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
P57791 UniProt NPD GO	FACE2_MOUSE	CAAX prenyl protease 2 (EC 3.4.22.-) (Prenyl protein-specific endoprotease 2) (Farnesylated proteins ...	0.08	-	vac	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				329
Q60809 UniProt NPD GO	CNOT7_MOUSE	CCR4-NOT transcription complex subunit 7 (CCR4-associated factor 1) (CAF1)	0.08	-	cyt	0	Nucleus	CCR4-NOT complex [IPI]			285
Q9UIV1 UniProt NPD GO	CNOT7_HUMAN	CCR4-NOT transcription complex subunit 7 (CCR4-associated factor 1) (CAF1) (BTG1-binding factor 1)	0.08	-	cyt	0	Nucleus	CCR4-NOT complex [NAS] nucleus [IEP]	604913		285
P18181 UniProt NPD GO	CD48_MOUSE	CD48 antigen precursor (MRC OX-45 surface antigen) (BCM1 surface antigen) (BLAST-1) (HM48-1) (sgp-60 ...	0.08	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor				240
Q9QWK4 UniProt NPD GO	CD5L_MOUSE	CD5 antigen-like precursor (SP-alpha) (CT-2) (Apoptosis inhibitory 6) (Apoptosis inhibitor expressed ...	0.08	-	exc	0	Secreted protein				352
P58019 UniProt NPD GO	CD59B_MOUSE	CD59B glycoprotein precursor (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory pro ...	0.08	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor				129
Q8W3E8 UniProt NPD GO	COBL4_ORYSA	COBRA-like 4 protein precursor (BRITTLE CULM1-like 9 protein)	0.08	-	nuc	1 *					425
Q5E9V6 UniProt NPD GO	COMD4_BOVIN	COMM domain-containing protein 4	0.08	-	mit	0					199
Q5KAS8 UniProt NPD GO	CSN12_CRYNE	COP9 signalosome complex subunit 12	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				403
Q6PC30 UniProt NPD GO	CSN5_BRARE	COP9 signalosome complex subunit 5 (EC 3.4.-.-) (Signalosome subunit 5)	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				334
Q9NRF8 UniProt NPD GO	PYRG2_HUMAN	CTP synthase 2 (EC 6.3.4.2) (UTP--ammonia ligase 2) (CTP synthetase 2)	0.08	-	cyt	0			300380		586
Q12864 UniProt NPD GO	CAD17_HUMAN	Cadherin-17 precursor (Liver-intestine-cadherin) (LI-cadherin) (Intestinal peptide-associated transp ...	0.08	-	end	1	Membrane; single-pass type I membrane protein (Potential)		603017		832
Q9FUQ7 UniProt NPD GO	CNBL8_ARATH	Calcineurin B-like protein 8	0.08	-	nuc	0					214
Q09460 UniProt NPD GO	SEB1_CAEEL	Calcitonin receptor-like protein seb-1	0.08	-	end	6	Membrane; multi-pass membrane protein (Potential)				546
Q04732 UniProt NPD GO	ARP_EUGGR	Calcium-binding acidic-repeat protein precursor (ARP)	0.08	-	exc	0	Or: Secreted protein. Or: Endoplasmic reticulum				695
P22700 UniProt NPD GO	ATC1_DROME	Calcium-transporting ATPase sarcoplasmic/endoplasmic reticulum type (EC 3.6.3.8) (Calcium pump)	0.08	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...	sarcoplasmic reticulum [ISS]			1020
Q9M8U1 UniProt NPD GO	CML18_ARATH	Calmodulin-like protein 18 (Calmodulin-15) (AtCaM-15)	0.08	-	cyt	0	Vacuole				165
P13135 UniProt NPD GO	CPNS1_BOVIN	Calpain small subunit 1 (CSS1) (Calcium-dependent protease small subunit 1) (Calcium-dependent prote ...	0.08	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon c ...				263
Q23858 UniProt NPD GO	CALR_DICDI	Calreticulin precursor	0.08	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				424
Q9SLY8 UniProt NPD GO	CALR_ORYSA	Calreticulin precursor	0.08	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum lumen [TAS]			424
O09165 UniProt NPD GO	CASQ1_MOUSE	Calsequestrin-1 precursor (Calsequestrin, skeletal muscle isoform)	0.08	-	mit	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen. This isoform of calsequestrin occurs in the sa ...	mitochondrion [IDA] sarcoplasmic reticulum [IDA]			399
P31415 UniProt NPD GO	CASQ1_HUMAN	Calsequestrin-1 precursor (Calsequestrin, skeletal muscle isoform) (Calmitin)	0.08	-	vac	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen. This isoform of calsequestrin occurs in the sa ...	mitochondrial matrix [TAS] smooth endoplasmic reticulum [TAS]	114250		390
Q3T0K1 UniProt NPD GO	CALU_BOVIN	Calumenin precursor	0.08	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				315
P32951 UniProt NPD GO	CARP1_CANPA	Candidapepsin-1 precursor (EC 3.4.23.24) (Aspartate protease 1) (ACP 1)	0.08	-	exc	0	Secreted protein				402
