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
Q9R045 UniProt NPD GO	ANGL2_MOUSE	Angiopoietin-related protein 2 precursor (Angiopoietin-like 2)	0.61	-	exc	0	Secreted protein (By similarity)				493
Q5T7N3 UniProt NPD GO	ANR38_HUMAN	Ankyrin repeat domain-containing protein 38	0.61	-	nuc	0					995
Q8BLS7 UniProt NPD GO	ANR43_MOUSE	Ankyrin repeat domain-containing protein 43	0.61	-	nuc	0					334
Q9R049 UniProt NPD GO	AMFR_MOUSE	Autocrine motility factor receptor (EC 6.3.2.19) (AMF receptor)	0.61	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	integral to endoplasmic reticulum membrane [ISS]			643
Q6FSJ9 UniProt NPD GO	ATG13_CANGA	Autophagy-related protein 13	0.61	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				660
Q06410 UniProt NPD GO	ATG17_YEAST	Autophagy-related protein 17	0.61	-	cyt	0	Cytoplasm. Punctate structures	cytoplasm [IDA]			417
P53855 UniProt NPD GO	ATG2_YEAST	Autophagy-related protein 2 (Sporulation-specific protein 72)	0.61	-	nuc	0		extrinsic to membrane [IDA]			1592
Q6CLZ2 UniProt NPD GO	ATG21_KLULA	Autophagy-related protein 21	0.61	+	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Vacuole; vacuolar ...				392
Q6FK56 UniProt NPD GO	ATG23_CANGA	Autophagy-related protein 23	0.61	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				440
Q9ZTX8 UniProt NPD GO	ARFF_ARATH	Auxin response factor 6	0.61	-	nuc	0	Nucleus				933
Q5XH61 UniProt NPD GO	BCL7A_XENLA	B-cell CLL/lymphoma 7 protein family member A	0.61	+	nuc	0					231
Q86UZ6 UniProt NPD GO	BTBD4_HUMAN	BTB/POZ domain-containing protein 4 (Zinc finger protein 340)	0.61	-	nuc	0	Nucleus (Potential)				589
Q961D9 UniProt NPD GO	BCL9_DROME	Bcl-9 homolog (Protein legless)	0.61	-	nuc	0	Nucleus	nucleus [IDA]			1469
P81182 UniProt NPD GO	BGBP_PENVA	Beta-1,3-glucan-binding protein precursor (BGBP) (Beta-1,3-glucan recognition protein) (BetaGRP) (Hi ...	0.61	-	nuc	0	Secreted protein	extracellular region [IDA]			1454
P26817 UniProt NPD GO	ARBK1_RAT	Beta-adrenergic receptor kinase 1 (EC 2.7.11.15) (Beta-ARK-1) (G-protein-coupled receptor kinase 2)	0.61	-	cyt	0		axon [IDA] dendritic shaft [IDA] dendritic spine [IDA] synapse [IDA]			689
Q9CY64 UniProt NPD GO	BIEA_MOUSE	Biliverdin reductase A precursor (EC 1.3.1.24) (Biliverdin-IX alpha-reductase) (BVR A)	0.61	-	cyt	0	Cytoplasm (By similarity)				295
Q9UHR4 UniProt NPD GO	BI2L1_HUMAN	Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 (BAI1-associated protein ...	0.61	-	nuc	0					511
O94308 UniProt NPD GO	CSN1_SCHPO	COP9 signalosome complex subunit 1 (CSN complex subunit 1) (SGN1)	0.61	-	cyt	0	Cytoplasm. Nucleus	signalosome complex [TAS]			422
Q8L5U0 UniProt NPD GO	CSN4_ARATH	COP9 signalosome complex subunit 4 (Signalosome subunit 4) (Constitutive photomorphogenesis protein ...	0.61	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)				397
Q90762 UniProt NPD GO	CADH6_CHICK	Cadherin-6 precursor (Cadherin-6B) (c-cad6B)	0.61	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				790
P57796 UniProt NPD GO	CABP4_HUMAN	Calcium-binding protein 4 (CaBP4)	0.61	+	nuc	0	Presynapses from both types of photoreceptors: rod spherules and cone pedicles (By similarity)		608965		275
P29295 UniProt NPD GO	HRR25_YEAST	Casein kinase I homolog HRR25 (EC 2.7.11.1)	0.61	-	nuc	0		nucleus [IDA] plasma membrane [IDA]			494
P56203 UniProt NPD GO	CATW_MOUSE	Cathepsin W precursor (EC 3.4.22.-) (Lymphopain)	0.61	+	cyt	0					371
O74957 UniProt NPD GO	AGO1_SCHPO	Cell cycle control protein ago1 (RNA interference pathway protein ago1)	0.61	-	cyt	0		centric heterochromatin [IDA] mating-type region heterochromatin [IDA] nuclear telomeric heterochromatin [IDA] RITS complex [IDA]			834
Q29537 UniProt NPD GO	P53_CANFA	Cellular tumor antigen p53 (Tumor suppressor p53)	0.61	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			381
Q96P48 UniProt NPD GO	CEND2_HUMAN	Centaurin-delta 2 (Cnt-d2) (Arf-GAP, Rho-GAP, ankyrin repeat and pleckstrin homology domain-containi ...	0.61	-	cyt	0	Cytoplasm. Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein. Associat ...		606646		1210
