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
P27084 UniProt NPD GO	SODM_PEA	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.05	-	mit	0	Mitochondrion; mitochondrial matrix				233
O75007 UniProt NPD GO	SODM_PENCH	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				210
Q6UW10 UniProt NPD GO	SFTPG_HUMAN	Surfactant-associated protein G precursor	0.05	-	exc	0	Secreted protein (Probable)				78
Q63564 UniProt NPD GO	SV2B_RAT	Synaptic vesicle glycoprotein 2B (Synaptic vesicle protein 2B)	0.05	-	end	12	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein. Associated with synaptic-l ...	membrane [IDA] synaptic vesicle [IDA]			683
Q27963 UniProt NPD GO	VMAT2_BOVIN	Synaptic vesicular amine transporter (Monoamine transporter) (Vesicular amine transporter 2) (VAT2) ...	0.05	-	end	11 *	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein				517
P36015 UniProt NPD GO	YKT6_YEAST	Synaptobrevin homolog YKT6	0.05	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	membrane [IDA] mitochondrion [IDA] soluble fraction [IDA] vacuole (sensu Fungi) [IDA]		1IOU	200
P57105 UniProt NPD GO	SYJ2B_HUMAN	Synaptojanin-2-binding protein (Mitochondrial outer membrane protein 25)	0.05	-	nuc	1	Mitochondrion; mitochondrial outer membrane (By similarity)				145
P81214 UniProt NPD GO	CARP_SYNRA	Syncephapepsin precursor (EC 3.4.23.-)	0.05	-	end	0					395
P49416 UniProt NPD GO	SDC4_CHICK	Syndecan-4 precursor	0.05	-	end	1	Membrane; single-pass type I membrane protein				197
Q9JI92 UniProt NPD GO	SDCB1_RAT	Syntenin-1 (Syndecan-binding protein 1)	0.05	-	cyt	1	Membrane; peripheral membrane protein (By similarity)	adherens junction [ISS] cytoskeleton [ISS] interleukin-5 receptor complex [ISS] membrane [ISS] nucleus [ISS]			300
P06324 UniProt NPD GO	TVC3_MOUSE	T-cell receptor gamma chain V region DFL12 precursor	0.05	-	end	0					132
P01740 UniProt NPD GO	TVC1_MOUSE	T-cell receptor gamma chain V region V108A precursor	0.05	-	end	0					135
P29017 UniProt NPD GO	CD1C_HUMAN	T-cell surface glycoprotein CD1c precursor (CD1c antigen)	0.05	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	188340		333
Q28072 UniProt NPD GO	CD3D_BOVIN	T-cell surface glycoprotein CD3 delta chain precursor (T-cell receptor T3 delta chain) (Fragment)	0.05	-	exc	0	Membrane; single-pass type I membrane protein				59
Q9TUF9 UniProt NPD GO	CD3E_RABIT	T-cell surface glycoprotein CD3 epsilon chain precursor	0.05	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				198
Q32L40 UniProt NPD GO	TCPA_BOVIN	T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha)	0.05	-	cyt	0	Cytoplasm (By similarity)				556
P12613 UniProt NPD GO	TCPA_DROME	T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha)	0.05	-	mit	0	Cytoplasm	proton-transporting ATP synthase complex (s... [NAS]			557
Q9W790 UniProt NPD GO	TCPA_PALPA	T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha)	0.05	-	cyt	0	Cytoplasm (By similarity)				559
Q94757 UniProt NPD GO	TCPA_SCHMA	T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha)	0.05	-	nuc	0	Cytoplasm				545
P11984 UniProt NPD GO	TCPA1_MOUSE	T-complex protein 1 subunit alpha A (TCP-1-alpha) (CCT-alpha) (Tailless complex polypeptide 1A) (TCP ...	0.05	-	cyt	0	Cytoplasm	chaperonin-containing T-complex [IDA] microtubule organizing center [IDA] nuclear heterochromatin [IDA] pericentriolar material [IDA]			556
P11983 UniProt NPD GO	TCPA2_MOUSE	T-complex protein 1 subunit alpha B (TCP-1-alpha) (CCT-alpha) (Tailless complex polypeptide 1B) (TCP ...	0.05	-	cyt	0	Cytoplasm	chaperonin-containing T-complex [IDA] microtubule organizing center [IDA] nuclear heterochromatin [IDA] pericentriolar material [IDA]			556
