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
Q7KV15 UniProt NPD GO	STEL4_DROME	Stellate protein CG33239	0.21	-	nuc	0		cytoplasm [ISS] nucleus [ISS] protein kinase CK2 complex [ISS]			171
Q6CYB3 UniProt NPD GO	ERG6_KLULA	Sterol 24-C-methyltransferase (EC 2.1.1.41) (Delta(24)-sterol C-methyltransferase)	0.21	-	cyt	0					371
P12437 UniProt NPD GO	PERX_SOLTU	Suberization-associated anionic peroxidase precursor (EC 1.11.1.7) (POPA)	0.21	-	exc	1 *	Secreted protein (By similarity)				363
P16064 UniProt NPD GO	ICI1_PHAAN	Subtilisin inhibitor 1 (Subtilisin inhibitor I) (ASI-I) [Contains: Subtilisin inhibitor 2 (Subtilisi ...	0.21	-	nuc	0	Secreted protein				92
Q99MT6 UniProt NPD GO	SUCR1_MOUSE	Succinate receptor 1 (G-protein coupled receptor 91)	0.21	-	end	6 *	Membrane; multi-pass membrane protein				317
O19069 UniProt NPD GO	SUCA_PIG	Succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial precursor (EC 6.2.1.4) (Succinyl-CoA ...	0.21	-	mit	0	Mitochondrion (By similarity)			2FPP	350
Q12325 UniProt NPD GO	SUL2_YEAST	Sulfate permease 2 (High-affinity sulfate transporter 2)	0.21	-	end	8	Membrane; multi-pass membrane protein	plasma membrane [IMP]			893
Q10357 UniProt NPD GO	CCS1_SCHPO	Superoxide dismutase 1 copper chaperone	0.21	-	nuc	0	Cytoplasm				297
O14508 UniProt NPD GO	SOCS2_HUMAN	Suppressor of cytokine signaling 2 (SOCS-2) (Cytokine-inducible SH2 protein 2) (CIS-2) (STAT-induced ...	0.21	-	nuc	0		cytoplasm [NAS]	605117	2C9W	198
P56677 UniProt NPD GO	ST14_MOUSE	Suppressor of tumorigenicity protein 14 (EC 3.4.21.-) (Serine protease 14) (Epithin)	0.21	-	mit	1	Membrane; single-pass type II membrane protein (Probable)	extracellular region [IDA] extrinsic to plasma membrane [IDA] integral to plasma membrane [TAS]			855
Q63769 UniProt NPD GO	SRPX_RAT	Sushi repeat-containing protein SRPX precursor (DRS protein) (Down-regulated by v-SRC)	0.21	-	exc	0					464
Q757A4 UniProt NPD GO	YKT6_ASHGO	Synaptobrevin homolog YKT6	0.21	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				200
Q9Z1L2 UniProt NPD GO	SNG4_MOUSE	Synaptogyrin-4	0.21	-	end	4 *	Membrane; multi-pass membrane protein				233
O75056 UniProt NPD GO	SDC3_HUMAN	Syndecan-3 (SYND3)	0.21	-	nuc	1	Membrane; single-pass type I membrane protein		186357		384
Q64519 UniProt NPD GO	SDC3_MOUSE	Syndecan-3 precursor (SYND3)	0.21	-	end	1	Membrane; single-pass type I membrane protein				442
P70323 UniProt NPD GO	TBX1_MOUSE	T-box transcription factor TBX1 (T-box protein 1) (Testis-specific T-box protein)	0.21	-	nuc	0	Nucleus (Potential)				479
Q9UMR3 UniProt NPD GO	TBX20_HUMAN	T-box transcription factor TBX20 (T-box protein 20) (Fragment)	0.21	-	nuc	0	Nucleus (Potential)		606061		251
P06323 UniProt NPD GO	TVA3_MOUSE	T-cell receptor alpha chain V region CTL-F3 precursor	0.21	-	exc	0				1AC6	132
P40200 UniProt NPD GO	TACT_HUMAN	T-cell surface protein tactile precursor (CD96 antigen)	0.21	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	606037		569
P40412 UniProt NPD GO	TCPE1_AVESA	T-complex protein 1 subunit epsilon (TCP-1-epsilon) (CCT-epsilon) (TCP-K19)	0.21	-	cyt	0	Cytoplasm				535
P50143 UniProt NPD GO	TCPG_XENLA	T-complex protein 1 subunit gamma (TCP-1-gamma) (CCT-gamma)	0.21	-	cyt	0	Cytoplasm				547
Q717B3 UniProt NPD GO	TDPZ1_MOUSE	TD and POZ domain-containing protein 1 (MAPP family protein 2)	0.21	-	cyt	0					365
Q925I4 UniProt NPD GO	TS1R2_MOUSE	Taste receptor type 1 member 2 precursor (G-protein coupled receptor 71) (Sweet taste receptor T1R2) ...	0.21	-	end	7	Membrane; multi-pass membrane protein				843
Q645V2 UniProt NPD GO	T2R14_PONPY	Taste receptor type 2 member 14 (T2R14)	0.21	-	end	7 *	Membrane; multi-pass membrane protein				318
