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
Q84TE9 UniProt NPD GO	DOF53_ARATH	Dof zinc finger protein DOF5.3 (AtDOF5.3)	0.51	-	nuc	0	Nucleus (Probable)				257
P57690 UniProt NPD GO	DMRT1_TRASC	Doublesex- and mab-3-related transcription factor 1 (Fragment)	0.51	-	nuc	0	Nucleus (Potential)				205
Q4QR87 UniProt NPD GO	DMRTC_RAT	Doublesex- and mab-3-related transcription factor C1	0.51	-	nuc	0					225
P31938 UniProt NPD GO	MP2K1_MOUSE	Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) (MAP kinase kinase 1) (MAPK ...	0.51	-	nuc	0					392
Q9XT09 UniProt NPD GO	MP2K1_PANTR	Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) (MAP kinase kinase 1) (MAPK ...	0.51	-	cyt	0					392
Q13115 UniProt NPD GO	DUS4_HUMAN	Dual specificity protein phosphatase 4 (EC 3.1.3.48) (EC 3.1.3.16) (Mitogen-activated protein kinase ...	0.51	-	nuc	0	Nucleus	nucleus [TAS]	602747		394
P38148 UniProt NPD GO	PPS1_YEAST	Dual specificity protein phosphatase PPS1 (EC 3.1.3.48) (EC 3.1.3.16)	0.51	-	nuc	0					807
Q39610 UniProt NPD GO	DYHA_CHLRE	Dynein alpha chain, flagellar outer arm (DHC alpha)	0.51	-	nuc	0	Flagellum				4499
P38632 UniProt NPD GO	MMS21_YEAST	E3 SUMO--protein ligase MMS21 (EC 6.-.-.-) (DNA repair protein MMS21)	0.51	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nuclear envelope [IDA] nucleus [IDA] Smc5-Smc6 complex [IPI]			267
Q9BUP0 UniProt NPD GO	EFHD1_HUMAN	EF-hand domain-containing protein 1 (Swiprosin-2)	0.51	-	nuc	0					239
Q9BY15 UniProt NPD GO	EMR3_HUMAN	EGF-like module-containing mucin-like hormone receptor-like 3 precursor (EGF-like module-containing ...	0.51	-	end	7	Cell membrane; multi-pass membrane protein. Subunit alpha: Secreted protein; extracellular space. A ...	integral to membrane [TAS]	606101		652
P06802 UniProt NPD GO	ENPP1_MOUSE	Ectonucleotide pyrophosphatase/phosphodiesterase 1 (E-NPP 1) (Phosphodiesterase I/nucleotide pyropho ...	0.51	-	nuc	1	Membrane; single-pass type II membrane protein				906
Q924C3 UniProt NPD GO	ENPP1_RAT	Ectonucleotide pyrophosphatase/phosphodiesterase 1 (E-NPP 1) (Phosphodiesterase I/nucleotide pyropho ...	0.51	-	nuc	1	Membrane; single-pass type II membrane protein				906
O13134 UniProt NPD GO	S4A4_AMBTI	Electrogenic sodium bicarbonate cotransporter 1 (Sodium bicarbonate cotransporter) (Na(+)/HCO3(-) co ...	0.51	+	end	9	Cell membrane; basolateral cell membrane; multi-pass membrane protein				1035
P14401 UniProt NPD GO	ENP2_TORCA	Electromotor neuron-associated protein 2 (Fragment)	0.51	-	nuc	0	Membrane; peripheral membrane protein. Associated with membranes of intracellular organelles				350
O08796 UniProt NPD GO	EF2K_MOUSE	Elongation factor 2 kinase (EC 2.7.11.20) (eEF-2 kinase) (eEF-2K) (Calcium/calmodulin-dependent euka ...	0.51	-	nuc	0					724
P25997 UniProt NPD GO	EF3_CANAL	Elongation factor 3 (EF-3)	0.51	+	nuc	0	Cytoplasm				1049
Q9HCU0 UniProt NPD GO	CD248_HUMAN	Endosialin precursor (Tumor endothelial marker 1) (CD248 antigen)	0.51	-	exc	1	Membrane; single-pass type I membrane protein (Probable)	extracellular matrix (sensu Metazoa) [TAS]	606064		757
Q01069 UniProt NPD GO	ESMB_DROME	Enhancer of split mbeta protein (E(spl)mbeta) (HLH-mbeta) (Split locus enhancer protein mA)	0.51	-	nuc	0	Nucleus (Probable)				195
O94142 UniProt NPD GO	KO1_GIBFU	Ent-kaurene oxidase (EC 1.14.13.78) (Cytochrome P450-4) (Cytochrome P450 503A1)	0.51	-	cyt	1 *					525
Q91571 UniProt NPD GO	EPB1A_XENLA	Ephrin type-B receptor 1-A precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor XEK)	0.51	-	end	0	Membrane; single-pass type I membrane protein				985
Q84XB3 UniProt NPD GO	ERF1_LYCES	Ethylene-responsive transcription factor 1 (Ethylene-responsive element-binding factor 1) (EREBP-1) ...	0.51	-	nuc	0	Nucleus (Probable)				244
Q9UL18 UniProt NPD GO	I2C1_HUMAN	Eukaryotic translation initiation factor 2C 1 (eIF2C 1) (eIF-2C 1) (Argonaute-1) (Putative RNA-bindi ...	0.51	-	cyt	0		eukaryotic translation initiation factor 2 ... [TAS]	606228	1SI3	857
Q26891 UniProt NPD GO	IF5_TRICA	Eukaryotic translation initiation factor 5 (eIF-5) (Fragment)	0.51	-	nuc	0					162
