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
P15330 UniProt NPD GO	DORS_DROME	Embryonic polarity protein dorsal	0.95	-	nuc	0	Cytoplasm. Nucleus. In ventral regions it is first cytoplasmic, then the protein is relocalized in t ...	cytoplasm [IDA] nucleus [IDA]			999
Q5K767 UniProt NPD GO	EPL1_CRYNE	Enhancer of polycomb-like protein 1	0.95	-	nuc	0	Nucleus (By similarity)				846
Q03769 UniProt NPD GO	ENT5_YEAST	Epsin-5	0.95	+	nuc	0	Cytoplasm. Endosome. Found predominantly on endosomal structures	clathrin vesicle coat [IDA] cytoplasm [IDA] endosome [IDA]			411
P19214 UniProt NPD GO	EBA1_PLAFC	Erythrocyte-binding antigen EBA-175	0.95	-	nuc	0					1435
Q14152 UniProt NPD GO	IF3A_HUMAN	Eukaryotic translation initiation factor 3 subunit 10 (eIF-3 theta) (eIF3 p167) (eIF3 p180) (eIF3 p1 ...	0.95	+	nuc	0	Cytoplasm	eukaryotic translation initiation factor 3 ... [TAS]	602039		1382
Q99613 UniProt NPD GO	IF38_HUMAN	Eukaryotic translation initiation factor 3 subunit 8 (eIF3 p110) (eIF3c)	0.95	-	nuc	0		eukaryotic translation initiation factor 3 ... [TAS]	603916		913
P41110 UniProt NPD GO	IF4G1_RABIT	Eukaryotic translation initiation factor 4 gamma 1 (eIF-4-gamma 1) (eIF-4G1) (eIF-4G 1) (p220)	0.95	-	nuc	0					1402
Q6FM00 UniProt NPD GO	EXO84_CANGA	Exocyst complex component EXO84	0.95	-	nuc	0	Secretory vesicle (By similarity). Cell periphery. The polarization of EXO84 requires actin cables ( ...				764
Q8VI60 UniProt NPD GO	SULF1_RAT	Extracellular sulfatase Sulf-1 precursor (EC 3.1.6.-) (Sulfatase FP) (RSulfFP1)	0.95	+	nuc	0	Endoplasmic reticulum. Golgi apparatus; Golgi stack. Cell surface. Also localized on the cell surfac ...	cell surface [NAS] endoplasmic reticulum [NAS] extracellular space [ISS] Golgi stack [NAS]			870
Q4G163 UniProt NPD GO	FBX43_HUMAN	F-box only protein 43 (Endogenous meiotic inhibitor 2)	0.95	-	nuc	0			609110		708
Q6BXE5 UniProt NPD GO	SPT16_DEBHA	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16)	0.95	+	nuc	0	Nucleus (By similarity)				1033
O14270 UniProt NPD GO	FHL1_SCHPO	Fork head transcription factor 1	0.95	-	nuc	0	Nucleus (Potential)				743
Q05859 UniProt NPD GO	FMN1B_MOUSE	Formin-1 isoform IV (Limb deformity protein)	0.95	+	nuc	0		adherens junction [IPI]			1206
P42774 UniProt NPD GO	GBF1_ARATH	G-box-binding factor 1 (AtbZIP41)	0.95	+	nuc	0	Nucleus				315
P39960 UniProt NPD GO	BEM2_YEAST	GTPase-activating protein BEM2/IPL2 (Bud emergence protein 2)	0.95	-	nuc	0		intracellular [TAS] mitochondrion [IDA]			2167
Q08484 UniProt NPD GO	GYP1_YEAST	GTPase-activating protein GYP1 (GAP for YPT1)	0.95	-	nuc	0	Golgi apparatus; Golgi stack	Golgi apparatus [IDA] mitochondrion [IDA]		1FKM	637
Q8BL74 UniProt NPD GO	TF3C2_MOUSE	General transcription factor 3C polypeptide 2 (Transcription factor IIIC-subunit beta) (TF3C-beta) ( ...	0.95	-	nuc	0	Nucleus (By similarity)				907
P34333 UniProt NPD GO	GEI8_CAEEL	Gex-3-interacting protein 8	0.95	-	nuc	0	Nucleus (Probable)				1780
Q06704 UniProt NPD GO	IMH1_YEAST	Golgin IMH1 (Integrins and myosins homology protein 1)	0.95	+	nuc	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein. IMH1 is recruited to the Go ...	cytosol [IDA] Golgi apparatus [IDA]			911
P27671 UniProt NPD GO	GNRP_MOUSE	Guanine nucleotide-releasing protein (GNRP) (Ras-specific nucleotide exchange factor CDC25) (CDC25Mm ...	0.95	-	nuc	0		plasma membrane [ISS] synaptosome [ISS]			1262
Q9BXL5 UniProt NPD GO	HEMGN_HUMAN	Hemogen (Hemopoietic gene protein) (Negative differentiation regulator protein) (Erythroid different ...	0.95	+	nuc	0	Nucleus				484
Q96MM7 UniProt NPD GO	H6ST2_HUMAN	Heparan-sulfate 6-O-sulfotransferase 2 (EC 2.8.2.-) (HS6ST-2)	0.95	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)		300545		605
