetase (EC 6.1.1.19) (Arginine--tRNA ligase) (ArgRS)	0.41	-	cyt	0	Cytoplasm	cytoplasm [TAS] soluble fraction [TAS]	107820		660
Q9Z2W0 UniProt NPD GO	DNPEP_MOUSE	Aspartyl aminopeptidase (EC 3.4.11.21)	0.41	-	nuc	0	Cytoplasm				473
Q6FMM7 UniProt NPD GO	ATG12_CANGA	Autophagy-related protein 12 (Autophagy-related ubiquitin-like modifier ATG12)	0.41	-	nuc	0	Cytoplasm (By similarity)				181
Q38824 UniProt NPD GO	IAA6_ARATH	Auxin-responsive protein IAA6 (Indoleacetic acid-induced protein 6)	0.41	-	cyt	0	Nucleus (By similarity)				189
O22152 UniProt NPD GO	YAB1_ARATH	Axial regulator YABBY1 (Protein ABNORMAL FLORAL ORGANS) (Protein FILAMENTOUS FLOWER) (Protein anther ...	0.41	-	nuc	0	Nucleus				229
O44739 UniProt NPD GO	BAG1_CAEEL	BAG-family molecular chaperone regulator 1	0.41	-	nuc	0				1T7S	210
Q8CJ69 UniProt NPD GO	BMPER_MOUSE	BMP-binding endothelial regulator protein precursor (Bone morphogenetic protein-binding endothelial ...	0.41	-	nuc	0	Secreted protein	extracellular region [IDA]			685
P13753 UniProt NPD GO	HA1B_BOVIN	BOLA class I histocompatibility antigen, alpha chain BL3-7 precursor	0.41	-	end	2 *	Membrane; single-pass type I membrane protein				364
P90846 UniProt NPD GO	BAT39_CAEEL	BTB and MATH domain-containing protein 39	0.41	-	nuc	0					370
Q32M84 UniProt NPD GO	BTBDG_HUMAN	BTB/POZ domain-containing protein 16	0.41	-	mit	0					506
Q8WMR7 UniProt NPD GO	VMD2_PIG	Bestrophin-1 (Vitelliform macular dystrophy protein 2 homolog) (Fragment)	0.41	-	nuc	2	Cell membrane; multi-pass membrane protein				428
Q92180 UniProt NPD GO	GCNT1_BOVIN	Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase (EC 2.4.1.102) ...	0.41	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				427
Q9HBI1 UniProt NPD GO	PARVB_HUMAN	Beta-parvin (Affixin)	0.41	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion; cytoplasmic side. Constituent of focal adhesion ...		608121		364
P07814 UniProt NPD GO	SYEP_HUMAN	Bifunctional aminoacyl-tRNA synthetase [Includes: Glutamyl-tRNA synthetase (EC 6.1.1.17) (Glutamate- ...	0.41	-	nuc	0		cytoplasm [TAS] soluble fraction [TAS]	138295	1FYJ	1440
Q6QNY0 UniProt NPD GO	BL1S3_HUMAN	Biogenesis of lysosome-related organelles complex-1 subunit 3 (BLOC subunit 3)	0.41	+	nuc	0	Cytoplasm (By similarity)		609762		202
P98063 UniProt NPD GO	BMP1_MOUSE	Bone morphogenetic protein 1 precursor (EC 3.4.24.19) (BMP-1) (Procollagen C-proteinase) (PCP) (Mamm ...	0.41	+	vac	0					991
O95393 UniProt NPD GO	BMP10_HUMAN	Bone morphogenetic protein 10 precursor (BMP-10)	0.41	-	exc	1 *	Secreted protein (By similarity)	extracellular region [ISS]	608748		424
P56945 UniProt NPD GO	BCAR1_HUMAN	Breast cancer anti-estrogen resistance protein 1 (CRK-associated substrate) (p130cas)	0.41	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion (By similarity). Cytoplasm (By similarity). Unph ...	cytoplasm [IDA] focal adhesion [ISS] membrane fraction [IDA] ruffle [IDA]	602941		870
Q9LUG5 UniProt NPD GO	BXDC1_ARATH	Brix domain-containing protein 1 homolog	0.41	-	nuc	0	Nucleus; nucleolus (By similarity)				314
Q9JL21 UniProt NPD GO	CCR10_MOUSE	C-C chemokine receptor type 10 (C-C CKR-10) (CC-CKR-10) (CCR-10) (Chemokine C-C receptor 9) (G-prote ...	0.41	-	end	7 *	Membrane; multi-pass membrane protein				362
P46092 UniProt NPD GO	CCR10_HUMAN	C-C chemokine receptor type 10 (C-C CKR-10) (CC-CKR-10) (CCR-10) (G-protein coupled receptor 2)	0.41	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600240		362
Q8NBL1 UniProt NPD GO	CLP46_HUMAN	CAP10-like 46 kDa protein precursor (Myelodysplastic syndromes relative protein)	0.41	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				392
P53566 UniProt NPD GO	CEBPA_MOUSE	CCAAT/enhancer-binding protein alpha (C/EBP alpha)	0.41	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			359
P53567 UniProt NPD GO	CEBPG_HUMAN	CCAAT/enhancer-binding protein gamma (C/EBP gamma)	0.41	+	nuc	0	Nucleus	nucleus [ISS]	138972		150
P53568 UniProt NPD GO	CEBPG_MOUSE	CCAAT/enhancer-binding protein gamma (C/EBP gamma) (Immunoglobulin enhancer-binding protein 1) (IG/E ...	0.41	+	nuc	0	Nucleus	nucleus [IDA]			150
Q8CJ91 UniProt NPD GO	C209B_MOUSE	CD209 antigen-like protein B (DC-SIGN-related protein 1) (DC-SIGNR1) (OtB7)	0.41	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)	external side of plasma membrane [IDA] integral to membrane [TAS]			325
Q6C1L4 UniProt NPD GO	CSN12_YARLI	COP9 signalosome complex subunit 12	0.41	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				396
Q7Z408 UniProt NPD GO	CSMD2_HUMAN	CUB and sushi domain-containing protein 2 (CUB and sushi multiple domains protein 2)	0.41	-	nuc	1			608398		3487
Q86UP6 UniProt NPD GO	CUZD1_HUMAN	CUB and zona pellucida-like domain-containing protein 1 precursor (Transmembrane protein UO-44)	0.41	-	end	1	Membrane; single-pass type I membrane protein (Potential). Associated with zymogen granule membranes ...	integral to membrane [NAS] zymogen granule membrane [ISS]			607

You are viewing entries 30901 to 30950 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.