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
P93171 UniProt NPD GO	CALM_HELAN	Calmodulin (CaM)	0.04	-	cyt	0					148
P62201 UniProt NPD GO	CALM_LILLO	Calmodulin (CaM)	0.04	-	cyt	0					148
P48976 UniProt NPD GO	CALM_MALDO	Calmodulin (CaM)	0.04	-	cyt	0					148
P17928 UniProt NPD GO	CALM_MEDSA	Calmodulin (CaM)	0.04	-	cyt	0					148
Q8X187 UniProt NPD GO	CALM_PAXIN	Calmodulin (CaM)	0.04	-	cyt	0					148
O94739 UniProt NPD GO	CALM_PLEOS	Calmodulin (CaM)	0.04	-	cyt	0					148
P21251 UniProt NPD GO	CALM_STIJA	Calmodulin (CaM)	0.04	-	cyt	0					148
O97341 UniProt NPD GO	CALM_SUBDO	Calmodulin (CaM)	0.04	-	cyt	0					148
P62202 UniProt NPD GO	CALM_BRYDI	Calmodulin (CaM) (BC329)	0.04	-	cyt	0					148
P53440 UniProt NPD GO	CALMF_NAEGR	Calmodulin, flagellar (CAM-1)	0.04	-	cyt	0					155
P62199 UniProt NPD GO	CALM1_PETHY	Calmodulin-1 (CaM-1)	0.04	-	cyt	0					148
P62200 UniProt NPD GO	CALM1_DAUCA	Calmodulin-1/11/16 (CaM-1/11/16)	0.04	-	cyt	0					148
P27163 UniProt NPD GO	CALM2_PETHY	Calmodulin-2 (CaM-2)	0.04	-	cyt	0					148
Q7DMN9 UniProt NPD GO	CALM5_SOLTU	Calmodulin-5/6/7/8 (CaM-5/6/7/8)	0.04	-	cyt	0					148
P59220 UniProt NPD GO	CALM7_ARATH	Calmodulin-7 (CaM-7)	0.04	-	cyt	0					148
P25070 UniProt NPD GO	TCH2_ARATH	Calmodulin-related protein 2, touch-induced	0.04	-	cyt	0				1AVJ	161
P19204 UniProt NPD GO	CASQ1_CHICK	Calsequestrin-1 precursor (Calsequestrin, skeletal muscle isoform) (Aspartactin) (Laminin-binding pr ...	0.04	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen. This isoform of calsequestrin occurs in the sa ...				406
P51868 UniProt NPD GO	CASQ2_RAT	Calsequestrin-2 precursor (Calsequestrin, cardiac muscle isoform)	0.04	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen. This isoform of calsequestrin occurs in the sa ...				413
Q8AY53 UniProt NPD GO	NXC1_BUNCA	Candiduxin-1 precursor	0.04	-	exc	0	Secreted protein				86
Q8AY52 UniProt NPD GO	NXC2_BUNCA	Candiduxin-2 precursor	0.04	-	exc	0	Secreted protein				86
P82803 UniProt NPD GO	TXCAN_BUNCN	Cangitoxin	0.04	-	nuc	0	Secreted protein. Found in nematocyst				48
P47746 UniProt NPD GO	CNR1_MOUSE	Cannabinoid receptor 1 (CB1) (CB-R) (Brain-type cannabinoid receptor)	0.04	-	end	7	Membrane; multi-pass membrane protein				473
P20272 UniProt NPD GO	CNR1_RAT	Cannabinoid receptor 1 (CB1) (CB-R) (Brain-type cannabinoid receptor)	0.04	-	end	7	Membrane; multi-pass membrane protein				473
Q91293 UniProt NPD GO	CPSM_RANCA	Carbamoyl-phosphate synthase [ammonia], mitochondrial precursor (EC 6.3.4.16) (Carbamoyl-phosphate s ...	0.04	-	mit	0	Mitochondrion				1496
P00918 UniProt NPD GO	CAH2_HUMAN	Carbonic anhydrase 2 (EC 4.2.1.1) (Carbonic anhydrase II) (Carbonate dehydratase II) (CA-II) (Carbon ...	0.04	-	cyt	0	Cytoplasm	cytoplasm [IDA]	259730	9CA2	259
P28651 UniProt NPD GO	CAH8_MOUSE	Carbonic anhydrase-related protein (CARP) (CA-VIII)	0.04	-	cyt	0		cytoplasm [IDA]			290
Q5RCU5 UniProt NPD GO	DHCA_PONPY	Carbonyl reductase [NADPH] 1 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase 1)	0.04	-	cyt	0	Cytoplasm (By similarity)				276
Q28960 UniProt NPD GO	DHCA_PIG	Carbonyl reductase [NADPH] 1 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase 1) (20-beta-hydroxys ...	0.04	-	cyt	0	Cytoplasm (By similarity)			1N5D	288