P34972 UniProt NPD GO	CNR2_HUMAN	Cannabinoid receptor 2 (CB2) (CB-2) (CX5)	0.08	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	605051		360
Q98895 UniProt NPD GO	CNR1B_FUGRU	Cannabinoid receptor type 1B	0.08	-	end	7	Membrane; multi-pass membrane protein				470
P46056 UniProt NPD GO	CARB_TRICU	Carbamoyl-phosphate synthase arginine-specific large chain (EC 6.3.5.5) (Arginine-specific carbamoyl ...	0.08	-	mit	0	Cytoplasm				1176
P80720 UniProt NPD GO	AWN_HORSE	Carbohydrate-binding protein AWN (Zona pellucida-binding protein AWN) (Spermadhesin AWN) (Seminal pl ...	0.08	-	nuc	0	Secreted protein. Predominantly localized on the membrane overlying the acrosomal cap region of the ...				133
P26776 UniProt NPD GO	AWN_PIG	Carbohydrate-binding protein AWN precursor (Zona pellucida-binding protein AWN) (Spermadhesin AWN) ( ...	0.08	-	mit	0	Secreted protein. Predominantly localized on the membrane overlying the acrosomal cap region of the ...				153
P47844 UniProt NPD GO	DHCA_RABIT	Carbonyl reductase [NADPH] 1 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase 1)	0.08	-	mit	0	Cytoplasm				276
P58466 UniProt NPD GO	CTDS1_MOUSE	Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 (EC 3.1.3.16) (Nuclear L ...	0.08	-	cyt	0	Nucleus (Potential)				261
Q9GZU7 UniProt NPD GO	CTDS1_HUMAN	Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 (EC 3.1.3.16) (Nuclear L ...	0.08	-	cyt	0	Nucleus (Potential)	nucleus [TAS]	605323	1TA0	261
O00748 UniProt NPD GO	EST2_HUMAN	Carboxylesterase 2 precursor (EC 3.1.1.1) (CE-2) (hCE-2)	0.08	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum [TAS]	605278		559
P19399 UniProt NPD GO	ICAA_ASCSU	Carboxypeptidase A inhibitor	0.08	-	nuc	0	Secreted protein				65
Q80V42 UniProt NPD GO	CBPM_MOUSE	Carboxypeptidase M precursor (EC 3.4.17.12)	0.08	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				443
P34946 UniProt NPD GO	CPS1_PENJA	Carboxypeptidase S1 (EC 3.4.16.6)	0.08	-	cyt	0					423
Q52QW2 UniProt NPD GO	CRTS2_ONCHC	Carotenoid isomerase 2, chloroplast precursor (EC 5.-.-.-) (CrtISO2) (OcrtISO24)	0.08	-	mit	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (By similarity)				587
O75601 UniProt NPD GO	CASPD_BOVIN	Caspase-13 precursor (EC 3.4.22.-) (CASP-13) (Evolutionary related interleukin-1-beta-converting enz ...	0.08	-	cyt	0					377
Q5E9C1 UniProt NPD GO	CASP4_BOVIN	Caspase-4 precursor (EC 3.4.22.-) (CASP-4) [Contains: Caspase-4 subunit 1; Caspase-4 subunit 2]	0.08	-	cyt	0					377
Q8X1P0 UniProt NPD GO	CATA_ERYGR	Catalase (EC 1.11.1.6)	0.08	-	exc	0					718
Q877A8 UniProt NPD GO	CATB_ASPOR	Catalase B precursor (EC 1.11.1.6)	0.08	-	end	0	Secreted protein (By similarity)				725
Q92405 UniProt NPD GO	CATB_ASPFU	Catalase B precursor (EC 1.11.1.6) (Slow catalase) (Antigenic catalase)	0.08	-	exc	0	Secreted protein (Probable)				728
P43510 UniProt NPD GO	CPR6_CAEEL	Cathepsin B-like cysteine proteinase 6 precursor (EC 3.4.22.-) (Cysteine protease-related 6)	0.08	+	exc	0					379
P18242 UniProt NPD GO	CATD_MOUSE	Cathepsin D precursor (EC 3.4.23.5)	0.08	-	mit	1 *	Lysosome	lysosome [IDA] mitochondrion [IDA]			410
Q9MZS8 UniProt NPD GO	CATD_SHEEP	Cathepsin D precursor (EC 3.4.23.5) (Fragment)	0.08	-	cyt	0	Lysosome				365
P06797 UniProt NPD GO	CATL_MOUSE	Cathepsin L precursor (EC 3.4.22.15) (Major excreted protein) (MEP) (p39 cysteine proteinase) [Conta ...	0.08	-	exc	0	Lysosome			1MVV	334
Q28944 UniProt NPD GO	CATL_PIG	Cathepsin L precursor (EC 3.4.22.15) [Contains: Cathepsin L heavy chain; Cathepsin L light chain]	0.08	-	vac	0	Lysosome				334
Q24940 UniProt NPD GO	CATLL_FASHE	Cathepsin L-like proteinase precursor (EC 3.4.22.-)	0.08	-	exc	0	Secreted protein	extracellular region [IDA]			326
P00760 UniProt NPD GO	TRY1_BOVIN	Cationic trypsin precursor (EC 3.4.21.4) (Beta-trypsin) [Contains: Alpha-trypsin chain 1; Alpha-tryp ...	0.08	-	exc	0	Secreted protein; extracellular space			5PTP	243
P97769 UniProt NPD GO	CITE1_MOUSE	Cbp/p300-interacting transactivator 1 (Melanocyte-specific protein 1)	0.08	-	nuc	0	Nucleus	nucleus [IDA]			203

You are viewing entries 67701 to 67750 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.