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
P47160 UniProt NPD GO	ENT3_YEAST	Epsin-3	0.58	-	nuc	0	Cytoplasm. Associates with the trans Golgi network (TGN) and endosomal clathrin coats	actin cortical patch [IPI] clathrin vesicle coat [IDA]			408
Q9NZJ5 UniProt NPD GO	E2AK3_HUMAN	Eukaryotic translation initiation factor 2-alpha kinase 3 precursor (EC 2.7.11.1) (PRKR-like endopla ...	0.58	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein		604032		1115
Q6QME8 UniProt NPD GO	I2C2_BOVIN	Eukaryotic translation initiation factor 2C 2 (eIF2C 2) (eIF-2C 2) (Argonaute-2)	0.58	-	cyt	0	Cytoplasm; cytoplasmic bodies (By similarity)				860
Q9QZ81 UniProt NPD GO	I2C2_RAT	Eukaryotic translation initiation factor 2C 2 (eIF2C 2) (eIF-2C 2) (Argonaute-2) (Golgi ER protein 9 ...	0.58	-	nuc	0	Cytoplasm; cytoplasmic bodies (By similarity)				860
Q8CJG0 UniProt NPD GO	I2C2_MOUSE	Eukaryotic translation initiation factor 2C 2 (eIF2C 2) (eIF-2C 2) (Argonaute-2) (Slicer protein) (P ...	0.58	-	nuc	0	Cytoplasm; cytoplasmic bodies (By similarity)				860
Q03690 UniProt NPD GO	IF3X_YEAST	Eukaryotic translation initiation factor 3 135 kDa subunit (eIF3 p135) (Translation initiation facto ...	0.58	-	nuc	0		cytoplasm [IDA] eukaryotic translation initiation factor 3 ... [IPI]			1277
Q9Z191 UniProt NPD GO	EYA4_MOUSE	Eyes absent homolog 4 (EC 3.1.3.48)	0.58	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				616
Q8CDU4 UniProt NPD GO	FXL13_MOUSE	F-box/LRR-repeat protein 13 (F-box and leucine-rich repeat protein 13)	0.58	-	nuc	0					790
Q6P050 UniProt NPD GO	FXL22_HUMAN	F-box/LRR-repeat protein 22 (F-box and leucine-rich repeat protein 22)	0.58	-	nuc	0			609088		241
Q8N878 UniProt NPD GO	FRMD1_HUMAN	FERM domain-containing protein 1	0.58	-	nuc	0					549
P46671 UniProt NPD GO	FAR3_YEAST	Factor arrest protein 3	0.58	-	nuc	0	Endoplasmic reticulum	endoplasmic reticulum [IDA]			204
Q8K0E8 UniProt NPD GO	FIBB_MOUSE	Fibrinogen beta chain precursor [Contains: Fibrinopeptide B]	0.58	-	exc	0	Secreted protein				481
Q8CIG3 UniProt NPD GO	AOF1_MOUSE	Flavin-containing amine oxidase domain-containing protein 1 (EC 1.-.-.-)	0.58	-	cyt	0					826
Q64733 UniProt NPD GO	FOXB2_MOUSE	Forkhead box protein B2 (Transcription factor FKH-4)	0.58	+	nuc	0	Nucleus				428
Q99958 UniProt NPD GO	FOXC2_HUMAN	Forkhead box protein C2 (Forkhead-related protein FKHL14) (Mesenchyme fork head protein 1) (MFH-1 pr ...	0.58	+	nuc	0	Nucleus (Probable)		153000	1D5V	501
Q6VFT5 UniProt NPD GO	FOXL2_RABIT	Forkhead box protein L2	0.58	-	nuc	0	Nucleus (Potential)				384
O70523 UniProt NPD GO	FXR1_CRIGR	Fragile X mental retardation syndrome-related protein 1	0.58	-	nuc	0	Cytoplasm (By similarity)				621
P51114 UniProt NPD GO	FXR1_HUMAN	Fragile X mental retardation syndrome-related protein 1 (hFXR1P)	0.58	-	nuc	0	Cytoplasm	cytoplasm [TAS] nucleolus [TAS] polysome [TAS]	600819	2CPQ	621
Q622Z7 UniProt NPD GO	GRK1_CAEBR	G protein-coupled receptor kinase 1 (EC 2.7.11.16)	0.58	+	cyt	0					640
P32866 UniProt NPD GO	GPRK2_DROME	G protein-coupled receptor kinase 2 (EC 2.7.11.16)	0.58	+	cyt	0		cytoplasm [IDA] plasma membrane [IDA]			714
P43249 UniProt NPD GO	GRK5_BOVIN	G protein-coupled receptor kinase 5 (EC 2.7.11.16) (G protein-coupled receptor kinase GRK5)	0.58	+	cyt	0					590
Q50DM8 UniProt NPD GO	GPR56_MACMU	G-protein coupled receptor 56 precursor	0.58	-	end	7 *	Membrane; multi-pass membrane protein				687
P70425 UniProt NPD GO	RIT2_MOUSE	GTP-binding protein Rit2 (Ras-like protein expressed in neurons) (Ras-like without CAAX protein 2)	0.58	+	cyt	0	Cell membrane				217
P38678 UniProt NPD GO	GS1_NEUCR	Glucan synthesis regulatory protein	0.58	-	nuc	0					532
Q9W3K5 UniProt NPD GO	GSH1_DROME	Glutamate--cysteine ligase (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) (Gamma-ECS) (GCS)	0.58	-	nuc	0					717
P24524 UniProt NPD GO	GLRA3_RAT	Glycine receptor alpha-3 chain precursor	0.58	-	end	4	Membrane; multi-pass membrane protein				464