Q5U247 UniProt NPD GO	EXOC8_XENLA	Exocyst complex component 8	0.51	-	nuc	0	Cytoplasm (By similarity)				685
Q5AH25 UniProt NPD GO	EXO70_CANAL	Exocyst complex protein EXO70	0.51	-	nuc	0	Bud (By similarity). Bud neck (By similarity)				667
Q06265 UniProt NPD GO	EXOS9_HUMAN	Exosome complex exonuclease RRP45 (EC 3.1.13.-) (Exosome component 9) (Polymyositis/scleroderma auto ...	0.51	+	nuc	0	Cytoplasm. Nucleus; nucleolus	nuclear exosome (RNase complex) [NAS] nucleolus [TAS] nucleus [TAS]	606180		423
P97767 UniProt NPD GO	EYA1_MOUSE	Eyes absent homolog 1 (EC 3.1.3.48)	0.51	-	nuc	0	Cytoplasm. Nucleus				591
Q8N4B4 UniProt NPD GO	FBX39_HUMAN	F-box only protein 39	0.51	-	cyt	0			609106		442
Q9UKT5 UniProt NPD GO	FBX4_HUMAN	F-box only protein 4	0.51	-	cyt	0		ubiquitin ligase complex [NAS]	609090		387
Q5MNV8 UniProt NPD GO	FBX47_HUMAN	F-box only protein 47	0.51	-	mit	0			609498		452
Q9UK97 UniProt NPD GO	FBX9_HUMAN	F-box only protein 9 (NY-REN-57 antigen) (Cross-immune reaction antigen 1)	0.51	-	cyt	0		ubiquitin ligase complex [NAS]	609091		447
Q9QZN1 UniProt NPD GO	FXL17_MOUSE	F-box/LRR-repeat protein 17 (F-box and leucine-rich repeat protein 17) (F-box only protein 13) (Frag ...	0.51	-	nuc	0					462
Q5XJY6 UniProt NPD GO	FANCB_MOUSE	Fanconi anemia group B protein homolog (Protein FACB)	0.51	-	mit	0	Nucleus (By similarity)				703
O76093 UniProt NPD GO	FGF18_HUMAN	Fibroblast growth factor 18 precursor (FGF-18) (zFGF5)	0.51	-	exc	0	Secreted protein (By similarity)	extracellular space [TAS]	603726		207
O89101 UniProt NPD GO	FGF18_MOUSE	Fibroblast growth factor 18 precursor (FGF-18) (zFGF5)	0.51	-	exc	0	Secreted protein (By similarity)				207
O55145 UniProt NPD GO	X3CL1_RAT	Fractalkine precursor (CX3CL1) (Neurotactin) (CX3C membrane-anchored chemokine) (Small inducible cyt ...	0.51	-	mit	2 *	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				393
Q92917 UniProt NPD GO	GPKOW_HUMAN	G patch domain and KOW motifs-containing protein (Protein T54)	0.51	-	nuc	0					378
Q3UNH4 UniProt NPD GO	GRIN1_MOUSE	G protein-regulated inducer of neurite outgrowth 1 (GRIN1)	0.51	-	nuc	0	Cell membrane; lipid-anchor. Highly enriched in growth cone	plasma membrane [IDA]			932
Q6MG88 UniProt NPD GO	GPSM3_RAT	G-protein signaling modulator 3	0.51	-	nuc	0	Cytoplasm (By similarity)				158
P20439 UniProt NPD GO	CCNB_DROME	G2/mitotic-specific cyclin-B	0.51	-	nuc	0		chromosome, pericentric region [TAS] pole plasm [TAS] spindle [TAS]			530
Q9EPI2 UniProt NPD GO	GFRA4_RAT	GDNF family receptor alpha-4 precursor (GFR-alpha-4) (Persephin receptor)	0.51	-	cyt	0	Isoform A: Cell membrane; lipid-anchor; GPI-anchor. Isoform B: Secreted protein (Potential)	extracellular region [IMP]			273
Q9NSN8 UniProt NPD GO	SNTG1_HUMAN	Gamma-1-syntrophin (G1SYN) (Syntrophin 4) (SYN4)	0.51	-	cyt	0	Cytoplasm. Nucleus. Mainly cytoplasmic and weakly nuclear	syntrophin complex [TAS]	608714		517
Q9D6F4 UniProt NPD GO	GBRA4_MOUSE	Gamma-aminobutyric-acid receptor alpha-4 subunit precursor (GABA(A) receptor)	0.51	-	exc	4 *	Membrane; multi-pass membrane protein				552
Q96RT8 UniProt NPD GO	GCP5_HUMAN	Gamma-tubulin complex component 5 (GCP-5)	0.51	-	nuc	0	Centrosome	gamma-tubulin ring complex [IDA]	608147		1024
P18713 UniProt NPD GO	ZG17_XENLA	Gastrula zinc finger protein XLCGF17.1 (Fragment)	0.51	-	nuc	0	Nucleus (Potential)				197
Q00618 UniProt NPD GO	BET4_YEAST	Geranylgeranyl transferase type-2 alpha subunit (EC 2.5.1.60) (Geranylgeranyl transferase type II al ...	0.51	-	nuc	0		Rab-protein geranylgeranyltransferase complex [IDA]			327
P39905 UniProt NPD GO	GDNF_HUMAN	Glial cell line-derived neurotrophic factor precursor (Astrocyte-derived trophic factor 1) (ATF-1)	0.51	-	nuc	0	Secreted protein		600837		211
Q4I061 UniProt NPD GO	NMT_GIBZE	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.51	+	cyt	0	Cytoplasm (By similarity)				564
Q9Z0J7 UniProt NPD GO	GDF15_MOUSE	Growth/differentiation factor 15 precursor (GDF-15)	0.51	-	nuc	0	Secreted protein (Probable)				303

You are viewing entries 24301 to 24350 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.