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
P18302 UniProt NPD GO	DREB_CHICK	Drebrin (Developmentally-regulated brain protein)	0.80	-	nuc	0	Cytoplasm				651
Q9JHU4 UniProt NPD GO	DYHC_MOUSE	Dynein heavy chain, cytosolic (DYHC) (Cytoplasmic dynein heavy chain 1) (DHC1) (Dynein heavy chain 1 ...	0.80	-	nuc	0	Cytoplasm				4644
P38650 UniProt NPD GO	DYHC_RAT	Dynein heavy chain, cytosolic (DYHC) (Cytoplasmic dynein heavy chain 1) (DHC1) (Dynein heavy chain 1 ...	0.80	-	nuc	0	Cytoplasm				4644
O75923 UniProt NPD GO	DYSF_HUMAN	Dysferlin (Dystrophy-associated fer-1-like protein) (Fer-1-like protein 1)	0.80	+	nuc	1	Sarcolemma; sarcolemmal membrane; single-pass type II membrane protein (Probable)	plasma membrane [TAS]	606768		2080
O60941 UniProt NPD GO	DTNB_HUMAN	Dystrobrevin beta (Beta-dystrobrevin) (DTN-B)	0.80	-	nuc	0	Cytoplasm		602415		627
Q96EV8 UniProt NPD GO	DTBP1_HUMAN	Dystrobrevin-binding protein 1 (Dysbindin) (Hermansky-Pudlak syndrome 7 protein)	0.80	-	nuc	0	Cytoplasm (By similarity)	axon [ISS] cytoplasm [ISS] nucleus [ISS] sarcolemma [ISS]	607145		351
Q9BG76 UniProt NPD GO	EDN1_SHEEP	Endothelin-1 precursor (ET-1) (Preproendothelin-1) (PPET1)	0.80	-	nuc	0	Secreted protein				202
Q5NRP8 UniProt NPD GO	EDN2_ATEAB	Endothelin-2 precursor (ET-2) (Preproendothelin-2) (PPET2)	0.80	-	exc	0	Secreted protein (By similarity)				180
Q92556 UniProt NPD GO	ELMO1_HUMAN	Engulfment and cell motility protein 1 (CED-12 homolog)	0.80	-	nuc	0	Cytoplasm. Cell membrane. Translocation to plasma membrane seems to be mediated by DOCK1 and CRK	cytoplasm [IDA] plasma membrane [IDA]	606420		727
Q8BPU7 UniProt NPD GO	ELMO1_MOUSE	Engulfment and cell motility protein 1 (CED-12 homolog)	0.80	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocation to plasma membrane seems to ...	cytoplasm [ISS] plasma membrane [ISS]			727
Q96BJ8 UniProt NPD GO	ELMO3_HUMAN	Engulfment and cell motility protein 3	0.80	-	cyt	0	Cytoplasm (By similarity)		606422		607
P42566 UniProt NPD GO	EP15_HUMAN	Epidermal growth factor receptor substrate 15 (Protein Eps15) (AF-1p protein)	0.80	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Recruited to the plasma membrane upon EGFR ...	coated pit [TAS] plasma membrane [IDA]	600051	1FF1	896
P42567 UniProt NPD GO	EP15_MOUSE	Epidermal growth factor receptor substrate 15 (Protein Eps15) (AF-1p protein)	0.80	-	nuc	0	Cytoplasm. Cell membrane. Recruited to the plasma membrane upon EGFR activation and localizes to coa ...			1QJT	897
Q9UBC2 UniProt NPD GO	EP15R_HUMAN	Epidermal growth factor receptor substrate 15-like 1 (Eps15-related protein) (Eps15R)	0.80	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Nucleus (By similarity). Localized to pl ...				864
P57782 UniProt NPD GO	ESR2_ONCMY	Estrogen receptor beta (ER-beta)	0.80	+	nuc	0	Nucleus				568
