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
Q5NRP9 UniProt NPD GO	EDN1_ATEAB	Endothelin-1 precursor (ET-1) (Preproendothelin-1) (PPET1)	0.63	-	nuc	0	Secreted protein (By similarity)				202
P29560 UniProt NPD GO	EDN1_RABIT	Endothelin-1 precursor (ET-1) (Preproendothelin-1) (PPET1)	0.63	-	nuc	0	Secreted protein				202
P07106 UniProt NPD GO	ENDR_BOVIN	Endozepine-related protein precursor (Membrane-associated diazepam-binding inhibitor) (MA-DBI)	0.63	-	nuc	1					533
Q14511 UniProt NPD GO	CASL_HUMAN	Enhancer of filamentation 1 (HEF1) (CRK-associated substrate-related protein) (CAS-L) (CasL) (p105) ...	0.63	-	nuc	0	Cytoplasm; cell cortex. Nucleus. Localizes to both the cell nucleus and the cell periphery and is di ...	cytoplasm [TAS] nucleus [TAS] spindle [TAS]	602265		834
Q91W69 UniProt NPD GO	EPN3_MOUSE	Epsin-3 (EPS-15-interacting protein 3)	0.63	-	nuc	0	Cytoplasm; cell cortex (By similarity). Cytoplasm; perinuclear region (By similarity). Concentrated ...				636
Q01842 UniProt NPD GO	POK_DROME	Ets DNA-binding protein pokkuri (Protein yan) (Protein anterior open)	0.63	-	nuc	0	Nucleus			1SV4	732
P23637 UniProt NPD GO	ERF2_PICPI	Eukaryotic peptide chain release factor GTP-binding subunit (ERF2) (Translation release factor 3) (P ...	0.63	-	nuc	0	Cytoplasm (Probable)				741
Q9BQI3 UniProt NPD GO	E2AK1_HUMAN	Eukaryotic translation initiation factor 2-alpha kinase 1 (EC 2.7.11.1) (Heme-regulated eukaryotic i ...	0.63	-	nuc	0					630
P32497 UniProt NPD GO	IF38_YEAST	Eukaryotic translation initiation factor 3 93 kDa subunit (eIF3 p93) (Nuclear transport protein NIP1 ...	0.63	-	nuc	0	Cytoplasm. Mainly	cytoplasm [IDA] eukaryotic translation initiation factor 3 ... [IDA] multi-eIF complex [IDA]			812
Q3TPX4 UniProt NPD GO	EXOC5_MOUSE	Exocyst complex component 5 (Exocyst complex component Sec10)	0.63	-	cyt	0	Cytoplasm (By similarity)				708
O00471 UniProt NPD GO	EXOC5_HUMAN	Exocyst complex component 5 (Exocyst complex component Sec10) (hSec10)	0.63	-	cyt	0	Cytoplasm	cytoplasm [TAS]	604469		708
Q6PGF7 UniProt NPD GO	EXOC8_MOUSE	Exocyst complex component 8 (Exocyst complex 84 kDa subunit)	0.63	-	nuc	0	Cytoplasm. Redistributes to growing neurites and growth cones during cell differentiation. Binds lip ...				716
Q6FJW2 UniProt NPD GO	EXO70_CANGA	Exocyst complex protein EXO70	0.63	-	nuc	0	Bud (By similarity). Bud neck (By similarity)				623
Q499Y0 UniProt NPD GO	XPO4_XENLA	Exportin-4	0.63	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				1150
P38246 UniProt NPD GO	ECM8_YEAST	Extracellular matrix protein 8	0.63	-	nuc	0					339
Q5XI67 UniProt NPD GO	FBX30_RAT	F-box only protein 30	0.63	-	nuc	0					742
Q9UKA2 UniProt NPD GO	FBXL4_HUMAN	F-box/LRR-repeat protein 4 (F-box and leucine-rich repeat protein 4) (F-box protein FBL4/FBL5)	0.63	+	nuc	0	Cytoplasm. Nucleus	ubiquitin ligase complex [TAS]	605654		621
Q924K2 UniProt NPD GO	FAF1_RAT	FAS-associated factor 1 (Protein FAF1)	0.63	-	cyt	0	Nucleus (Potential)	CD95 death-inducing signaling complex [ISS] cytosol [ISS] nucleus [ISS] perinuclear region [ISS]			649
Q6FKH7 UniProt NPD GO	FKBP3_CANGA	FK506-binding protein 3 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.63	+	nuc	0	Nucleus; nucleolus (By similarity)				437
Q9ZSZ8 UniProt NPD GO	FIP37_ARATH	FKBP12-interacting protein of 37 kDa (FIP-37) (Immunophilin-interacting protein AtFIP37)	0.63	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Nuclear with a speckled distribution pattern				330
Q61555 UniProt NPD GO	FBN2_MOUSE	Fibrillin-2 precursor	0.63	-	nuc	0		extracellular region [TAS] microfibril [TAS]			2907
Q8R5L7 UniProt NPD GO	FGF14_RAT	Fibroblast growth factor 14 (FGF-14)	0.63	-	nuc	0	Nucleus (Probable)				247
P36386 UniProt NPD GO	FGF3_XENLA	Fibroblast growth factor 3 precursor (FGF-3) (HBGF-3) (INT-2)	0.63	-	exc	0					237
P23706 UniProt NPD GO	DEFA_ANTMA	Floral homeotic protein DEFICIENS	0.63	-	nuc	0	Nucleus				227
Q03378 UniProt NPD GO	GLOB_ANTMA	Floral homeotic protein GLOBOSA	0.63	-	nuc	0	Nucleus				215
O00358 UniProt NPD GO	FOXE1_HUMAN	Forkhead box protein E1 (Thyroid transcription factor 2) (TTF-2) (Forkhead-related protein FKHL15)	0.63	-	nuc	0	Nucleus (Potential)		602617		376