Q4PB56 UniProt NPD GO	NMT_USTMA	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.58	+	mit	0	Cytoplasm (By similarity)				706
P35053 UniProt NPD GO	GPC1_RAT	Glypican-1 precursor (HSPG M12)	0.58	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				558
Q07104 UniProt NPD GO	GDF3_MOUSE	Growth/differentiation factor 3 precursor (GDF-3) (VG-1-related protein 2)	0.58	-	nuc	0	Secreted protein (Probable)				366
P43444 UniProt NPD GO	GNA11_XENLA	Guanine nucleotide-binding protein alpha-11 subunit	0.58	-	cyt	0					359
Q9TU29 UniProt NPD GO	GNA15_RABIT	Guanine nucleotide-binding protein alpha-15 subunit (G alpha-15)	0.58	-	mit	0		heterotrimeric G-protein complex [NAS]			374
P19686 UniProt NPD GO	GCYA3_RAT	Guanylate cyclase soluble subunit alpha-3 (EC 4.6.1.2) (GCS-alpha-3) (Soluble guanylate cyclase larg ...	0.58	-	cyt	0	Cytoplasm	guanylate cyclase complex, soluble [TAS]			690
P61579 UniProt NPD GO	REC17_HUMAN	HERV-K_11q22.1 provirus Rec protein	0.58	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity). Shuttles between the nucleus and cyto ...				105
P61571 UniProt NPD GO	REC1_HUMAN	HERV-K_12q14.1 provirus Rec protein	0.58	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity). Shuttles between the nucleus and the ...				104
P61565 UniProt NPD GO	ENK1_HUMAN	HERV-K_12q14.1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (EnvK1 protein) [ ...	0.58	-	end	2					698
Q902F9 UniProt NPD GO	ENK5_HUMAN	HERV-K_19p13.11 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (HERV-K113 envel ...	0.58	-	end	2					699
P61572 UniProt NPD GO	REC3_HUMAN	HERV-K_19q12 provirus Rec protein (HERV-K(C19) Rec protein)	0.58	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity). Shuttles between the nucleus and the ...				105
O71037 UniProt NPD GO	ENK3_HUMAN	HERV-K_19q12 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (HERV-K(C19) envelo ...	0.58	-	mit	2					699
P61580 UniProt NPD GO	NP10_HUMAN	HERV-K_5q33.3 provirus Np9 protein (HERV-K10 Np9 protein) (HERV-K107 Np9 protein)	0.58	-	nuc	0	Nucleus (By similarity). When overexpressed (By similarity)				75
P61573 UniProt NPD GO	REC4_HUMAN	HERV-K_6q14.1 provirus Rec protein (HERV-K109 Rec protein) (HERV-K(C6) Rec protein)	0.58	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity). Shuttles between the nucleus and the ...				105
Q69384 UniProt NPD GO	ENK2_HUMAN	HERV-K_7p22.1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (HERV-K(HML-2.HOM) ...	0.58	-	end	2			605626		699
Q69383 UniProt NPD GO	REC2_HUMAN	HERV-K_7q22.1 provirus Rec protein (HERV-K(HML-2.HOM) Rec protein) (HERV-K108 Rec protein) (HERV-K(C ...	0.58	-	nuc	0	Cytoplasm. Nucleus; nucleolus. Shuttles between the nucleus and the cytoplasm. When in the nucleus, ...				105
P61575 UniProt NPD GO	REC6_HUMAN	HERV-K_8p23.1 provirus Rec protein (HERV-K115 Rec protein)	0.58	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity). Shuttles between the nucleus and the ...				105
Q902F8 UniProt NPD GO	ENK6_HUMAN	HERV-K_8p23.1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (HERV-K115 envelop ...	0.58	-	mit	2					699
O73615 UniProt NPD GO	HAND1_XENLA	Heart- and neural crest derivatives-expressed protein 1 (Extraembryonic tissues, heart, autonomic ne ...	0.58	+	nuc	0					197
Q92260 UniProt NPD GO	HSP70_PENCI	Heat shock 70 kDa protein (Allergen Pen c 19) (Fragment)	0.58	-	cyt	0					503
P30218 UniProt NPD GO	HS30C_XENLA	Heat shock protein 30C	0.58	-	nuc	0					213
P33416 UniProt NPD GO	HSP78_YEAST	Heat shock protein 78, mitochondrial precursor	0.58	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			811
P41235 UniProt NPD GO	HNF4A_HUMAN	Hepatocyte nuclear factor 4-alpha (HNF-4-alpha) (Transcription factor HNF-4) (Transcription factor 1 ...	0.58	-	nuc	0	Nucleus	nucleus [TAS]	125850	1PZL	465
Q60HF3 UniProt NPD GO	HPS1_MACFA	Hermansky-Pudlak syndrome 1 protein homolog	0.58	-	cyt	0					667

You are viewing entries 20151 to 20200 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.