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
P11120 UniProt NPD GO	CALM_PLECO	Calmodulin (CaM)	0.05	-	cyt	0					148
Q5RAD2 UniProt NPD GO	CALM_PONPY	Calmodulin (CaM)	0.05	-	cyt	0					148
P11121 UniProt NPD GO	CALM_PYUSP	Calmodulin (CaM)	0.05	-	cyt	0					148
P62160 UniProt NPD GO	CALM_RABIT	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]			148
P62161 UniProt NPD GO	CALM_RAT	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]		1QX7	148
P62184 UniProt NPD GO	CALM_RENRE	Calmodulin (CaM)	0.05	-	cyt	0					148
P05933 UniProt NPD GO	CALM_SCHPO	Calmodulin (CaM)	0.05	-	cyt	0	In the growing tips and spindle pole body during interphase and in the septum during septation. Comp ...	spindle pole body [IDA]			150
Q6YNX6 UniProt NPD GO	CALM_SHEEP	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]			148
P02598 UniProt NPD GO	CALM_TETPY	Calmodulin (CaM)	0.05	-	cyt	0					148
P62151 UniProt NPD GO	CALM_TORCA	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]			148
P62155 UniProt NPD GO	CALM_XENLA	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]		2COL	148
P62147 UniProt NPD GO	CALM1_BRAFL	Calmodulin-1 (CaM 1)	0.05	-	cyt	0					148
P62148 UniProt NPD GO	CALM1_BRALA	Calmodulin-1 (CaM 1)	0.05	-	cyt	0					148
P62153 UniProt NPD GO	CALMA_HALRO	Calmodulin-A (CaM A)	0.05	-	cyt	0					148
O96081 UniProt NPD GO	CALMB_HALRO	Calmodulin-B (CaM B)	0.05	-	cyt	0					148
P62146 UniProt NPD GO	CALMA_ARBPU	Calmodulin-alpha (CaM A) (Fragment)	0.05	-	cyt	0					141
Q9S744 UniProt NPD GO	CML9_ARATH	Calmodulin-like protein 9 (AtCaM-9)	0.05	-	cyt	0					151
P36581 UniProt NPD GO	CALX_SCHPO	Calnexin homolog precursor	0.05	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	endoplasmic reticulum membrane [TAS]			560
O09161 UniProt NPD GO	CASQ2_MOUSE	Calsequestrin-2 precursor (Calsequestrin, cardiac muscle isoform)	0.05	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen. This isoform of calsequestrin occurs in the sa ...	sarcoplasmic reticulum [TAS]			415
P43092 UniProt NPD GO	CARP3_CANAL	Candidapepsin-3 precursor (EC 3.4.23.24) (Aspartate protease 3) (ACP 3) (Secreted aspartic protease ...	0.05	-	exc	0	Secreted protein				398
P47936 UniProt NPD GO	CNR2_MOUSE	Cannabinoid receptor 2 (CB2) (CB-2)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				347
O96432 UniProt NPD GO	CBK_TRIVA	Carbamate kinase (EC 2.7.2.2)	0.05	-	cyt	0					314
P00919 UniProt NPD GO	CAH2_RABIT	Carbonic anhydrase 2 (EC 4.2.1.1) (Carbonic anhydrase II) (Carbonate dehydratase II) (CA-II)	0.05	-	cyt	0	Cytoplasm				259
P07451 UniProt NPD GO	CAH3_HUMAN	Carbonic anhydrase 3 (EC 4.2.1.1) (Carbonic anhydrase III) (Carbonate dehydratase III) (CA-III)	0.05	-	cyt	0	Cytoplasm		114750	1Z97	259
P48758 UniProt NPD GO	DHCA_MOUSE	Carbonyl reductase [NADPH] 1 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase 1)	0.05	-	cyt	0	Cytoplasm				276
P36035 UniProt NPD GO	JEN1_YEAST	Carboxylic acid transporter protein homolog	0.05	-	end	12	Membrane; multi-pass membrane protein (Probable)	mitochondrion [IDA] plasma membrane [IMP]			616
P19628 UniProt NPD GO	CBPB_PROAT	Carboxypeptidase B precursor (EC 3.4.17.2) (Fragment)	0.05	-		0	Secreted protein				15
P04836 UniProt NPD GO	CBPE_BOVIN	Carboxypeptidase E (EC 3.4.17.10) (CPE) (Carboxypeptidase H) (CPH) (Enkephalin convertase) (Prohormo ...	0.05	-	cyt	0	Secretory granules of pancreatic islets, adrenal gland, pituitary and brain				434