P16152 UniProt NPD GO	DHCA_HUMAN	Carbonyl reductase [NADPH] 1 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase 1) (Prostaglandin-E( ...	0.04	-	cyt	0	Cytoplasm		114830	1WMA	276
P38677 UniProt NPD GO	CMLE_NEUCR	Carboxy-cis,cis-muconate cyclase (EC 5.5.1.5) (3-carboxy-cis,cis-muconate lactonizing enzyme) (CMLE) ...	0.04	-	cyt	0				1JOF	365
Q8VCT4 UniProt NPD GO	CES3_MOUSE	Carboxylesterase 3 precursor (EC 3.1.1.1) (Triacylglycerol hydrolase) (TGH)	0.04	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				565
P56683 UniProt NPD GO	CP23_SPOER	Cardioactive peptide CAP23	0.04	-	nuc	0					23
P38498 UniProt NPD GO	FAR2_PROCL	Cardioexcitatory FMRFamide homolog DF2	0.04	-		0	Secreted protein				7
Q9PW19 UniProt NPD GO	CXL_BUNMM	Cardiotoxin-like protein BMLCL precursor	0.04	-	nuc	0	Secreted protein (By similarity)				103
P10056 UniProt NPD GO	PAPA3_CARPA	Caricain precursor (EC 3.4.22.30) (Papaya proteinase omega) (Papaya proteinase III) (PPIII) (Papaya ...	0.04	-	end	0				1PPO	348
O19175 UniProt NPD GO	KC1A_PIG	Casein kinase I isoform alpha (EC 2.7.11.1) (CKI-alpha) (CK1) (Fragment)	0.04	-	cyt	0	Cytoplasm				125
O77229 UniProt NPD GO	CATA_DICDI	Catalase (EC 1.11.1.6)	0.04	-	cyt	0	Peroxisome (By similarity)				496
Q9C169 UniProt NPD GO	CAT3_NEUCR	Catalase-3 precursor (EC 1.11.1.6)	0.04	-	exc	0					719
P21964 UniProt NPD GO	COMT_HUMAN	Catechol O-methyltransferase (EC 2.1.1.6)	0.04	-	nuc	1 *	Isoform S-COMT: Cytoplasm. Isoform MB-COMT: Cell membrane; single-pass type II membrane protein; ext ...	microsome [TAS] soluble fraction [TAS]	116790		271
P07858 UniProt NPD GO	CATB_HUMAN	Cathepsin B precursor (EC 3.4.22.1) (Cathepsin B1) (APP secretase) (APPS) [Contains: Cathepsin B lig ...	0.04	-	exc	0	Lysosome	intracellular [TAS]	116810	3PBH	339
P00787 UniProt NPD GO	CATB_RAT	Cathepsin B precursor (EC 3.4.22.1) (Cathepsin B1) (RSG-2) [Contains: Cathepsin B light chain; Cathe ...	0.04	-	end	0	Lysosome	apical plasma membrane [IDA] external side of plasma membrane [IDA] extracellular region [IDA] lysosome [IDA]		1THE	339
Q95029 UniProt NPD GO	CATL_DROME	Cathepsin L precursor (EC 3.4.22.15) (Cysteine proteinase 1) [Contains: Cathepsin L heavy chain; Cat ...	0.04	-	exc	0	Lysosome				341
Q26636 UniProt NPD GO	CATL_SARPE	Cathepsin L precursor (EC 3.4.22.15) [Contains: Cathepsin L heavy chain; Cathepsin L light chain]	0.04	-	exc	0	Lysosome				339
Q94714 UniProt NPD GO	CATL1_PARTE	Cathepsin L1 precursor (EC 3.4.22.15)	0.04	-	cyt	0	Secreted protein				314
P25326 UniProt NPD GO	CATS_BOVIN	Cathepsin S precursor (EC 3.4.22.27)	0.04	-	exc	0	Lysosome				331
Q8HY82 UniProt NPD GO	CATS_SAIBB	Cathepsin S precursor (EC 3.4.22.27)	0.04	-	exc	0	Lysosome (By similarity)				330
P70423 UniProt NPD GO	CTR3_MOUSE	Cationic amino acid transporter 3 (CAT-3) (Solute carrier family 7 member 3) (Cationic amino acid tr ...	0.04	-	end	14 *	Cell membrane; multi-pass membrane protein				618
O08812 UniProt NPD GO	CTR3_RAT	Cationic amino acid transporter 3 (CAT-3) (Solute carrier family 7 member 3) (Cationic amino acid tr ...	0.04	-	end	14 *	Cell membrane; multi-pass membrane protein (By similarity)				619
Q2QL79 UniProt NPD GO	CAV1_DIDMA	Caveolin-1	0.04	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				178
P83420 UniProt NPD GO	CEC_OIKKI	Cecropin (Fragment)	0.04	-	nuc	0	Secreted protein				32

You are viewing entries 76451 to 76500 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.