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
P34944 UniProt NPD GO	NUGM_MARPO	NADH-ubiquinone oxidoreductase 27 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-27KD) (CI-27KD) ...	0.68	-	cyt	0	Mitochondrion; mitochondrial inner membrane				195
Q8BZN4 UniProt NPD GO	NUAK2_MOUSE	NUAK family SNF1-like kinase 2 (EC 2.7.11.1)	0.68	-	nuc	0					639
P55160 UniProt NPD GO	NCKPL_HUMAN	Nck-associated protein 1-like (Membrane-associated protein HEM-1) (Hematopoietic protein 1)	0.68	-	nuc	0		integral to plasma membrane [TAS] membrane fraction [TAS]	141180		1127
Q9TU19 UniProt NPD GO	NPHP1_CANFA	Nephrocystin-1 (Fragment)	0.68	+	cyt	0	Cell membrane; cell-cell junction; adherens junction (By similarity). Localizes at or near the cell- ...				565
Q24567 UniProt NPD GO	NETA_DROME	Netrin-A precursor	0.68	-	exc	0	Secreted protein; extracellular space				726
Q24568 UniProt NPD GO	NETB_DROME	Netrin-B precursor	0.68	-	exc	1 *	Secreted protein; extracellular space				793
O17611 UniProt NPD GO	NH100_CAEEL	Nuclear hormone receptor family member nhr-100	0.68	-	mit	0	Nucleus (Potential)				437
P27476 UniProt NPD GO	NSR1_YEAST	Nuclear localization sequence-binding protein (p67)	0.68	+	nuc	0	Nucleus. Nucleus; nucleolus (Potential). Possibly at the nucleolus	mitochondrion [IDA] nucleolus [TAS] nucleus [IDA]			414
P49790 UniProt NPD GO	NU153_HUMAN	Nuclear pore complex protein Nup153 (Nucleoporin Nup153) (153 kDa nucleoporin)	0.68	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex. Located to the terminal ring structure of the nucle ...	nuclear pore [TAS]	603948		1475
Q13772 UniProt NPD GO	NCOA4_HUMAN	Nuclear receptor coactivator 4 (NCoA-4) (70 kDa androgen receptor coactivator) (70 kDa AR-activator) ...	0.68	-	nuc	0		nucleus [TAS]	188550	1T5Z	614
Q80YV2 UniProt NPD GO	NIPA_MOUSE	Nuclear-interacting partner of ALK (Nuclear-interacting partner of anaplastic lymphoma kinase) (mNIP ...	0.68	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			501
P38181 UniProt NPD GO	NU170_YEAST	Nucleoporin NUP170 (Nuclear pore protein NUP170)	0.68	-	end	0	Nucleus; nuclear envelope; nuclear pore complex; central core structure; multi-pass membrane protein ...	nuclear pore [IDA]			1502
Q2HJF3 UniProt NPD GO	ORC6_BOVIN	Origin recognition complex subunit 6	0.68	-	nuc	0	Nucleus (By similarity)				252
Q8C437 UniProt NPD GO	PEX5R_MOUSE	PEX5-related protein (Peroxin-5-related protein) (Pex5Rp) (PEX5-like protein) (PEX2-related protein) ...	0.68	-	nuc	0	Cytoplasm. Some fraction is membrane associated via its interaction with RAB8B (By similarity)				567
O75626 UniProt NPD GO	PRDM1_HUMAN	PR domain zinc finger protein 1 (PR domain-containing protein 1) (Beta-interferon gene positive-regu ...	0.68	-	nuc	0	Nucleus (By similarity)		603423		789
O95521 UniProt NPD GO	PRAM1_HUMAN	PRAME family member 1	0.68	-	mit	0					474
