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
Q9USZ1 UniProt NPD GO	EFG1_SCHPO	Elongation factor G 1, mitochondrial precursor (mEF-G-1)	0.43	-	nuc	0					770
P38874 UniProt NPD GO	IKI1_YEAST	Elongator complex protein 5 (Gamma-toxin target 5) (Protein IKI1) (HAT-associated protein 2)	0.43	-	nuc	0	Cytoplasm. Nucleus	DNA-directed RNA polymerase II, holoenzyme [TAS] transcription elongation factor complex [IDA]			309
O35980 UniProt NPD GO	NTHL1_MOUSE	Endonuclease III-like protein 1 (EC 4.2.99.18)	0.43	-	mit	0	Mitochondrion	mitochondrion [IDA] nucleus [IDA]			300
P12294 UniProt NPD GO	ENS2_YEAST	Endonuclease SceI small subunit (EC 3.1.21.-) (Endo.SceI 50 kDa subunit) (Maturase-like RF3 protein) ...	0.43	-	nuc	0					559
Q9JMI0 UniProt NPD GO	ECEL1_MOUSE	Endothelin-converting enzyme-like 1 (EC 3.4.24.-) (Xce protein) (Damage-induced neuronal endopeptida ...	0.43	-	cyt	1	Membrane; single-pass type II membrane protein (By similarity)				775
P13098 UniProt NPD GO	ESM8_DROME	Enhancer of split m8 protein (E(spl)m8)	0.43	-	nuc	0	Nucleus (Probable)				179
Q15768 UniProt NPD GO	EFNB3_HUMAN	Ephrin-B3 precursor (EPH-related receptor tyrosine kinase ligand 8) (LERK-8) (EPH-related receptor t ...	0.43	-	end	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	602297		340
P08641 UniProt NPD GO	CADH1_CHICK	Epithelial-cadherin precursor (E-cadherin) (Cadherin-1) (Liver cell adhesion molecule) (L-CAM)	0.43	-	end	1	Membrane; single-pass type I membrane protein				887
Q9Z2R9 UniProt NPD GO	E2AK1_MOUSE	Eukaryotic translation initiation factor 2-alpha kinase 1 (EC 2.7.11.1) (Heme-regulated eukaryotic i ...	0.43	-	cyt	0		cytoplasm [IDA]			619
Q56JZ5 UniProt NPD GO	IF33_BOVIN	Eukaryotic translation initiation factor 3 subunit 3 (eIF-3 gamma)	0.43	-	nuc	0					352
Q9Y262 UniProt NPD GO	IF3I_HUMAN	Eukaryotic translation initiation factor 3 subunit 6-interacting protein	0.43	-	cyt	0					564
Q62622 UniProt NPD GO	4EBP1_RAT	Eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) (eIF4E-binding protein 1) (Ph ...	0.43	-	nuc	0					116
Q8RVQ5 UniProt NPD GO	EXOC5_ARATH	Exocyst complex component 5 (Exocyst complex component Sec10)	0.43	-	mit	0					829
Q6CC70 UniProt NPD GO	EXO70_YARLI	Exocyst complex protein EXO70	0.43	-	cyt	0	Bud (By similarity). Bud neck (By similarity)				603
P53256 UniProt NPD GO	RRP46_YEAST	Exosome complex exonuclease RRP46 (EC 3.1.13.-) (Ribosomal RNA-processing protein 46)	0.43	-	nuc	0	Cytoplasm. Nucleus; nucleolus	cytoplasmic exosome (RNase complex) [IDA] nuclear exosome (RNase complex) [IDA]			256
Q61508 UniProt NPD GO	ECM1_MOUSE	Extracellular matrix protein 1 precursor (Secretory component p85)	0.43	-	exc	0	Secreted protein; extracellular space	extracellular space [IDA]			559
Q9UKB1 UniProt NPD GO	FBW1B_HUMAN	F-box/WD repeat protein 11 (F-box/WD repeat protein 1B) (F-box and WD repeats protein beta-TrCP2)	0.43	-	mit	0	Cytoplasm (Potential)	ubiquitin ligase complex [NAS]	605651		542
Q6CMY2 UniProt NPD GO	YFAS1_KLULA	FAS1 domain-containing protein KLLA0E16841g precursor	0.43	-	mit	0	Vacuole (By similarity)				266
P0C091 UniProt NPD GO	FREM3_HUMAN	FRAS1-related extracellular matrix protein 3 precursor	0.43	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		608946		2135
Q14296 UniProt NPD GO	FASTK_HUMAN	Fas-activated serine/threonine kinase (EC 2.7.11.8) (FAST kinase)	0.43	-	mit	0			606965		549
P14480 UniProt NPD GO	FIBB_RAT	Fibrinogen beta chain precursor [Contains: Fibrinopeptide B]	0.43	-	exc	0	Secreted protein				479
P15656 UniProt NPD GO	FGF5_MOUSE	Fibroblast growth factor 5 precursor (FGF-5) (HBGF-5)	0.43	-	exc	0					264
Q802A9 UniProt NPD GO	FGFP2_CHICK	Fibroblast growth factor-binding protein 2 precursor (FGF-binding protein 2) (FGF-BP2) (FGFBP-2)	0.43	-	nuc	0	Secreted protein; extracellular space (By similarity)				208
Q61086 UniProt NPD GO	FZD3_MOUSE	Frizzled-3 precursor (Fz-3) (mFz3)	0.43	-	end	8 *	Membrane; multi-pass membrane protein	apical part of cell [IDA]			666