O49160 UniProt NPD GO	IF38_ARATH	Eukaryotic translation initiation factor 3 subunit 8 (eIF3 p110) (eIF3c) (p105)	0.80	-	nuc	0					900
P23588 UniProt NPD GO	IF4B_HUMAN	Eukaryotic translation initiation factor 4B (eIF-4B)	0.80	-	nuc	0		eukaryotic translation initiation factor 4F... [TAS]	603928	1WI8	611
Q9VQQ9 UniProt NPD GO	EXOC2_DROME	Exocyst complex component 2 (Exocyst complex component Sec5)	0.80	-	nuc	0		exocyst [NAS]			894
Q6CNM8 UniProt NPD GO	EXO84_KLULA	Exocyst complex component EXO84	0.80	-	nuc	0	Secretory vesicle (By similarity). Cell periphery. The polarization of EXO84 requires actin cables ( ...				720
Q803U7 UniProt NPD GO	EXO1_BRARE	Exonuclease 1 (EC 3.1.-.-) (Exonuclease I)	0.80	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			806
P26040 UniProt NPD GO	EZRI_MOUSE	Ezrin (p81) (Cytovillin) (Villin-2)	0.80	-	nuc	0	Membrane (By similarity). Localization to the apical membrane of parietal cells depends on the inter ...	actin cytoskeleton [ISS] apical plasma membrane [IDA] basal body [IDA] uropod [IDA]			585
P31977 UniProt NPD GO	EZRI_RAT	Ezrin (p81) (Cytovillin) (Villin-2)	0.80	-	nuc	0	Membrane. Localization to the apical membrane of parietal cells depends on the interaction with MPP5 ...	actin cytoskeleton [ISS]			585
Q9VZF4 UniProt NPD GO	FBXW7_DROME	F-box/WD repeat protein 7 (F-box and WD-40 domain protein 7) (Protein archipelago)	0.80	-	nuc	0	Nucleus (By similarity)	SCF ubiquitin ligase complex [NAS]			1326
Q65WY8 UniProt NPD GO	SSP1B_ORYSA	FACT complex subunit SSRP1-B (Facilitates chromatin transcription complex subunit SSRP1-B) (Recombin ...	0.80	+	nuc	0	Nucleus (By similarity)				640
Q61E63 UniProt NPD GO	SPT16_CAEBR	FACT complex subunit spt-16 (Facilitates chromatin transcription complex subunit spt-16)	0.80	+	mit	0	Nucleus (By similarity)				1034
Q9R1E0 UniProt NPD GO	FOXO1_MOUSE	Forkhead box protein O1A (Forkhead in rhabdomyosarcoma)	0.80	-	nuc	0	Cytoplasm. Nucleus. Shuttles between cytoplasm and nucleus	cytoplasm [IDA] nucleus [IDA]			652
P58462 UniProt NPD GO	FOXP1_MOUSE	Forkhead box protein P1 (Forkhead-related transcription factor 1)	0.80	-	nuc	0	Nucleus (Probable)	nucleus [IC]			705
P18625 UniProt NPD GO	FOSL2_CHICK	Fos-related antigen 2	0.80	+	nuc	0	Nucleus				323
P47930 UniProt NPD GO	FOSL2_MOUSE	Fos-related antigen 2	0.80	+	nuc	0	Nucleus				326
P30430 UniProt NPD GO	FUR1C_DROME	Furin-like protease 1, isoform 1-CRR precursor (EC 3.4.21.75) (Furin-1) (Kex2-like endoprotease 1) ( ...	0.80	-	mit	2	Golgi apparatus; Golgi membrane; multi-pass membrane protein	plasma membrane [IDA]			1101
P63250 UniProt NPD GO	IRK3_MOUSE	G protein-activated inward rectifier potassium channel 1 (GIRK1) (Potassium channel, inwardly rectif ...	0.80	+	end	3	Membrane; multi-pass membrane protein			1U4E	501