P59535 UniProt NPD GO	T2R40_HUMAN	Taste receptor type 2 member 40 (T2R40) (T2R58) (G-protein coupled receptor 60)	0.21	-	end	6 *	Membrane; multi-pass membrane protein				323
Q2MV58 UniProt NPD GO	TECT1_HUMAN	Tectonic-1 precursor	0.21	-	exc	0	Secreted protein (By similarity)		609863		587
P82354 UniProt NPD GO	THBI_THETS	Theromin (Thrombin inhibitor)	0.21	-	nuc	0	Secreted protein				67
Q3T0L2 UniProt NPD GO	TXND4_BOVIN	Thioredoxin domain-containing protein 4 precursor	0.21	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				406
P52709 UniProt NPD GO	SYTC_CAEEL	Threonyl-tRNA synthetase, cytoplasmic (EC 6.1.1.3) (Threonine--tRNA ligase) (ThrRS)	0.21	-	mit	0	Cytoplasm (Potential)				725
O04630 UniProt NPD GO	SYTM_ARATH	Threonyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.3) (Threonine--tRNA ligase) (ThrRS)	0.21	-	mit	0	Mitochondrion. Cytoplasm				709
Q8JHW2 UniProt NPD GO	TSP3A_BRARE	Thrombospondin-3a precursor (Thbs3a)	0.21	-	nuc	0		extracellular region [NAS]			962
Q9QXE5 UniProt NPD GO	TSSP_MOUSE	Thymus-specific serine protease precursor (EC 3.4.-.-)	0.21	-	mit	1 *	Cytoplasmic vesicle. Vesicular, either lysosomal or endosomal				509
Q62264 UniProt NPD GO	THRSP_MOUSE	Thyroid hormone-inducible hepatic protein (Spot 14 protein) (SPOT14) (S14 protein)	0.21	-	mit	0	Nucleus				150
Q15654 UniProt NPD GO	TRIP6_HUMAN	Thyroid receptor-interacting protein 6 (TRIP6) (OPA-interacting protein 1) (Zyxin-related protein 1) ...	0.21	-	nuc	0		focal adhesion [IDA]	602933	1X61	476
P25684 UniProt NPD GO	TX022_DENAN	Toxin C10S2C2	0.21	-	mit	0	Secreted protein				60
P48522 UniProt NPD GO	TCMO_CATRO	Trans-cinnamate 4-monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) ...	0.21	-	end	0					505
Q43240 UniProt NPD GO	TCMO_ZINEL	Trans-cinnamate 4-monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) ...	0.21	+	end	0					505
Q5KB83 UniProt NPD GO	SPT4_CRYNE	Transcription elongation factor SPT4 (Chromatin elongation factor SPT4)	0.21	-	cyt	0	Nucleus. Centromere and heterochromatin (By similarity)				113
Q94C60 UniProt NPD GO	SPT42_ARATH	Transcription elongation factor SPT4 homolog 2	0.21	-	cyt	0	Nucleus (By similarity)				116
Q92371 UniProt NPD GO	BTF3_SCHPO	Transcription factor BTF3 homolog	0.21	-	nuc	0	Nucleus (Probable)				151
Q9ERZ8 UniProt NPD GO	TRPV4_RAT	Transient receptor potential cation channel subfamily V member 4 (TrpV4) (osm-9-like TRP channel 4) ...	0.21	+	end	6	Membrane; multi-pass membrane protein (Probable)	plasma membrane [ISS]			871
Q95GN9 UniProt NPD GO	IF1C_AMBTC	Translation initiation factor IF-1, chloroplast	0.21	-	nuc	0	Plastid; chloroplast				77
Q95GM7 UniProt NPD GO	IF1C_CORMA	Translation initiation factor IF-1, chloroplast	0.21	-	nuc	0	Plastid; chloroplast				77
Q7ICQ5 UniProt NPD GO	IF1C_FOUSP	Translation initiation factor IF-1, chloroplast	0.21	-	nuc	0	Plastid; chloroplast				77
Q95GM4 UniProt NPD GO	IF1C_GAREL	Translation initiation factor IF-1, chloroplast	0.21	-	nuc	0	Plastid; chloroplast				77
Q95GN7 UniProt NPD GO	IF1C_ILLPA	Translation initiation factor IF-1, chloroplast	0.21	-	cyt	0	Plastid; chloroplast				80
Q332U2 UniProt NPD GO	IF1C_LACSA	Translation initiation factor IF-1, chloroplast	0.21	-	nuc	0	Plastid; chloroplast				77
Q94PL3 UniProt NPD GO	IF1C_MONCA	Translation initiation factor IF-1, chloroplast	0.21	-	nuc	0	Plastid; chloroplast				77
Q95GM5 UniProt NPD GO	IF1C_SAMCA	Translation initiation factor IF-1, chloroplast	0.21	-	nuc	0	Plastid; chloroplast				77
P40071 UniProt NPD GO	YEU3_YEAST	Transmembrane 9 superfamily protein YER113C precursor	0.21	-	end	10 *	Membrane; multi-pass membrane protein (Probable)	Golgi apparatus [IDA]			706

You are viewing entries 50101 to 50150 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.