Q13461 UniProt NPD GO	FOXE3_HUMAN	Forkhead box protein E3 (Forkhead-related protein FKHL12) (Forkhead-related transcription factor 8) ...	0.63	-	nuc	0	Nucleus	nucleus [NAS] transcription factor complex [IDA]	601094		319
Q90964 UniProt NPD GO	FOXGB_CHICK	Forkhead box protein G1B (Forkhead-related protein FKHL1) (Transcription factor BF-1) (Brain factor ...	0.63	-	nuc	0	Nucleus (Potential)				451
O15353 UniProt NPD GO	FOXN1_HUMAN	Forkhead box protein N1 (Transcription factor winged-helix nude)	0.63	-	nuc	0	Nucleus	nucleus [TAS]	600838		648
Q90854 UniProt NPD GO	IRK3_CHICK	G protein-activated inward rectifier potassium channel 1 (GIRK1) (Potassium channel, inwardly rectif ...	0.63	-	mit	3	Membrane; multi-pass membrane protein				492
Q8K209 UniProt NPD GO	GPR56_MOUSE	G-protein coupled receptor 56 precursor (Serpentine receptor cyt28)	0.63	-	end	7	Membrane; multi-pass membrane protein				687
O96001 UniProt NPD GO	GSUB_HUMAN	G-substrate	0.63	-	nuc	0		soluble fraction [TAS]	604088		155
P20438 UniProt NPD GO	CG12_YEAST	G1/S-specific cyclin CLN2	0.63	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			545
P42524 UniProt NPD GO	CCNB_DICDI	G2/mitotic-specific cyclin-B	0.63	-	nuc	0					436
Q86XJ1 UniProt NPD GO	GA2L3_HUMAN	GAS2-like protein 3 (Growth arrest-specific 2-like 3)	0.63	-	nuc	0					694
Q8LC79 UniProt NPD GO	GAT19_ARATH	GATA transcription factor 19	0.63	-	nuc	0	Nucleus (Probable)				295
Q9LRH6 UniProt NPD GO	GAT26_ARATH	GATA transcription factor 26 (Protein ZIM)	0.63	-	nuc	0	Nucleus				309
Q86UU5 UniProt NPD GO	GGN_HUMAN	Gametogenetin	0.63	-	nuc	0		integral to membrane [ISS] nuclear envelope [ISS]	609966		652
P47742 UniProt NPD GO	GBRR2_RAT	Gamma-aminobutyric-acid receptor rho-2 subunit precursor (GABA(A) receptor)	0.63	-	end	4	Membrane; multi-pass membrane protein				465
Q00959 UniProt NPD GO	NMDE1_RAT	Glutamate [NMDA] receptor subunit epsilon 1 precursor (N-methyl D-aspartate receptor subtype 2A) (NR ...	0.63	-	end	4	Membrane; multi-pass membrane protein	N-methyl-D-aspartate selective glutamate re... [IDA] neuron projection [IDA] plasma membrane [IMP] presynaptic membrane [IEP] synapse [TAS]		2A5T	1464
P35438 UniProt NPD GO	NMDZ1_MOUSE	Glutamate [NMDA] receptor subunit zeta 1 precursor (N-methyl-D-aspartate receptor subunit NR1)	0.63	+	end	3	Cell membrane; multi-pass membrane protein (By similarity). Enriched in post-synaptic plasma membran ...	cytoplasm [IDA] dendrite [ISS] growth cone [NAS] membrane fraction [IDA] N-methyl-D-aspartate selective glutamate re... [ISS] postsynaptic membrane [IDA] synaptic vesicle [IDA]			938
Q5R1P0 UniProt NPD GO	NMDZ1_CANFA	Glutamate [NMDA] receptor subunit zeta 1 precursor (N-methyl-D-aspartate receptor subunit NR1) (NMD- ...	0.63	+	end	3	Cell membrane; multi-pass membrane protein (By similarity). Enriched in post-synaptic plasma membran ...				943
Q925T6 UniProt NPD GO	GRIP1_MOUSE	Glutamate receptor-interacting protein 1 (GRIP1 protein)	0.63	-	nuc	0	Cytoplasmic and membrane-associated with vesicles, peri-Golgi complexes and endoplasmic reticulum. E ...	lipid raft [IDA]			1127
Q9HF78 UniProt NPD GO	GSH1_CANAL	Glutamate--cysteine ligase (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) (Gamma-ECS) (GCS)	0.63	-	nuc	0					690
Q9XZV5 UniProt NPD GO	GNAS_GEOCY	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.63	-	cyt	0					381
Q12373 UniProt NPD GO	HIF1_YEAST	HAT1-interacting factor 1	0.63	-	nuc	0	Nucleus	histone acetyltransferase complex [IPI] nucleus [IDA]			385
O17468 UniProt NPD GO	HIRA_DROME	HIRA protein homolog (dHIRA)	0.63	-	nuc	0	Nucleus (Potential)				1047
P38529 UniProt NPD GO	HSF1_CHICK	Heat shock factor protein 1 (HSF 1) (Heat shock transcription factor 1) (HSTF 1) (HSF 3A) (HSTF 3A)	0.63	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic during normal growth and moves to th ...				491
P30219 UniProt NPD GO	HS30D_XENLA	Heat shock protein 30D	0.63	-	nuc	0					215
Q76LV2 UniProt NPD GO	HS90A_BOVIN	Heat shock protein HSP 90-alpha	0.63	-	nuc	0	Cytoplasm (By similarity)				732

You are viewing entries 17351 to 17400 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.