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
Q5BBF1 UniProt NPD GO	CSN5_EMENI	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	0.19	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				335
Q6FUD0 UniProt NPD GO	PYRG_CANGA	CTP synthase (EC 6.3.4.2) (UTP--ammonia ligase) (CTP synthetase)	0.19	-	cyt	0					578
Q63315 UniProt NPD GO	CAD22_RAT	Cadherin-22 precursor (Pituitary and brain cadherin) (PB-cadherin)	0.19	-	end	2 *	Membrane; single-pass type I membrane protein				813
Q6FLU4 UniProt NPD GO	CANB_CANGA	Calcineurin subunit B (Protein phosphatase 2B regulatory subunit) (Calcineurin regulatory subunit)	0.19	-	cyt	0					175
P25296 UniProt NPD GO	CANB_YEAST	Calcineurin subunit B (Protein phosphatase 2B regulatory subunit) (Calcineurin regulatory subunit)	0.19	-	cyt	0		calcineurin complex [IPI]			174
Q9N0V5 UniProt NPD GO	CALC_HORSE	Calcitonin precursor	0.19	-	exc	0	Secreted protein				140
Q9WU49 UniProt NPD GO	CHSP1_RAT	Calcium-regulated heat stable protein 1 (Calcium-regulated heat-stable protein of 24 kDa) (CRHSP-24) ...	0.19	-	nuc	0	Cytoplasm	cytosol [TAS]			147
Q5R440 UniProt NPD GO	CALX_PONPY	Calnexin precursor	0.19	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				592
P27824 UniProt NPD GO	CALX_HUMAN	Calnexin precursor (Major histocompatibility complex class I antigen-binding protein p88) (p90) (IP9 ...	0.19	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	cytoplasm [IDA] endoplasmic reticulum [IDA]	114217		592
P24643 UniProt NPD GO	CALX_CANFA	Calnexin precursor (pp90)	0.19	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein			1JHN	593
Q9ER56 UniProt NPD GO	CAN12_MOUSE	Calpain-12 (EC 3.4.22.-)	0.19	-	cyt	0					720
Q9BQT9 UniProt NPD GO	CSTN3_HUMAN	Calsyntenin-3 precursor	0.19	-	end	1	Membrane; single-pass type I membrane protein (Potential)				956
Q8R553 UniProt NPD GO	CSTN3_RAT	Calsyntenin-3 precursor	0.19	-	end	1	Membrane; single-pass type I membrane protein (Potential)	postsynaptic membrane [IDA]			957
O88563 UniProt NPD GO	MRP3_RAT	Canalicular multispecific organic anion transporter 2 (Multidrug resistance-associated protein 3) (M ...	0.19	-	end	16 *	Membrane; multi-pass membrane protein				1522
Q6AXM1 UniProt NPD GO	CHSTA_BRARE	Carbohydrate sulfotransferase 10 (EC 2.8.2.-) (HNK-1 sulfotransferase) (HNK1ST) (HNK-1ST)	0.19	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				365
Q9GZX3 UniProt NPD GO	CHST6_HUMAN	Carbohydrate sulfotransferase 6 (EC 2.8.2.-) (N-acetylglucosamine 6-O-sulfotransferase 5) (GlcNAc6ST ...	0.19	-	exc	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi apparatus [TAS] intrinsic to Golgi membrane [ISS]	605294		395
P49747 UniProt NPD GO	COMP_HUMAN	Cartilage oligomeric matrix protein precursor (COMP)	0.19	-	nuc	0	Secreted protein	extracellular matrix (sensu Metazoa) [TAS]	600310		757
P35444 UniProt NPD GO	COMP_RAT	Cartilage oligomeric matrix protein precursor (COMP)	0.19	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [IDA]		1VDF	755
O01382 UniProt NPD GO	ICE_DROME	Caspase precursor (EC 3.4.22.-) (drICE) [Contains: Caspase subunit p21; Caspase subunit p12]	0.19	-	nuc	0					339
Q60431 UniProt NPD GO	CASP3_CRILO	Caspase-3 precursor (EC 3.4.22.-) (CASP-3) (Apopain) (Cysteine protease CPP32) (Yama protein) (CPP-3 ...	0.19	-	nuc	0	Cytoplasm				277
P55304 UniProt NPD GO	CATA_BOTCI	Catalase (EC 1.11.1.6)	0.19	-	cyt	0	Peroxisome (By similarity)				479
P18122 UniProt NPD GO	CATA1_MAIZE	Catalase isozyme 1 (EC 1.11.1.6)	0.19	-	cyt	0	Peroxisome				492
P55312 UniProt NPD GO	CATA2_SOLTU	Catalase isozyme 2 (EC 1.11.1.6)	0.19	-	cyt	0	Peroxisome (By similarity). Glyoxysome (By similarity)				492