P14306 UniProt NPD GO	CPYI_YEAST	Carboxypeptidase Y inhibitor (CPY inhibitor) (Ic) (I(C)) (Protein DKA1) (Protein NSP1) (Protein TFS1 ...	0.05	-	nuc	0	Cytoplasm	soluble fraction [IDA]		1WPX	219
Q14002 UniProt NPD GO	CEAM7_HUMAN	Carcinoembryonic antigen-related cell adhesion molecule 7 precursor (Carcinoembryonic antigen CGM2)	0.05	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	integral to membrane [TAS] plasma membrane [TAS]			265
P38499 UniProt NPD GO	FAR1_PROCL	Cardioexcitatory FMRFamide homolog NF1	0.05	-		0	Secreted protein				7
Q80ZM8 UniProt NPD GO	CRLS1_MOUSE	Cardiolipin synthetase (EC 2.7.8.-) (Cardiolipin synthase) (CLS)	0.05	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				303
Q5U2V5 UniProt NPD GO	CRLS1_RAT	Cardiolipin synthetase (EC 2.7.8.-) (Cardiolipin synthase) (CLS)	0.05	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				302
P83345 UniProt NPD GO	CX1_NAJSG	Cardiotoxin sagitoxin I	0.05	-	nuc	0	Secreted protein				60
Q9PRP9 UniProt NPD GO	CAR1_ECHCA	Carinactivase-1 (EC 3.4.24.-) (CA-1) (Fragment)	0.05	-	cyt	0					32
P35508 UniProt NPD GO	KC1D_BOVIN	Casein kinase I isoform delta (EC 2.7.11.1) (CKI-delta) (CKId) (Fragment)	0.05	-	nuc	0	Cytoplasm				42
P19454 UniProt NPD GO	CSK22_YEAST	Casein kinase II subunit alpha' (EC 2.7.11.1) (CK II)	0.05	-	mit	0		protein kinase CK2 complex [IDA]			338
O02002 UniProt NPD GO	CASP1_DROME	Caspase-1 precursor (EC 3.4.22.-) [Contains: Caspase-1 subunit p22; Caspase-1 subunit p13]	0.05	-	cyt	0					323
P78619 UniProt NPD GO	CATB_EMENI	Catalase B precursor (EC 1.11.1.6)	0.05	-	end	0					722
P10420 UniProt NPD GO	CARP_MYTED	Catch-relaxing peptide (CARP)	0.05	-		0					7
Q4LAL9 UniProt NPD GO	CATD_CANFA	Cathepsin D precursor (EC 3.4.23.5)	0.05	-	mit	1 *	Lysosome				410
P49935 UniProt NPD GO	CATH_MOUSE	Cathepsin H precursor (EC 3.4.22.16) (Cathepsin B3) (Cathepsin BA) [Contains: Cathepsin H mini chain ...	0.05	-	mit	0	Lysosome				333
P00786 UniProt NPD GO	CATH_RAT	Cathepsin H precursor (EC 3.4.22.16) (Cathepsin B3) (Cathepsin BA) [Contains: Cathepsin H mini chain ...	0.05	-	end	0	Lysosome	lysosome [TAS]			333
O46427 UniProt NPD GO	CATH_PIG	Cathepsin H precursor (EC 3.4.22.16) [Contains: Cathepsin H mini chain; Cathepsin H heavy chain; Cat ...	0.05	-	end	0	Lysosome			8PCH	335
P07711 UniProt NPD GO	CATL_HUMAN	Cathepsin L precursor (EC 3.4.22.15) (Major excreted protein) (MEP) [Contains: Cathepsin L heavy cha ...	0.05	-	vac	0	Lysosome	extracellular region [NAS] lysosome [NAS]	116880	1MHW	333
P43234 UniProt NPD GO	CATO_HUMAN	Cathepsin O precursor (EC 3.4.22.42)	0.05	-	end	0			600550		321
Q9QZE3 UniProt NPD GO	CATQ_RAT	Cathepsin Q precursor (EC 3.4.22.-)	0.05	-	exc	0	Lysosome (Potential)	lysosome [NAS]			343
P25774 UniProt NPD GO	CATS_HUMAN	Cathepsin S precursor (EC 3.4.22.27)	0.05	-	end	0	Lysosome	extracellular region [NAS] lysosome [NAS]	116845	2G6D	331
O70370 UniProt NPD GO	CATS_MOUSE	Cathepsin S precursor (EC 3.4.22.27)	0.05	-	mit	0	Lysosome	lysosome [IDA] membrane [IDA]		1M0H	340
P08426 UniProt NPD GO	TRY3_RAT	Cationic trypsin-3 precursor (EC 3.4.21.4) (Cationic trypsin III) (Pretrypsinogen III)	0.05	-	exc	0	Secreted protein; extracellular space				247

You are viewing entries 74001 to 74050 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.