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
P58131 UniProt NPD GO	RPOC1_ASTLO	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.57	-	nuc	0	Plastid				575
Q49L07 UniProt NPD GO	RPOC1_EUCGG	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.57	-	cyt	0	Plastid; chloroplast				682
P60288 UniProt NPD GO	RPOC1_PHYPA	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.57	-	cyt	0	Plastid; chloroplast				679
Q9CZT4 UniProt NPD GO	RPC5_MOUSE	DNA-directed RNA polymerases III 80 kDa polypeptide (EC 2.7.7.6) (RNA polymerase III subunit 5) (RPC ...	0.57	-	nuc	0	Nucleus (By similarity)				710
O55188 UniProt NPD GO	DMP1_MOUSE	Dentin matrix acidic phosphoprotein 1 precursor (Dentin matrix protein 1) (DMP-1) (AG1)	0.57	-	exc	0					503
Q62936 UniProt NPD GO	DLG3_RAT	Discs large homolog 3 (Synapse-associated protein 102) (SAP102) (PSD-95/SAP90-related protein 1)	0.57	-	nuc	0		cell soma [IDA] dendritic shaft [IDA] growth cone [IDA] postsynaptic density [IDA] synapse [IDA]			849
Q6R005 UniProt NPD GO	DLG4_BRARE	Discs large homolog 4 (Postsynaptic density protein 95) (PSD-95)	0.57	-	cyt	0	Cell membrane; peripheral membrane protein. High levels in postsynaptic density of neuronal cells	synapse [IDA]			801
Q9D832 UniProt NPD GO	DNJB4_MOUSE	DnaJ homolog subfamily B member 4	0.57	-	nuc	0					337
Q99704 UniProt NPD GO	DOK1_HUMAN	Docking protein 1 (Downstream of tyrosine kinase 1) (p62(dok)) (pp62)	0.57	-	nuc	0			602919		481
Q9D6N5 UniProt NPD GO	DRAP1_MOUSE	Dr1-associated corepressor (Dr1-associated protein 1) (Negative co-factor 2 alpha) (NC2 alpha)	0.57	-	nuc	0		nucleus [IDA]			204
Q4U116 UniProt NPD GO	S4A4_PIG	Electrogenic sodium bicarbonate cotransporter 1 (Sodium bicarbonate cotransporter) (Na(+)/HCO3(-) co ...	0.57	+	end	9	Cell membrane; basolateral cell membrane; multi-pass membrane protein (By similarity)				1079
Q9JI66 UniProt NPD GO	S4A4_RAT	Electrogenic sodium bicarbonate cotransporter 1 (Sodium bicarbonate cotransporter) (Na(+)/HCO3(-) co ...	0.57	+	end	9	Cell membrane; basolateral cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			1079
P58107 UniProt NPD GO	EPIPL_HUMAN	Epiplakin (450 kDa epidermal antigen)	0.57	-	nuc	0		cytoskeleton [NAS]	607553		5065
P49885 UniProt NPD GO	ESR1_SHEEP	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha) (Fragment)	0.57	+	nuc	0	Nucleus				111
Q9LW48 UniProt NPD GO	ERF5_NICSY	Ethylene-responsive transcription factor 5 (Ethylene-responsive element-binding factor 5 homolog) (E ...	0.57	-	nuc	0	Nucleus (Probable)				282
Q41969 UniProt NPD GO	IF2B_ARATH	Eukaryotic translation initiation factor 2 subunit beta (eIF-2-beta)	0.57	+	nuc	0					268
O60573 UniProt NPD GO	IF4E3_HUMAN	Eukaryotic translation initiation factor 4E type 3 (eIF4E type 3) (eIF-4E type 3) (mRNA cap-binding ...	0.57	-	nuc	0			605895		245
Q924Z6 UniProt NPD GO	XPO6_MOUSE	Exportin-6 (Exp6) (Ran-binding protein 20)	0.57	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Shuttles between the nucleus and the cytoplasm ( ...				1125
Q39601 UniProt NPD GO	SSRP1_CATRO	FACT complex subunit SSRP1 (Facilitates chromatin transcription complex subunit SSRP1) (Recombinatio ...	0.57	+	nuc	0	Nucleus (By similarity)				639
Q9LEF5 UniProt NPD GO	SSRP1_MAIZE	FACT complex subunit SSRP1 (Facilitates chromatin transcription complex subunit SSRP1) (Recombinatio ...	0.57	+	cyt	0	Nucleus				639
Q9ESQ8 UniProt NPD GO	RFRP_MOUSE	FMRFamide-related peptides precursor [Contains: Neuropeptide NPSF (Neuropeptide RFRP-1); Neuropeptid ...	0.57	-	nuc	0	Secreted protein				188
Q96DB9 UniProt NPD GO	FXYD5_HUMAN	FXYD domain-containing ion transport regulator 5 precursor (Dysadherin)	0.57	-	exc	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [IDA]	606669		178
P02675 UniProt NPD GO	FIBB_HUMAN	Fibrinogen beta chain precursor [Contains: Fibrinopeptide B]	0.57	-	mit	0	Secreted protein	extracellular region [NAS] fibrinogen complex [TAS] soluble fraction [TAS]	134830	1RF1	491
Q90722 UniProt NPD GO	FGF8_CHICK	Fibroblast growth factor 8 precursor (FGF-8) (HBGF-8)	0.57	-	nuc	0	Secreted protein				214