P09958 UniProt NPD GO	FURIN_HUMAN	Furin precursor (EC 3.4.21.75) (Paired basic amino acid residue cleaving enzyme) (PACE) (Dibasic-pro ...	0.43	-	end	1 *	Golgi apparatus; trans-Golgi network. Seems to be localized intracellularly to the trans Golgi netwo ...	Golgi apparatus [TAS] trans-Golgi network transport vesicle [IDA]	136950		794
P30183 UniProt NPD GO	CCNBL_ARATH	G2/mitotic-specific cyclin (B-like cyclin)	0.43	-	cyt	0					428
Q9W589 UniProt NPD GO	OFUT2_DROME	GDP-fucose protein O-fucosyltransferase 2 precursor (EC 2.4.1.221) (Peptide-O-fucosyltransferase) (O ...	0.43	+	exc	0	Endoplasmic reticulum	endoplasmic reticulum [IDA]			490
P33153 UniProt NPD GO	CRL1_CANAL	GTP-binding RHO-like protein	0.43	+	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				346
P10065 UniProt NPD GO	CRGA_RAT	Gamma crystallin A (Gamma crystallin 1-1)	0.43	-	nuc	0					173
Q96MZ0 UniProt NPD GO	GD1L1_HUMAN	Ganglioside-induced differentiation-associated protein 1-like 1 (GDAP1-L1)	0.43	-	nuc	1					367
Q96QA5 UniProt NPD GO	GSDM1_HUMAN	Gasdermin	0.43	-	cyt	0					445
P18725 UniProt NPD GO	ZG5_XENLA	Gastrula zinc finger protein 5-1 (XLCGF5.1)	0.43	-	nuc	0					445
P18717 UniProt NPD GO	ZG29_XENLA	Gastrula zinc finger protein XLCGF29.1 (Fragment)	0.43	-	nuc	0	Nucleus (Potential)				139
Q5EA80 UniProt NPD GO	PGTA_BOVIN	Geranylgeranyl transferase type-2 alpha subunit (EC 2.5.1.60) (Geranylgeranyl transferase type II al ...	0.43	-	nuc	0					567
Q5NVK5 UniProt NPD GO	PGTA_PONPY	Geranylgeranyl transferase type-2 alpha subunit (EC 2.5.1.60) (Geranylgeranyl transferase type II al ...	0.43	-	nuc	0					567
P41585 UniProt NPD GO	PACA_ONCNE	Glucagon family neuropeptides precursor [Contains: Growth hormone-releasing factor (GRF) (Growth hor ...	0.43	-	nuc	0	Secreted protein				173
P55095 UniProt NPD GO	GLUC_MOUSE	Glucagon precursor [Contains: Glicentin; Glicentin-related polypeptide (GRPP); Oxyntomodulin (OXY) ( ...	0.43	-	exc	0	Secreted protein				180
Q9JL60 UniProt NPD GO	GMEB1_MOUSE	Glucocorticoid modulatory element-binding protein 1 (GMEB-1)	0.43	-	cyt	0	Nucleus. Cytoplasm. May be also cytoplasmic	nucleus [IDA]			562
Q43727 UniProt NPD GO	G6PD1_ARATH	Glucose-6-phosphate 1-dehydrogenase 1, chloroplast precursor (EC 1.1.1.49) (G6PD1) (G6PDH1)	0.43	-	mit	0	Plastid; chloroplast				576
P48507 UniProt NPD GO	GSH0_HUMAN	Glutamate--cysteine ligase regulatory subunit (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) (Gamm ...	0.43	-	nuc	0			601176		274
P13188 UniProt NPD GO	SYQ_YEAST	Glutaminyl-tRNA synthetase (EC 6.1.1.18) (Glutamine--tRNA ligase) (GlnRS)	0.43	-	cyt	0		cytoplasm [IC]			809
Q02897 UniProt NPD GO	GLUB2_ORYSA	Glutelin type-B 2 precursor (Glutelin type-B 7) [Contains: Glutelin type-B 2 acidic chain; Glutelin ...	0.43	-	mit	0					495
P10388 UniProt NPD GO	GLT5_WHEAT	Glutenin, high molecular weight subunit DX5 precursor	0.43	-	exc	1 *					839
Q00766 UniProt NPD GO	PHS1_DICDI	Glycogen phosphorylase 1 (EC 2.4.1.1) (GP1)	0.43	-	nuc	0					853
O35165 UniProt NPD GO	GOSR2_RAT	Golgi SNAP receptor complex member 2 (27 kDa Golgi SNARE protein) (Membrin)	0.43	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (Potential)				212
Q5FWH3 UniProt NPD GO	GRHL3_MOUSE	Grainyhead-like protein 3 homolog (Transcription factor CP2-like 4)	0.43	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			603
Q8UWE0 UniProt NPD GO	GDF8_ANAPL	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.43	+	cyt	0	Secreted protein (By similarity)				375
O42220 UniProt NPD GO	GDF8_CHICK	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.43	+	cyt	0	Secreted protein (By similarity)				375
O42221 UniProt NPD GO	GDF8_MELGA	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.43	+	cyt	0	Secreted protein (By similarity)				375
Q8CGK7 UniProt NPD GO	GNAL_MOUSE	Guanine nucleotide-binding protein G(olf) subunit alpha (Adenylate cyclase-stimulating G alpha prote ...	0.43	-	nuc	0					381

You are viewing entries 29601 to 29650 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.