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
Q9UU93 UniProt NPD GO	CANB_SCHPO	Calcineurin subunit B (Protein phosphatase 2B regulatory subunit) (Calcineurin regulatory subunit)	0.28	-	cyt	0					174
P01257 UniProt NPD GO	CALC_RAT	Calcitonin precursor	0.28	-	exc	0	Secreted protein				136
O14408 UniProt NPD GO	KCC1_METAN	Calcium/calmodulin-dependent protein kinase (EC 2.7.11.17)	0.28	-	cyt	0					382
O70150 UniProt NPD GO	KCC1B_RAT	Calcium/calmodulin-dependent protein kinase type 1B (EC 2.7.11.17) (CaM kinase IB) (CaM kinase I bet ...	0.28	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)	calcium- and calmodulin-dependent protein k... [TAS]			343
Q13557 UniProt NPD GO	KCC2D_HUMAN	Calcium/calmodulin-dependent protein kinase type II delta chain (EC 2.7.11.17) (CaM-kinase II delta ...	0.28	-	mit	0		calcium- and calmodulin-dependent protein k... [TAS]	607708		499
P34652 UniProt NPD GO	CALX_CAEEL	Calnexin homolog precursor	0.28	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				619
Q9GLG2 UniProt NPD GO	CAN1_MACFA	Calpain-1 catalytic subunit (EC 3.4.22.52) (Calpain-1 large subunit) (Calcium-activated neutral prot ...	0.28	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...				714
P97571 UniProt NPD GO	CAN1_RAT	Calpain-1 catalytic subunit (EC 3.4.22.52) (Calpain-1 large subunit) (Calcium-activated neutral prot ...	0.28	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...			2G8J	713
Q06814 UniProt NPD GO	CALR_SCHMA	Calreticulin precursor (SM4 protein)	0.28	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				393
Q9QXT8 UniProt NPD GO	CSEN_MOUSE	Calsenilin (DRE-antagonist modulator) (DREAM) (Kv channel-interacting protein 3) (A-type potassium c ...	0.28	-	cyt	0	Cytoplasm. Cell membrane; lipid-anchor. Endoplasmic reticulum. Golgi apparatus. In the presence of P ...				256
Q6B940 UniProt NPD GO	CARA_GRATL	Carbamoyl-phosphate synthase small chain (EC 6.3.5.5) (Carbamoyl-phosphate synthetase glutamine chai ...	0.28	-	nuc	0	Plastid; chloroplast				395
O93403 UniProt NPD GO	CHST3_TORCA	Carbohydrate sulfotransferase 3 (EC 2.8.2.17) (Chondroitin 6-O-sulfotransferase 1) (C6ST-1) (Nervous ...	0.28	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				441
Q9GZS9 UniProt NPD GO	CHST5_HUMAN	Carbohydrate sulfotransferase 5 (EC 2.8.2.-) (N-acetylglucosamine 6-O-sulfotransferase 3) (GlcNAc6ST ...	0.28	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane (Probable). Golgi membrane, early secr ...	Golgi apparatus [IDA] integral to membrane [NAS] intrinsic to Golgi membrane [NAS]	604817		390
Q9QZA0 UniProt NPD GO	CAH5B_MOUSE	Carbonic anhydrase 5B, mitochondrial precursor (EC 4.2.1.1) (Carbonic anhydrase VB) (Carbonate dehyd ...	0.28	-	mit	0	Mitochondrion	mitochondrion [IDA]			317
P18761 UniProt NPD GO	CAH6_MOUSE	Carbonic anhydrase 6 precursor (EC 4.2.1.1) (Carbonic anhydrase VI) (Carbonate dehydratase VI) (CA-V ...	0.28	-	exc	0	Secreted protein				317
Q00493 UniProt NPD GO	CBPE_MOUSE	Carboxypeptidase E precursor (EC 3.4.17.10) (CPE) (Carboxypeptidase H) (CPH) (Enkephalin convertase) ...	0.28	-	exc	0	Secretory granules of pancreatic islets, adrenal gland, pituitary and brain				476
P47934 UniProt NPD GO	CACP_MOUSE	Carnitine O-acetyltransferase (EC 2.3.1.7) (Carnitine acetylase) (CAT) (Carnitine acetyltransferase) ...	0.28	-	pox	0	Endoplasmic reticulum (Potential). Peroxisome (Potential). Mitochondrion; mitochondrial inner membra ...	mitochondrion [IDA]		1T7Q	626
P97633 UniProt NPD GO	KC1A_RAT	Casein kinase I isoform alpha (EC 2.7.11.1) (CKI-alpha) (CK1)	0.28	-	nuc	0	Cytoplasm				325
P08182 UniProt NPD GO	CSK2B_DROME	Casein kinase II subunit beta (CK II beta)	0.28	-	cyt	0		cytosol [IDA] nucleus [IDA] protein kinase CK2 complex [IDA]			235
P57730 UniProt NPD GO	ICBR_HUMAN	Caspase-1 inhibitor Iceberg	0.28	-	mit	0			605354	1DGN	90
Q5RF10 UniProt NPD GO	CATA_PONPY	Catalase (EC 1.11.1.6)	0.28	-	cyt	0	Peroxisome (By similarity)				526