Q9BUJ2 UniProt NPD GO	HNRL1_HUMAN	Heterogeneous nuclear ribonucleoprotein U-like protein 1 (Adenovirus early region 1B-associated prot ...	0.95	-	nuc	0	Nucleus		605800		856
Q6AZF8 UniProt NPD GO	HM20A_XENLA	High mobility group protein 20A (HMG box-containing protein 20A)	0.95	-	nuc	0	Nucleus (By similarity)				345
Q6DIJ5 UniProt NPD GO	HM20A_XENTR	High mobility group protein 20A (HMG box-containing protein 20A)	0.95	-	nuc	0	Nucleus (By similarity)				345
Q8TEK3 UniProt NPD GO	DOT1L_HUMAN	Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) (Histone H3-K79 methyltransf ...	0.95	-	nuc	0	Nucleus (Probable)		607375	1NW3	1739
P41817 UniProt NPD GO	CUP9_YEAST	Homeobox protein CUP9	0.95	-	nuc	0	Nucleus (Probable)				306
Q00400 UniProt NPD GO	DTH1_DUGTI	Homeobox protein DTH-1	0.95	+	nuc	0	Nucleus (Probable)				533
P10035 UniProt NPD GO	HMH2_DROME	Homeobox protein H2.0	0.95	+	nuc	0	Nucleus (Potential)				418
Q90471 UniProt NPD GO	HXDCA_BRARE	Homeobox protein Hox-D12a (Hox-D12)	0.95	+	nuc	0	Nucleus				276
P39770 UniProt NPD GO	SALM_DROME	Homeotic protein spalt-major	0.95	-	nuc	0	Nucleus (Probable)				1365
P53836 UniProt NPD GO	YN18_YEAST	Hypothetical 118.3 kDa protein in ERG24-MET2 intergenic region	0.95	-	nuc	0		CCR4-NOT complex [IPI]			1060
P12223 UniProt NPD GO	YCF1B_MARPO	Hypothetical 57 kDa protein ycf1 (ORF 464)	0.95	+	nuc	0	Plastid; chloroplast				464
O94693 UniProt NPD GO	LIN1_SCHPO	Hypothetical Lin1-like protein	0.95	-	nuc	0					408
Q09856 UniProt NPD GO	YAF2_SCHPO	Hypothetical protein C29E6.02 in chromosome I	0.95	+	nuc	0					542
Q03573 UniProt NPD GO	YLF3_CAEEL	Hypothetical protein C40H1.3	0.95	-	nuc	0					504
O14196 UniProt NPD GO	YDQ2_SCHPO	Hypothetical protein C5D6.02c in chromosome I	0.95	+	nuc	0		nucleus [IDA]			300
O14210 UniProt NPD GO	YDT5_SCHPO	Hypothetical protein C6B12.05c in chromosome I	0.95	+	nuc	0					295
P34515 UniProt NPD GO	YMX7_CAEEL	Hypothetical protein K06H7.7	0.95	+	nuc	0					322
P30651 UniProt NPD GO	YOW5_CAEEL	Hypothetical protein ZK643.5	0.95	+	nuc	0					487
Q9YIB9 UniProt NPD GO	HIF1A_CHICK	Hypoxia-inducible factor 1 alpha (HIF-1 alpha) (HIF1 alpha)	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in normoxia, nuclear translocation i ...				811
O35800 UniProt NPD GO	HIF1A_RAT	Hypoxia-inducible factor 1 alpha (HIF-1 alpha) (HIF1 alpha)	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in normoxia, nuclear translocation i ...				825
Q6FRX4 UniProt NPD GO	TIM50_CANGA	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.95	+	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				485
P24350 UniProt NPD GO	IPOU_DROME	Inhibitory POU protein (I-POU) (Abnormal chemosensory jump 6 protein)	0.95	+	nuc	0	Nucleus				396
Q9WVE9 UniProt NPD GO	ITSN1_RAT	Intersectin-1 (EH domain and SH3 domain regulator of endocytosis 1)	0.95	+	nuc	0	Intracytoplasmic membrane. Synaptosome. Enriched in synaptosomes				1217
Q15811 UniProt NPD GO	ITSN1_HUMAN	Intersectin-1 (SH3 domain-containing protein 1A) (SH3P17)	0.95	+	nuc	0	Intracytoplasmic membrane (By similarity). Synaptosome (By similarity). Enriched in synaptosomes (By ...		602442	1KI1	1721
P83829 UniProt NPD GO	IFT81_RAT	Intraflagellar transport 81 (Carnitine deficiency-associated protein expressed in ventricle 1) (CDV- ...	0.95	-	nuc	0					675
P53863 UniProt NPD GO	JJJ1_YEAST	J protein type 1	0.95	+	nuc	0	Nucleus (Potential)	cytoplasm [IDA] mitochondrion [IDA]			590
P34307 UniProt NPD GO	YKR1_CAEEL	KH domain-containing protein C06G4.1	0.95	+	nuc	0					886
Q61595 UniProt NPD GO	KTN1_MOUSE	Kinectin	0.95	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Vesicle ...	endoplasmic reticulum [IDA]			1327

You are viewing entries 1851 to 1900 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.