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
Q08834 UniProt NPD GO	MGAT5_RAT	Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V (EC 2.4.1.155) (Mannoside ac ...	0.53	+	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				740
P11615 UniProt NPD GO	ADA1B_CANFA	Alpha-1B adrenergic receptor (Alpha 1B-adrenoceptor) (Alpha 1B-adrenoreceptor) (Fragment)	0.53	+	end	5 *	Membrane; multi-pass membrane protein				417
Q99068 UniProt NPD GO	AMRP_RAT	Alpha-2-macroglobulin receptor-associated protein precursor (Alpha-2-MRAP) (Low density lipoprotein ...	0.53	-	nuc	0	Endoplasmic reticulum (By similarity). Cytoplasm (By similarity). Cell surface (By similarity). Intr ...				360
P39194 UniProt NPD GO	ALU7_HUMAN	Alu subfamily SQ sequence contamination warning entry	0.53	-	exc	0					593
Q6X1Y6 UniProt NPD GO	ACCN3_MOUSE	Amiloride-sensitive cation channel 3 (Acid-sensing ion channel 3) (ASIC3) (Dorsal root ASIC) (DRASIC ...	0.53	-	nuc	0	Cell membrane; multi-pass membrane protein. Cell surface expression may be stabilized by interaction ...	integral to plasma membrane [IDA]			530
P41889 UniProt NPD GO	CUT9_SCHPO	Anaphase-promoting complex subunit cut9 (20S cyclosome/APC complex protein cut9) (Cell untimely torn ...	0.53	-	nuc	0	Nucleus (Probable)	anaphase-promoting complex [IDA]			671
Q9WVH6 UniProt NPD GO	ANGP4_MOUSE	Angiopoietin-4 precursor (ANG-4) (ANG-3)	0.53	-	nuc	0	Secreted protein (Probable)				509
P12821 UniProt NPD GO	ACE_HUMAN	Angiotensin-converting enzyme, somatic isoform precursor (EC 3.4.15.1) (Dipeptidyl carboxypeptidase ...	0.53	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein. A soluble form ...	membrane fraction [TAS] plasma membrane [TAS] soluble fraction [TAS]	106180	1O8A	1306
Q96NS5 UniProt NPD GO	ASB16_HUMAN	Ankyrin repeat and SOCS box protein 16 (ASB-16)	0.53	-	mit	0					453
P61800 UniProt NPD GO	APTX_FUGRU	Aprataxin homolog (Forkhead-associated domain histidine triad-like protein) (FHA-HIT)	0.53	-	nuc	0	Nucleus (Probable)				356
Q4R684 UniProt NPD GO	AMZ2_MACFA	Archaemetzincin-2 (EC 3.-.-.-) (Archeobacterial metalloproteinase-like protein 2)	0.53	-	cyt	0					360
Q5R4A6 UniProt NPD GO	AMZ2_PONPY	Archaemetzincin-2 (EC 3.-.-.-) (Archeobacterial metalloproteinase-like protein 2)	0.53	-	cyt	0					360
P20749 UniProt NPD GO	BCL3_HUMAN	B-cell lymphoma 3-encoded protein (Protein Bcl-3)	0.53	-	nuc	0	Nucleus		109560	1K1B	446
O55003 UniProt NPD GO	BNIP3_MOUSE	BCL2/adenovirus E1B 19 kDa protein-interacting protein 3	0.53	-	cyt	1	Mitochondrion (By similarity). Coexpression with the EIB 19-kDa protein results in a shift in NIP3 l ...	cytoplasm [ISS] dendrite [ISS] integral to mitochondrial outer membrane [ISS] mitochondrial membrane [IDA] mitochondrion [ISS] nuclear envelope [ISS] nucleoplasm [ISS] nucleus [ISS]			187
Q8BID6 UniProt NPD GO	BTBD4_MOUSE	BTB/POZ domain-containing protein 4	0.53	-	nuc	0	Nucleus (Potential)				600
Q9JMC8 UniProt NPD GO	E41LB_MOUSE	Band 4.1-like protein 4B (Protein EHM2)	0.53	-	mit	0					527
Q21973 UniProt NPD GO	BES1_CAEEL	Bestrophin-1	0.53	-	end	4 *					525
Q9TVD0 UniProt NPD GO	CASB_CAMDR	Beta-casein precursor	0.53	-	nuc	0	Secreted protein				232
P28550 UniProt NPD GO	CASB_MACEU	Beta-casein precursor	0.53	-	exc	0	Secreted protein				302
Q3KPK4 UniProt NPD GO	BORAB_XENLA	Borealin-B (Dasra-B) (DasraB) (xDasraB) (Cell division cycle-associated protein 8-B)	0.53	-	nuc	0	Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metaphase and then ...				280
P47974 UniProt NPD GO	TISD_HUMAN	Butyrate response factor 2 (TIS11D protein) (EGF-response factor 2) (ERF-2)	0.53	-	nuc	0	Nucleus (Potential)			1RGO	492
Q13387 UniProt NPD GO	JIP2_HUMAN	C-jun-amino-terminal kinase-interacting protein 2 (JNK-interacting protein 2) (JIP-2) (JNK MAP kinas ...	0.53	-	nuc	0	Cytoplasm. Accumulates in cell surface projections	cytoplasm [IEP]	607755		824
P17676 UniProt NPD GO	CEBPB_HUMAN	CCAAT/enhancer-binding protein beta (C/EBP beta) (Nuclear factor NF-IL6) (Transcription factor 5)	0.53	+	nuc	0	Nucleus	nucleus [TAS]	189965	1IO4	345