Q91740 UniProt NPD GO	FINC_XENLA	Fibronectin precursor (FN)	0.57	-	mit	0					2481
O04064 UniProt NPD GO	FLLH_POPTR	Floricaula/leafy homolog (PTLF)	0.57	-	cyt	0	Nucleus (Probable)				377
Q61850 UniProt NPD GO	FOXC2_MOUSE	Forkhead box protein C2 (Forkhead-related protein FKHL14) (Mesenchyme fork head protein 1) (MFH-1 pr ...	0.57	+	nuc	0	Nucleus (Probable)				494
Q63250 UniProt NPD GO	FOXE3_RAT	Forkhead box protein E3 (Forkhead-related protein FKHL12) (Forkhead-related transcription factor 8) ...	0.57	-	mit	0	Nucleus				101
Q5JY77 UniProt NPD GO	GASP1_HUMAN	G-protein coupled receptor-associated sorting protein 1 (GASP-1)	0.57	-	nuc	0	Cytoplasm		300417		1395
P49707 UniProt NPD GO	CCNE1_CHICK	G1/S-specific cyclin-E1	0.57	-	nuc	0	Nucleus (By similarity)				407
P51986 UniProt NPD GO	CCNA_CHLVR	G2/mitotic-specific cyclin-A (Fragment)	0.57	-	nuc	0					420
O75628 UniProt NPD GO	REM1_HUMAN	GTP-binding protein REM 1 (Rad and Gem-like GTP-binding protein 1) (GTPase-regulating endothelial ce ...	0.57	-	nuc	0					298
Q5BJQ5 UniProt NPD GO	RIT2_RAT	GTP-binding protein Rit2	0.57	+	cyt	0	Cell membrane (By similarity)				217
P48365 UniProt NPD GO	GYP7_YEAST	GTPase-activating protein GYP7 (GAP for YPT7)	0.57	-	mit	0		cytoplasm [IDA]			746
Q96A11 UniProt NPD GO	G3ST3_HUMAN	Galactose-3-O-sulfotransferase 3 (EC 2.8.2.-) (Gal3ST-3) (Galbeta1-3GalNAc 3'-sulfotransferase 3) (B ...	0.57	-	nuc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)	integral to membrane [NAS]	608234		431
Q921G8 UniProt NPD GO	GCP2_MOUSE	Gamma-tubulin complex component 2 (GCP-2)	0.57	-	cyt	0	Centrosome (By similarity)				905
P16242 UniProt NPD GO	ANTA_HAEGH	Ghilanten	0.57	-	nuc	0	Secreted protein				119
Q6CT96 UniProt NPD GO	GNT1B_KLULA	Glucose N-acetyltransferase 1-B (EC 2.4.1.-) (N-acetylglucosaminyltransferase B)	0.57	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity). Vacuole; vacu ...				453
Q09768 UniProt NPD GO	GSH1_SCHPO	Glutamate--cysteine ligase (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) (Gamma-ECS) (GCS)	0.57	-	cyt	0					669
Q91XP5 UniProt NPD GO	GLRA3_MOUSE	Glycine receptor alpha-3 chain precursor	0.57	-	end	4	Membrane; multi-pass membrane protein	glycine-gated chloride channel complex [ISS]			464
Q5XPT3 UniProt NPD GO	LARG2_MOUSE	Glycosyltransferase-like protein LARGE2 (EC 2.4.-.-) (Glycosyltransferase-like 1B)	0.57	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				690
P40009 UniProt NPD GO	YND1_YEAST	Golgi apyrase (EC 3.6.1.5) (ATP-diphosphatase) (Adenosine diphosphatase) (ADPase) (ATP-diphosphohydr ...	0.57	+	nuc	1	Golgi apparatus; Golgi membrane	Golgi apparatus [IDA]			630
P21279 UniProt NPD GO	GNAQ_MOUSE	Guanine nucleotide-binding protein G(q) subunit alpha (Guanine nucleotide-binding protein alpha-q)	0.57	-	cyt	0		heterotrimeric G-protein complex [TAS]		2BCJ	353
P82471 UniProt NPD GO	GNAQ_RAT	Guanine nucleotide-binding protein G(q) subunit alpha (Guanine nucleotide-binding protein alpha-q)	0.57	-	cyt	0		heterotrimeric G-protein complex [TAS]			353
P38409 UniProt NPD GO	GNA11_BOVIN	Guanine nucleotide-binding protein alpha-11 subunit (GL2)	0.57	-	cyt	0					359
P34042 UniProt NPD GO	GPA4_DICDI	Guanine nucleotide-binding protein alpha-4 subunit (G alpha-4) (Fragment)	0.57	-	mit	0					345
O14435 UniProt NPD GO	GBB_CRYPA	Guanine nucleotide-binding protein subunit beta	0.57	-	cyt	0					359
P33322 UniProt NPD GO	CBF5_YEAST	H/ACA ribonucleoprotein complex subunit 4 (EC 5.4.99.-) (Centromere/microtubule-binding protein CBF5 ...	0.57	+	nuc	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [IPI]			483
P61296 UniProt NPD GO	HAND2_HUMAN	Heart- and neural crest derivatives-expressed protein 2 (Deciduum, heart, autonomic nervous system a ...	0.57	+	nuc	0			602407		217
P61295 UniProt NPD GO	HAND2_RAT	Heart- and neural crest derivatives-expressed protein 2 (Deciduum, heart, autonomic nervous system a ...	0.57	+	nuc	0					217

You are viewing entries 20701 to 20750 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.