Q4WWN2 UniProt NPD GO	ERFB_ASPFU	Palmitoyltransferase erf2 (EC 2.3.1.-) (DHHC cysteine-rich domain-containing protein erf2) (Ras prot ...	0.68	-	mit	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				607
P0C1J1 UniProt NPD GO	PPIL2_RHIOR	Peptidyl-prolyl cis-trans isomerase-like 2 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-60) (Cyclop ...	0.68	+	nuc	0	Nucleus (By similarity)				533
Q24767 UniProt NPD GO	PER_DROYA	Period circadian protein	0.68	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				1208
Q9BYK8 UniProt NPD GO	PR285_HUMAN	Peroxisomal proliferator-activated receptor A-interacting complex 285 kDa protein (EC 3.6.1.-) (ATP- ...	0.68	-	nuc	0	Nucleus				2649
O94325 UniProt NPD GO	PEX5_SCHPO	Peroxisomal targeting signal receptor (Peroxin-5) (PTS1 receptor)	0.68	-	nuc	0	Cytoplasm (By similarity). Peroxisome; peroxisomal membrane; peripheral membrane protein (By similar ...				598
Q05568 UniProt NPD GO	PEX10_YEAST	Peroxisome assembly protein 10 (Peroxin-10) (Peroxisome biogenesis factor 10)	0.68	-	nuc	1	Peroxisome; peroxisomal membrane; peripheral membrane protein (Potential)	peroxisomal membrane [TAS]			337
P07270 UniProt NPD GO	PHO4_YEAST	Phosphate system positive regulatory protein PHO4	0.68	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]		1A0A	312
P30694 UniProt NPD GO	CAPP2_FLATR	Phosphoenolpyruvate carboxylase (EC 4.1.1.31) (PEPCase) (PEPC)	0.68	-	nuc	0	Cytoplasm				966
Q42730 UniProt NPD GO	CAPP_FLAAU	Phosphoenolpyruvate carboxylase (EC 4.1.1.31) (PEPCase) (PEPC)	0.68	-	nuc	0	Cytoplasm				966
P70496 UniProt NPD GO	PLD1_RAT	Phospholipase D1 (EC 3.1.4.4) (PLD 1) (Choline phosphatase 1) (Phosphatidylcholine-hydrolyzing phosp ...	0.68	-	cyt	0	Perinuclear regions: endoplasmic reticulum, Golgi apparatus and late endosomes (By similarity). Memb ...				1074
P18688 UniProt NPD GO	KPB1_RABIT	Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform (Phosphorylase kinase alpha ...	0.68	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				1237
Q99959 UniProt NPD GO	PKP2_HUMAN	Plakophilin-2	0.68	-	nuc	0	Nucleus. Cell membrane; cell-cell junction; anchoring junction; desmosome. Nuclear and associated wi ...	desmosome [NAS] integral to membrane [TAS] nucleus [NAS] plasma membrane [TAS]	609040		881
O18783 UniProt NPD GO	PLMN_MACEU	Plasminogen precursor (EC 3.4.21.7) [Contains: Plasmin heavy chain A; Activation peptide; Plasmin he ...	0.68	-	exc	0	Secreted protein				806
Q9H4M7 UniProt NPD GO	PKHA4_HUMAN	Pleckstrin homology domain-containing family A member 4 (Phosphoinositol 3-phosphate-binding protein ...	0.68	+	mit	0	Cytoplasm (Probable). Membrane; peripheral membrane protein (Probable)		607769	1UPR	779
Q9QXS1 UniProt NPD GO	PLEC1_MOUSE	Plectin-1 (PLTN) (PCN) (Fragment)	0.68	-	cyt	0		contractile fiber [IDA] insoluble fraction [IDA]		1SH6	964
O35245 UniProt NPD GO	PKD2_MOUSE	Polycystin-2 (Polycystic kidney disease 2 protein homolog)	0.68	+	end	6	Membrane; multi-pass membrane protein (Potential)	cilium [IDA] endoplasmic reticulum [TAS]			966
