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
P22074 UniProt NPD GO	CALT_CAVPO	Caltrin-like protein 1 (Caltrin-like protein I)	0.02	-	nuc	0	Secreted protein				45
P22572 UniProt NPD GO	CARA_NEUCR	Carbamoyl-phosphate synthase arginine-specific small chain, mitochondrial precursor (EC 6.3.5.5) (Ar ...	0.02	-	nuc	0	Mitochondrion; mitochondrial matrix				453
P87183 UniProt NPD GO	CARA_TRIVE	Carbamoyl-phosphate synthase arginine-specific small chain, mitochondrial precursor (EC 6.3.5.5) (Ar ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix				453
P46510 UniProt NPD GO	CAHX_FLABI	Carbonic anhydrase (EC 4.2.1.1) (Carbonate dehydratase)	0.02	-	mit	0	Cytoplasm (Potential)				330
P46511 UniProt NPD GO	CAHX_FLABR	Carbonic anhydrase (EC 4.2.1.1) (Carbonate dehydratase)	0.02	-	mit	0	Cytoplasm (Potential)				330
P46281 UniProt NPD GO	CAHX_FLAPR	Carbonic anhydrase (EC 4.2.1.1) (Carbonate dehydratase)	0.02	-	mit	0	Cytoplasm (Potential)				329
P46512 UniProt NPD GO	CAH1_FLALI	Carbonic anhydrase 1 (EC 4.2.1.1) (Carbonate dehydratase 1)	0.02	-	mit	0	Cytoplasm (Potential)				330
P00917 UniProt NPD GO	CAH1_HORSE	Carbonic anhydrase 1 (EC 4.2.1.1) (Carbonic anhydrase I) (Carbonate dehydratase I) (CA-I)	0.02	-	nuc	0	Cytoplasm				260
P42737 UniProt NPD GO	CAH2_ARATH	Carbonic anhydrase 2 (EC 4.2.1.1) (Carbonate dehydratase 2)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein. Plastid; chloroplast; chlor ...				259
P07630 UniProt NPD GO	CAH2_CHICK	Carbonic anhydrase 2 (EC 4.2.1.1) (Carbonic anhydrase II) (Carbonate dehydratase II) (CA-II)	0.02	-	cyt	0	Cytoplasm			1Q4I	259
P07450 UniProt NPD GO	CAH3_HORSE	Carbonic anhydrase 3 (EC 4.2.1.1) (Carbonic anhydrase III) (Carbonate dehydratase III) (CA-III)	0.02	-	cyt	0	Cytoplasm				259
P14141 UniProt NPD GO	CAH3_RAT	Carbonic anhydrase 3 (EC 4.2.1.1) (Carbonic anhydrase III) (Carbonate dehydratase III) (CA-III)	0.02	-	cyt	0	Cytoplasm			1FLJ	259
P47727 UniProt NPD GO	DHCA_RAT	Carbonyl reductase [NADPH] 1 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase 1)	0.02	-	cyt	0	Cytoplasm	cytosol [TAS] microsome [IDA]			276
P14384 UniProt NPD GO	CBPM_HUMAN	Carboxypeptidase M precursor (EC 3.4.17.12)	0.02	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor	plasma membrane [TAS]	114860	1UWY	443
Q5RFD6 UniProt NPD GO	CBPM_PONPY	Carboxypeptidase M precursor (EC 3.4.17.12)	0.02	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				443
P40198 UniProt NPD GO	CEAM3_HUMAN	Carcinoembryonic antigen-related cell adhesion molecule 3 precursor (Carcinoembryonic antigen CGM1) ...	0.02	-	nuc	1	Membrane; single-pass type I membrane protein		609142		252
P81816 UniProt NPD GO	ALL13_CARMA	Carcinustatin-13	0.02	-		0	Secreted protein				18
Q98965 UniProt NPD GO	CTX6_NAJAT	Cardiotoxin 6 precursor	0.02	-	mit	0	Secreted protein				82
Q91996 UniProt NPD GO	CX7P_NAJAT	Cardiotoxin 7'' precursor	0.02	-	nuc	0	Secreted protein				83
Q91126 UniProt NPD GO	CX7A_NAJAT	Cardiotoxin 7a precursor	0.02	-	nuc	0	Secreted protein				83
P62375 UniProt NPD GO	CXH_NAJAT	Cardiotoxin V precursor (CTX V) (CTXV) (CTX A5) (Cardiotoxin-like basic polypeptide) (CLBP)	0.02	-	nuc	0	Secreted protein			1KXI	83
P81494 UniProt NPD GO	CATB_COTJA	Cathepsin B (EC 3.4.22.1) (Cathepsin B1) (Fragments)	0.02	-	nuc	0	Lysosome				48
P92131 UniProt NPD GO	CATB1_GIALA	Cathepsin B-like CP1 precursor (EC 3.4.22.-) (Cathepsin B-like protease B1)	0.02	-	nuc	0	Vacuole				303
Q05744 UniProt NPD GO	CATD_CHICK	Cathepsin D precursor (EC 3.4.23.5) [Contains: Cathepsin D light chain; Cathepsin D heavy chain]	0.02	-	end	1 *	Lysosome				398