O43101 UniProt NPD GO	CBF5_CANAL	Centromere/microtubule-binding protein CBF5 (Centromere-binding factor 5) (Small nucleolar RNP prote ...	0.61	+	nuc	0	Nucleus; nucleolus (By similarity)				479
P51789 UniProt NPD GO	CLCN2_RABIT	Chloride channel protein 2 (ClC-2) (PKA-activated chloride channel)	0.61	-	end	12	Membrane; multi-pass membrane protein				898
Q8WHX2 UniProt NPD GO	RR15_PSINU	Chloroplast 30S ribosomal protein S15	0.61	+	nuc	0	Plastid; chloroplast				86
Q9GFL3 UniProt NPD GO	RR7_GINBI	Chloroplast 30S ribosomal protein S7	0.61	-	nuc	0	Plastid; chloroplast				155
P41634 UniProt NPD GO	RR8_PINTH	Chloroplast 30S ribosomal protein S8	0.61	+	nuc	0	Plastid; chloroplast				132
Q9TL17 UniProt NPD GO	RK23_NEPOL	Chloroplast 50S ribosomal protein L23	0.61	+	cyt	0	Plastid; chloroplast				92
Q85C28 UniProt NPD GO	RK32_ANTFO	Chloroplast 50S ribosomal protein L32	0.61	-	nuc	0	Plastid; chloroplast				69
Q95H45 UniProt NPD GO	RK32_WHEAT	Chloroplast 50S ribosomal protein L32	0.61	-	mit	0	Plastid; chloroplast				63
P28329 UniProt NPD GO	CLAT_HUMAN	Choline O-acetyltransferase (EC 2.3.1.6) (CHOACTase) (Choline acetylase) (ChAT)	0.61	-	nuc	0		cytoplasm [TAS] nucleus [TAS]	254210		748
Q8NDY6 UniProt NPD GO	BHLH4_HUMAN	Class B basic helix-loop-helix protein 4 (bHLHB4)	0.61	-	nuc	0	Nucleus (Probable)		609331		225
Q8BGW3 UniProt NPD GO	BHLH4_MOUSE	Class B basic helix-loop-helix protein 4 (bHLHB4)	0.61	+	nuc	0	Nucleus (Probable)				223
Q04962 UniProt NPD GO	FA12_CAVPO	Coagulation factor XII precursor (EC 3.4.21.38) (Hageman factor) (HAF) [Contains: Coagulation factor ...	0.61	-	exc	0	Secreted protein				603
Q9UMD9 UniProt NPD GO	COHA1_HUMAN	Collagen alpha-1(XVII) chain (Bullous pemphigoid antigen 2) (180 kDa bullous pemphigoid antigen 2)	0.61	-	nuc	1	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS] intercellular junction [TAS]	226650		1497
P21180 UniProt NPD GO	CO2_MOUSE	Complement C2 precursor (EC 3.4.21.43) (C3/C5 convertase) [Contains: Complement C2b fragment; Comple ...	0.61	-	mit	0	Secreted protein				760
P17927 UniProt NPD GO	CR1_HUMAN	Complement receptor type 1 precursor (C3b/C4b receptor) (CD35 antigen)	0.61	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	120620	1PPQ	2039
Q8WTW3 UniProt NPD GO	COG1_HUMAN	Conserved oligomeric Golgi complex component 1	0.61	-	nuc	0	Golgi apparatus	Golgi transport complex [NAS]	606973		980
Q9UP83 UniProt NPD GO	COG5_HUMAN	Conserved oligomeric Golgi complex component 5 (13S Golgi transport complex 90 kDa subunit) (GTC-90) ...	0.61	-	nuc	0	Cytoplasm; cytosol. Golgi apparatus; Golgi membrane; peripheral membrane protein	Golgi transport complex [NAS]	606821		839
Q5R6L5 UniProt NPD GO	CAND1_PONPY	Cullin-associated NEDD8-dissociated protein 1 (Cullin-associated and neddylation-dissociated protein ...	0.61	-	mit	0	Nucleus (By similarity)				1230
Q8IX94 UniProt NPD GO	CTGE4_HUMAN	Cutaneous T-cell lymphoma-associated antigen 4 (cTAGE-4 protein)	0.61	-	nuc	0			608910		504
Q99KY4 UniProt NPD GO	GAK_MOUSE	Cyclin G-associated kinase (EC 2.7.11.1)	0.61	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Golgi apparatus; trans-Golgi network (By similarity). ...				1305
P36613 UniProt NPD GO	CGM2_SCHPO	Cyclin mcs2 (Mitotic catastrophe suppressor 2)	0.61	-	nuc	0	Nucleus				322
Q61458 UniProt NPD GO	CCNH_MOUSE	Cyclin-H	0.61	+	nuc	0	Nucleus	nucleus [IDA]			323
O35926 UniProt NPD GO	CD5R2_MOUSE	Cyclin-dependent kinase 5 activator 2 precursor (CDK5 activator 2) (Cyclin-dependent kinase 5 regula ...	0.61	-	nuc	0					369
P49918 UniProt NPD GO	CDN1C_HUMAN	Cyclin-dependent kinase inhibitor 1C (Cyclin-dependent kinase inhibitor p57) (p57KIP2)	0.61	-	nuc	0	Nucleus (By similarity)		600856		316

You are viewing entries 18351 to 18400 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.)

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