Q9TTT5 UniProt NPD GO	KCND3_RABIT	Potassium voltage-gated channel subfamily D member 3 (Voltage-gated potassium channel subunit Kv4.3) ...	0.68	-	end	6	Membrane; multi-pass membrane protein				655
O35219 UniProt NPD GO	KCNH2_MOUSE	Potassium voltage-gated channel subfamily H member 2 (Voltage-gated potassium channel subunit Kv11.1 ...	0.68	-	ves	4	Membrane; multi-pass membrane protein	cytoplasm [IDA] nuclear envelope [IDA] plasma membrane [IDA]			1162
Q9Z351 UniProt NPD GO	KCNQ2_MOUSE	Potassium voltage-gated channel subfamily KQT member 2 (Voltage-gated potassium channel subunit Kv7. ...	0.68	-	nuc	5	Membrane; multi-pass membrane protein				759
Q750X3 UniProt NPD GO	CLF1_ASHGO	Pre-mRNA-splicing factor CLF1	0.68	-	cyt	0	Nucleus (By similarity)				683
Q6CVR3 UniProt NPD GO	CWC21_KLULA	Pre-mRNA-splicing factor CWC21	0.68	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				113
Q03375 UniProt NPD GO	CWC21_YEAST	Pre-mRNA-splicing factor CWC21 (Complexed with CEF1 protein 21)	0.68	-	mit	0	Cytoplasm. Nucleus	spliceosome complex [IPI]			135
Q6BYK1 UniProt NPD GO	RSE1_DEBHA	Pre-mRNA-splicing factor RSE1	0.68	-	nuc	0	Nucleus (By similarity)				1256
P87312 UniProt NPD GO	CLF1_SCHPO	Pre-mRNA-splicing factor clf1 (Complexed with cdc5 protein 4) (Cell cycle control protein cwf4)	0.68	+	cyt	0	Nucleus (By similarity)	spliceosome complex [IDA]			674
Q5AU50 UniProt NPD GO	PRP45_EMENI	Pre-mRNA-splicing factor prp45 (Pre-mRNA-processing protein 45)	0.68	-	nuc	0	Nucleus (By similarity)				583
Q22000 UniProt NPD GO	PDE4_CAEEL	Probable 3',5'-cyclic phosphodiesterase pde-4 (EC 3.1.4.17)	0.68	-	mit	0					674
Q9LXD7 UniProt NPD GO	MYST2_ARATH	Probable MYST-like histone acetyltransferase 2 (EC 2.3.1.48)	0.68	-	nuc	0	Nucleus (Probable)				445
Q9C646 UniProt NPD GO	RX24L_ARATH	Probable disease resistance protein RXW24L	0.68	-	nuc	0					899
Q6CEY7 UniProt NPD GO	NDC80_YARLI	Probable kinetochore protein NDC80	0.68	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				631
O74526 UniProt NPD GO	KJ45_SCHPO	Probable serine/threonine-protein kinase C70.05c (EC 2.7.11.1)	0.68	-	nuc	0	Cytoplasm				781
P47042 UniProt NPD GO	KJF7_YEAST	Probable serine/threonine-protein kinase YJL057C (EC 2.7.11.1)	0.68	-	nuc	0					667
Q08217 UniProt NPD GO	KOE5_YEAST	Probable serine/threonine-protein kinase YOL045W (EC 2.7.11.1)	0.68	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA]			1101
O60079 UniProt NPD GO	UBP12_SCHPO	Probable ubiquitin carboxyl-terminal hydrolase 12 (EC 3.1.2.15) (Ubiquitin thioesterase 12) (Ubiquit ...	0.68	-	nuc	0		nucleus [TAS]			979
Q6MG07 UniProt NPD GO	PRR3_RAT	Proline-rich protein 3 (MHC class I region proline-rich protein CAT56)	0.68	-	nuc	0					186

You are viewing entries 14851 to 14900 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.