O17473 UniProt NPD GO	CATL_BRUPA	Cathepsin L-like precursor (EC 3.4.22.15)	0.19	-	exc	0				1BMU	395
Q99966 UniProt NPD GO	CITE1_HUMAN	Cbp/p300-interacting transactivator 1 (Melanocyte-specific protein 1)	0.19	-	nuc	0	Nucleus	nucleus [IDA]	300149		193
Q9WUL8 UniProt NPD GO	CITE4_MOUSE	Cbp/p300-interacting transactivator 4 (MSG1-related protein 2) (MRG-2)	0.19	-	nuc	0	Nucleus. Cytoplasm (By similarity)	cytoplasm [IDA] nucleus [IDA]			182
O94620 UniProt NPD GO	CWF17_SCHPO	Cell cycle control protein cwf17	0.19	-	cyt	0	Nucleus (Probable)	spliceosome complex [IDA]			340
P38973 UniProt NPD GO	CC2H1_TRYBB	Cell division control protein 2 homolog 1 (EC 2.7.11.22)	0.19	-	cyt	0					301
Q91727 UniProt NPD GO	CDK4_XENLA	Cell division protein kinase 4 (EC 2.7.11.22) (Cyclin-dependent kinase 4)	0.19	-	cyt	0					319
Q99674 UniProt NPD GO	CGRE1_HUMAN	Cell growth regulator with EF hand domain 1 (Cell growth regulatory gene 11 protein)	0.19	-	exc	0			606137		301
Q9CQA0 UniProt NPD GO	CENPM_MOUSE	Centromere protein M (CENP-M) (Proliferation-associated nuclear element protein 1)	0.19	-	mit	0	Nucleus. Nuclear in non-confluent cells and cytoplasmic in confluent or dividing cells				180
O22586 UniProt NPD GO	CHSY_ONOVI	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.19	-	nuc	0					390
P16107 UniProt NPD GO	CHSY_PETCR	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.19	-	cyt	0					398
P13416 UniProt NPD GO	CHS1_SINAL	Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1)	0.19	-	cyt	0					395
Q9XGX2 UniProt NPD GO	CHS1_SORBI	Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1)	0.19	-	cyt	0					401
Q9SBL6 UniProt NPD GO	CHS3_SORBI	Chalcone synthase 3 (EC 2.3.1.74) (Naringenin-chalcone synthase 3)	0.19	-	cyt	0					401
Q9SBL4 UniProt NPD GO	CHS5_SORBI	Chalcone synthase 5 (EC 2.3.1.74) (Naringenin-chalcone synthase 5)	0.19	-	cyt	0					401
Q9SBL3 UniProt NPD GO	CHS6_SORBI	Chalcone synthase 6 (EC 2.3.1.74) (Naringenin-chalcone synthase 6)	0.19	-	cyt	0					401
P48394 UniProt NPD GO	CHSB_IPOCO	Chalcone synthase B (EC 2.3.1.74) (Naringenin-chalcone synthase B) (CHS-B) (Fragment)	0.19	-	mit	0					363
P24825 UniProt NPD GO	CHS2_MAIZE	Chalcone synthase C2 (EC 2.3.1.74) (Naringenin-chalcone synthase C2)	0.19	-	mit	0					400
P78955 UniProt NPD GO	HUS1_SCHPO	Checkpoint protein hus1	0.19	-	nuc	0	Nucleus (Probable)	checkpoint clamp complex [IDA]			287
P00993 UniProt NPD GO	IBP_CARCR	Chelonianin (Basic protease inhibitor) (RTPI)	0.19	-	nuc	0					110
P81859 UniProt NPD GO	CBLE_VISAL	Chitin-binding lectin	0.19	-	nuc	0					49
Q8MX41 UniProt NPD GO	IDGF1_DROSI	Chitinase-like protein Idgf1 precursor (Imaginal disk growth factor protein 1)	0.19	-	exc	0	Secreted protein (By similarity). Secreted in hemolymph (By similarity). It is probably transported ...	extracellular region [ISS]			439
P58125 UniProt NPD GO	RR16_LOTJA	Chloroplast 30S ribosomal protein S16	0.19	-	mit	0	Plastid; chloroplast				80
Q2PMP7 UniProt NPD GO	RR3_SOYBN	Chloroplast 30S ribosomal protein S3	0.19	-	mit	0	Plastid; chloroplast				216
Q5SD16 UniProt NPD GO	RR8_HUPLU	Chloroplast 30S ribosomal protein S8	0.19	-	cyt	0	Plastid; chloroplast				132
P21512 UniProt NPD GO	RK16_EUGGR	Chloroplast 50S ribosomal protein L16	0.19	-	mit	0	Plastid; chloroplast				135
O98449 UniProt NPD GO	RK19_THAWE	Chloroplast 50S ribosomal protein L19	0.19	-	nuc	0	Plastid; chloroplast				120
P51209 UniProt NPD GO	RK21_PORPU	Chloroplast 50S ribosomal protein L21	0.19	-	nuc	0	Plastid; chloroplast				104

You are viewing entries 51651 to 51700 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.