P04762 UniProt NPD GO	CATA_RAT	Catalase (EC 1.11.1.6)	0.28	-	cyt	0	Peroxisome				526
P25793 UniProt NPD GO	CYSP2_HAECO	Cathepsin B-like cysteine proteinase 2 precursor (EC 3.4.22.-)	0.28	-	vac	0					342
P06243 UniProt NPD GO	CDC7_YEAST	Cell division control protein 7 (EC 2.7.11.1)	0.28	-	nuc	0		nucleoplasm [TAS]			507
P51953 UniProt NPD GO	CDK7_CARAU	Cell division protein kinase 7 (EC 2.7.11.22) (EC 2.7.11.23) (40 kDa protein kinase) (P40 MO15) (CDC ...	0.28	+	cyt	0	Nucleus (By similarity)				344
P47179 UniProt NPD GO	DAN4_YEAST	Cell wall protein DAN4 precursor	0.28	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA]			1161
P13635 UniProt NPD GO	CERU_RAT	Ceruloplasmin precursor (EC 1.16.3.1) (Ferroxidase)	0.28	-	exc	0	Secreted protein	anchored to plasma membrane [IDA] extracellular region [IDA]			1059
Q9TLT1 UniProt NPD GO	DNAK_CYACA	Chaperone protein dnaK (Heat shock protein 70) (Heat shock 70 kDa protein) (HSP70)	0.28	+	cyt	0	Plastid; chloroplast				618
Q6DF27 UniProt NPD GO	CHM1B_XENTR	Charged multivesicular body protein 1b (Chromatin-modifying protein 1b) (CHMP1b)	0.28	-	nuc	0	Cytoplasm (By similarity)				199
Q9CQD4 UniProt NPD GO	CH1B2_MOUSE	Charged multivesicular body protein 1b-2 (Chromatin-modifying protein 1b-2) (CHMP1b-2)	0.28	-	nuc	0	Cytoplasm; cytosol (By similarity). Endosome (By similarity)				199
P30594 UniProt NPD GO	CHS1_RHIOL	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1)	0.28	-	end	7	Cell membrane; multi-pass membrane protein				858
Q33BZ9 UniProt NPD GO	RR11_NICTO	Chloroplast 30S ribosomal protein S11	0.28	-	mit	0	Plastid; chloroplast				138
P06587 UniProt NPD GO	RR11_PEA	Chloroplast 30S ribosomal protein S11	0.28	-	mit	0	Plastid; chloroplast				138
Q8MA18 UniProt NPD GO	RR12_CHAGL	Chloroplast 30S ribosomal protein S12	0.28	-	nuc	0	Plastid; chloroplast				123
P48856 UniProt NPD GO	RR12_HORVU	Chloroplast 30S ribosomal protein S12	0.28	-	mit	0	Plastid; chloroplast				124
P24066 UniProt NPD GO	RR12_WHEAT	Chloroplast 30S ribosomal protein S12	0.28	-	mit	0	Plastid; chloroplast				122
Q9TLY9 UniProt NPD GO	RR16_CYACA	Chloroplast 30S ribosomal protein S16	0.28	-	nuc	0	Plastid; chloroplast				75
P28521 UniProt NPD GO	RR16_GALSU	Chloroplast 30S ribosomal protein S16	0.28	-	nuc	0	Plastid; chloroplast				77
P10359 UniProt NPD GO	RR16_SINAL	Chloroplast 30S ribosomal protein S16	0.28	-	nuc	0	Plastid; chloroplast				88
P56798 UniProt NPD GO	RR3_ARATH	Chloroplast 30S ribosomal protein S3	0.28	-	mit	0	Plastid; chloroplast				218
Q49KW0 UniProt NPD GO	RR3_EUCGG	Chloroplast 30S ribosomal protein S3	0.28	-	mit	0	Plastid; chloroplast				216
Q2MI62 UniProt NPD GO	RR3_LYCES	Chloroplast 30S ribosomal protein S3	0.28	-	cyt	0	Plastid; chloroplast				218
O62951 UniProt NPD GO	RR3_PICAB	Chloroplast 30S ribosomal protein S3	0.28	-	mit	0	Plastid; chloroplast				218
Q3BAJ9 UniProt NPD GO	RK16_PHAAO	Chloroplast 50S ribosomal protein L16	0.28	-	mit	0	Plastid; chloroplast				135
O46897 UniProt NPD GO	RK2_GUITH	Chloroplast 50S ribosomal protein L2	0.28	-	nuc	0	Plastid; chloroplast				275
O78429 UniProt NPD GO	RK21_GUITH	Chloroplast 50S ribosomal protein L21	0.28	+	nuc	0	Plastid; chloroplast				104
Q6YXM3 UniProt NPD GO	RK33_PHYPA	Chloroplast 50S ribosomal protein L33	0.28	-	nuc	0	Plastid; chloroplast				66
P80345 UniProt NPD GO	CCKN_TRASC	Cholecystokinins precursor (CCK) [Contains: Cholecystokinin 58 (CCK58); Cholecystokinin 40 (CCK40); ...	0.28	-	exc	0	Secreted protein				130
Q42884 UniProt NPD GO	AROC1_LYCES	Chorismate synthase 1, chloroplast precursor (EC 4.2.3.5) (5-enolpyruvylshikimate-3-phosphate phosph ...	0.28	-	nuc	0	Plastid; chloroplast				440
P13712 UniProt NPD GO	MSI1_YEAST	Chromatin assembly factor 1 subunit p50 (CAF-1 p50 subunit) (Protein MSI1) (IRA1 multicopy suppresso ...	0.28	-	nuc	0	Cytoplasm. Nucleus	chromatin assembly complex [IDA] chromatin silencing complex [IMP]			422

You are viewing entries 42101 to 42150 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.