P63251 UniProt NPD GO	IRK3_RAT	G protein-activated inward rectifier potassium channel 1 (GIRK1) (Potassium channel, inwardly rectif ...	0.80	+	end	3	Membrane; multi-pass membrane protein				501
P70507 UniProt NPD GO	GRK4_RAT	G protein-coupled receptor kinase 4 (EC 2.7.11.16) (G protein-coupled receptor kinase GRK4)	0.80	-	cyt	0					575
Q9EQH1 UniProt NPD GO	GAB2_RAT	GRB2-associated-binding protein 2 (GRB2-associated binder 2)	0.80	-	nuc	0					665
P58854 UniProt NPD GO	GCP3_MOUSE	Gamma-tubulin complex component 3 (GCP-3)	0.80	-	nuc	0	Centrosome (By similarity)				905
P18723 UniProt NPD GO	ZG48_XENLA	Gastrula zinc finger protein XLCGF48.2 (Fragment)	0.80	-	nuc	0	Nucleus (Potential)				647
P18726 UniProt NPD GO	ZG5A_XENLA	Gastrula zinc finger protein XLCGF51.1A (Fragment)	0.80	-	nuc	0	Nucleus (Potential)				172
Q8TEQ6 UniProt NPD GO	GEMI5_HUMAN	Gem-associated protein 5 (Gemin5)	0.80	+	nuc	0	Nucleus. Found both in the nucleoplasm and in nuclear bodies called gems (Gemini of Cajal bodies) th ...	cytoplasm [IDA] nuclear body [IDA] nucleoplasm [IDA]	607005		1508
P25655 UniProt NPD GO	NOT1_YEAST	General negative regulator of transcription subunit 1	0.80	-	end	0	Cytoplasm. Nucleus	CCR4-NOT core complex [IPI] cytoplasm [IDA] nucleus [IDA]			2108
P04150 UniProt NPD GO	GCR_HUMAN	Glucocorticoid receptor (GR)	0.80	+	nuc	0	Cytoplasm. Nucleus. Cytoplasmic in the absence of ligand; nuclear after ligand-binding	cytoplasm [TAS] mitochondrial matrix [TAS] nucleus [TAS]	138040	1P93	777
O70311 UniProt NPD GO	NMT2_MOUSE	Glycylpeptide N-tetradecanoyltransferase 2 (EC 2.3.1.97) (Peptide N-myristoyltransferase 2) (Myristo ...	0.80	+	cyt	0	Cytoplasm	cytoplasm [TAS]			529
Q6GNT7 UniProt NPD GO	GOGA5_XENLA	Golgin subfamily A member 5 (Golgin-84)	0.80	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)	Golgi apparatus [ISS]			722
O13166 UniProt NPD GO	TLE2_BRARE	Groucho 2 protein	0.80	-	nuc	0	Nucleus (Probable)				761
O42611 UniProt NPD GO	HIRA_FUGRU	HIRA protein (TUP1-like enhancer of split protein 1)	0.80	+	nuc	0	Nucleus (Potential)				1025
P79987 UniProt NPD GO	HIRA_CHICK	HIRA protein (TUP1-like enhancer of split protein 1) (CHIRA)	0.80	+	nuc	0	Nucleus (Potential)				1018
P57100 UniProt NPD GO	HAND1_RABIT	Heart- and neural crest derivatives-expressed protein 1 (Extraembryonic tissues, heart, autonomic ne ...	0.80	+	nuc	0					215
Q90867 UniProt NPD GO	HNF1A_CHICK	Hepatocyte nuclear factor 1-alpha (HNF-1A) (HNF-1-alpha)	0.80	-	nuc	0	Nucleus (By similarity)				634
P19376 UniProt NPD GO	H1S_STRPU	Histone H1, sperm (Fragment)	0.80	+	nuc	0	Nucleus				34
Q9PWD6 UniProt NPD GO	HXA10_MORSA	Homeobox protein Hox-A10	0.80	+	nuc	0	Nucleus (By similarity)				289
Q9DDU0 UniProt NPD GO	HXABA_BRARE	Homeobox protein Hox-A11a	0.80	+	nuc	0	Nucleus (By similarity)				284

You are viewing entries 8851 to 8900 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.