P00795 UniProt NPD GO	CATD_PIG	Cathepsin D precursor (EC 3.4.23.5) [Contains: Cathepsin D light chain; Cathepsin D heavy chain]	0.02	-	cyt	0	Lysosome				345
Q9R014 UniProt NPD GO	CATJ_MOUSE	Cathepsin J precursor (EC 3.4.22.-) (Cathepsin P) (Cathepsin L-related protein) (Catlrp-p)	0.02	-	exc	0	Lysosome (Potential)				334
Q63088 UniProt NPD GO	CATJ_RAT	Cathepsin J precursor (EC 3.4.22.-) (Cathepsin P) (Cathepsin L-related protein) (Catlrp-p)	0.02	-	end	0	Lysosome (Potential)				334
P09648 UniProt NPD GO	CATL_CHICK	Cathepsin L (EC 3.4.22.15) [Contains: Cathepsin L heavy chain; Cathepsin L light chain] (Fragments)	0.02	-	cyt	0	Lysosome				218
Q26534 UniProt NPD GO	CATL_SCHMA	Cathepsin L precursor (EC 3.4.22.15) (SMCL1)	0.02	-	cyt	0	Lysosome				319
Q09093 UniProt NPD GO	CATL1_FASHE	Cathepsin L1 (EC 3.4.22.15) (Fragment)	0.02	-		0	Lysosome				20
P11456 UniProt NPD GO	MPRD_BOVIN	Cation-dependent mannose-6-phosphate receptor precursor (CD Man-6-P receptor) (CD-MPR) (46 kDa manno ...	0.02	-	end	1	Lysosome; lysosomal membrane; single-pass type I membrane protein			1M6P	279
Q2QL90 UniProt NPD GO	CAV1_MICMU	Caveolin-1	0.02	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				179
Q66WT7 UniProt NPD GO	CAV2_BOVIN	Caveolin-2	0.02	-	end	2	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				162
Q9YGM9 UniProt NPD GO	CAV2_FUGRU	Caveolin-2	0.02	-	nuc	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				162
P51636 UniProt NPD GO	CAV2_HUMAN	Caveolin-2	0.02	-	end	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...	caveolar membrane [NAS] integral to plasma membrane [IDA] lipid raft [IDA] perinuclear region [IDA] plasma membrane [IDA]	601048		162
Q2QLF3 UniProt NPD GO	CAV2_PANTR	Caveolin-2	0.02	-	end	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				162
P14666 UniProt NPD GO	CEC4_BOMMO	Cecropin (Antibacterial peptide CM-IV)	0.02	-	nuc	0	Secreted protein				35
Q06590 UniProt NPD GO	CEC2_CERCA	Cecropin-2 precursor	0.02	-	end	1 *	Secreted protein				63
Q94990 UniProt NPD GO	CEC2_DROVI	Cecropin-2 precursor	0.02	-	vac	1 *	Secreted protein				63
Q94558 UniProt NPD GO	CEC3_DROVI	Cecropin-3 precursor	0.02	-	exc	1 *	Secreted protein				63
P82592 UniProt NPD GO	CECA_AEDAE	Cecropin-A precursor	0.02	-	exc	0	Secreted protein				59
P14954 UniProt NPD GO	CECA_DROME	Cecropin-A1/A2 precursor	0.02	-	vac	1 *	Secreted protein	extracellular region [IDA]			63
O61281 UniProt NPD GO	CECA2_DROYA	Cecropin-A2 (Fragment)	0.02	-	vac	0	Secreted protein	extracellular region [ISS]			56
Q86PR5 UniProt NPD GO	CECB1_CULPP	Cecropin-B1 precursor	0.02	-	exc	1 *	Secreted protein (By similarity)				59
Q86PR4 UniProt NPD GO	CECB2_CULPP	Cecropin-B2 precursor	0.02	-	exc	1 *	Secreted protein (By similarity)				59
P83415 UniProt NPD GO	CECC_HELVI	Cecropin-C (Fragment)	0.02	-	cyt	0	Secreted protein				33
P34112 UniProt NPD GO	CDC2_DICDI	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase)	0.02	-	cyt	0					296
P54666 UniProt NPD GO	CC2H3_TRYBB	Cell division control protein 2 homolog 3 (EC 2.7.11.22)	0.02	-	mit	0					311
P35567 UniProt NPD GO	CDC2A_XENLA	Cell division control protein 2-A (EC 2.7.11.22) (EC 2.7.11.23) (Cell division control protein 2 hom ...	0.02	-	cyt	0	Nucleus (By similarity)				302
P48280 UniProt NPD GO	FTSW_CYAPA	Cell division protein ftsW homolog	0.02	-	end	10 *	Plastid; cyanelle; cyanelle membrane; multi-pass membrane protein (Potential)				397

You are viewing entries 82701 to 82750 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.