Q9JLH6 UniProt NPD GO	CK5P1_RAT	CDK5 regulatory subunit-associated protein 1 (CDK5 activator-binding protein C42)	0.53	-	mit	0					586
Q94899 UniProt NPD GO	CSN2_DROME	COP9 signalosome complex subunit 2 (Signalosome subunit 2) (Dch2) (Alien protein)	0.53	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)	cytoplasm [IDA] signalosome complex [IDA]			444
Q9Z1Y3 UniProt NPD GO	CADH2_RAT	Cadherin-2 precursor (Neural-cadherin) (N-cadherin) (CDw325 antigen)	0.53	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				906
O18867 UniProt NPD GO	KCMA1_MACMU	Calcium-activated potassium channel subunit alpha 1 (Calcium-activated potassium channel, subfamily ...	0.53	-	end	6	Membrane; multi-pass membrane protein (By similarity)				1151
Q28204 UniProt NPD GO	KCMA1_BOVIN	Calcium-activated potassium channel subunit alpha 1 (Calcium-activated potassium channel, subfamily ...	0.53	-	end	6	Membrane; multi-pass membrane protein (By similarity)				1166
Q8HZJ4 UniProt NPD GO	CABP4_BOVIN	Calcium-binding protein 4 (CaBP4)	0.53	-	nuc	0	Presynapses from both types of photoreceptors: rod spherules and cone pedicles (By similarity)				279
Q08853 UniProt NPD GO	ATC_PLAFK	Calcium-transporting ATPase (EC 3.6.3.8) (Calcium pump)	0.53	-	end	8	Membrane; multi-pass membrane protein				1228
P37801 UniProt NPD GO	CLPH_ONCVO	Calponin homolog OV9M	0.53	-	nuc	0					378
Q2KJB7 UniProt NPD GO	CPT2_BOVIN	Carnitine O-palmitoyltransferase 2, mitochondrial precursor (EC 2.3.1.21) (Carnitine palmitoyltransf ...	0.53	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				658
P28293 UniProt NPD GO	CATG_MOUSE	Cathepsin G precursor (EC 3.4.21.20) (Vimentin-specific protease) (VSP)	0.53	-	exc	0	Membrane. Strongly associated with membranes				261
Q86WG3 UniProt NPD GO	ATCAY_HUMAN	Caytaxin (Ataxia Cayman type protein) (BNIP-H)	0.53	-	cyt	2			608179		371
Q9NQS1 UniProt NPD GO	AVEN_HUMAN	Cell death regulator Aven	0.53	+	nuc	0	Membrane; peripheral membrane protein. Associated with intracellular membranes	intracellular [IDA] membrane fraction [IDA]	605265		362
Q42545 UniProt NPD GO	FTSZ_ARATH	Cell division protein ftsZ homolog, chloroplast precursor	0.53	-	mit	0	Plastid; chloroplast				433
Q5EAB2 UniProt NPD GO	CDK9_BOVIN	Cell division protein kinase 9 (EC 2.7.11.22) (EC 2.7.11.23) (Cyclin-dependent kinase 9)	0.53	-	cyt	0	Nucleus (By similarity)				372
Q99J95 UniProt NPD GO	CDK9_MOUSE	Cell division protein kinase 9 (EC 2.7.11.22) (EC 2.7.11.23) (Cyclin-dependent kinase 9)	0.53	-	cyt	0	Nucleus (By similarity)				372
Q641Z4 UniProt NPD GO	CDK9_RAT	Cell division protein kinase 9 (EC 2.7.11.22) (EC 2.7.11.23) (Cyclin-dependent kinase 9)	0.53	-	cyt	0	Nucleus (By similarity)				372
Q6IQY5 UniProt NPD GO	CEP70_MOUSE	Centrosomal protein of 70 kDa (Cep70 protein)	0.53	-	nuc	0	Centrosome (By similarity)				616
Q9DB34 UniProt NPD GO	CHM2A_MOUSE	Charged multivesicular body protein 2a (Chromatin-modifying protein 2a) (CHMP2a) (Vacuolar protein s ...	0.53	-	nuc	0	Cytoplasm				222
O43633 UniProt NPD GO	CHM2A_HUMAN	Charged multivesicular body protein 2a (Chromatin-modifying protein 2a) (CHMP2a) (Vacuolar protein s ...	0.53	-	nuc	0	Cytoplasm (By similarity)				222
Q69VG1 UniProt NPD GO	CIGR1_ORYSA	Chitin-inducible gibberellin-responsive protein 1	0.53	-	nuc	0	Nucleus				571
Q9R0A1 UniProt NPD GO	CLCN2_MOUSE	Chloride channel protein 2 (ClC-2)	0.53	-	end	11	Membrane; multi-pass membrane protein				908
P69662 UniProt NPD GO	RR15_SECCE	Chloroplast 30S ribosomal protein S15	0.53	+	nuc	0	Plastid; chloroplast				90
P69661 UniProt NPD GO	RR15_WHEAT	Chloroplast 30S ribosomal protein S15	0.53	+	nuc	0	Plastid; chloroplast				90
Q6B8R9 UniProt NPD GO	RR20_GRATL	Chloroplast 30S ribosomal protein S20	0.53	-	nuc	0	Plastid; chloroplast				97
Q6YXK8 UniProt NPD GO	RR3_PHYPA	Chloroplast 30S ribosomal protein S3	0.53	-	cyt	0	Plastid; chloroplast				218
P59136 UniProt NPD GO	RR4_CANTA	Chloroplast 30S ribosomal protein S4	0.53	-	mit	0	Plastid; chloroplast				202
Q6H9K7 UniProt NPD GO	RR4_EQUPT	Chloroplast 30S ribosomal protein S4	0.53	-	nuc	0	Plastid; chloroplast				207

You are viewing entries 22951 to 23000 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.