P26355 UniProt NPD GO	TBP_DICDI	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.05	-	mit	0	Nucleus				205
Q9R0X0 UniProt NPD GO	TRFP_MOUSE	TRF-proximal protein homolog	0.05	-	cyt	0	Nucleus (Probable)	Srb-mediator complex [ISS]			212
P81735 UniProt NPD GO	TRP3_LEUMA	Tachykinin-related peptide 3 (LemTRP 3)	0.05	-		0	Secreted protein				19
Q9R233 UniProt NPD GO	TPSN_MOUSE	Tapasin precursor (TPSN) (TPN) (TAP-binding protein) (TAP-associated protein)	0.05	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (Probable ...	integral to plasma membrane [TAS]			465
Q00762 UniProt NPD GO	A9_ARATH	Tapetum-specific protein A9 precursor	0.05	-	exc	0					91
Q49KI5 UniProt NPD GO	TS1R3_FELCA	Taste receptor type 1 member 3 precursor (Taste receptor T1R3)	0.05	-	end	7	Membrane; multi-pass membrane protein				865
Q9JKU0 UniProt NPD GO	T2R16_RAT	Taste receptor type 2 member 16 (T2R16) (T2R18) (T2R3)	0.05	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			299
Q646E9 UniProt NPD GO	T2R38_PAPHA	Taste receptor type 2 member 38 (T2R38)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				333
Q646G3 UniProt NPD GO	T2R42_PAPHA	Taste receptor type 2 member 42 (T2R42) (T2R55)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				314
Q645T3 UniProt NPD GO	T2R43_MACMU	Taste receptor type 2 member 43 (T2R43)	0.05	-	end	6 *	Membrane; multi-pass membrane protein				308
P59537 UniProt NPD GO	T2R43_HUMAN	Taste receptor type 2 member 43 (T2R43) (T2R52)	0.05	-	end	6 *	Membrane; multi-pass membrane protein				309
Q645Z6 UniProt NPD GO	T2R44_GORGO	Taste receptor type 2 member 44 (T2R44)	0.05	-	end	6 *	Membrane; multi-pass membrane protein				309
Q645Z7 UniProt NPD GO	T2R46_GORGO	Taste receptor type 2 member 46 (T2R46)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				309
P59540 UniProt NPD GO	T2R46_HUMAN	Taste receptor type 2 member 46 (T2R46) (T2R54)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				309
Q5Y4Y8 UniProt NPD GO	T2R66_PANPA	Taste receptor type 2 member 66 (T2R66)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				309
Q96GX1 UniProt NPD GO	TECT2_HUMAN	Tectonic-2 precursor	0.05	-	end	0	Membrane; single-pass type I membrane protein (Potential)				697
P48622 UniProt NPD GO	FAD3D_ARATH	Temperature-sensitive omega-3 fatty acid desaturase, chloroplast precursor (EC 1.14.19.-)	0.05	-	mit	3	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (Probable)				435
Q8VCF5 UniProt NPD GO	TSN10_MOUSE	Tetraspanin-10 (Tspan-10) (Oculospanin)	0.05	-	end	3	Membrane; multi-pass membrane protein (Potential)				331
P83957 UniProt NPD GO	TLP_CASCH	Thaumatin-like protein (Fragment)	0.05	-		0	Secreted protein (By similarity)				15
O80327 UniProt NPD GO	TLP1_PYRPY	Thaumatin-like protein 1 precursor	0.05	-	nuc	0	Secreted protein				244
P83335 UniProt NPD GO	TLP2_PRUPE	Thaumatin-like protein 2 precursor (PpAZ8)	0.05	-	exc	0	Secreted protein (Potential)				242
P50699 UniProt NPD GO	TLPH_ARATH	Thaumatin-like protein precursor	0.05	-	nuc	1 *					243
Q8MKF1 UniProt NPD GO	THTPA_BOVIN	Thiamine-triphosphatase (EC 3.6.1.28) (ThTPase)	0.05	-	nuc	0	Cytoplasm				218
Q9XGS0 UniProt NPD GO	TRXM_BRANA	Thioredoxin M-type, chloroplast precursor (TRX-M)	0.05	-	nuc	0	Plastid; chloroplast				177
Q8NBS9 UniProt NPD GO	TXND5_HUMAN	Thioredoxin domain-containing protein 5 precursor (Thioredoxin-like protein p46) (Endoplasmic reticu ...	0.05	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum [TAS]			432
Q9D531 UniProt NPD GO	CI121_MOUSE	Thioredoxin domain-containing protein C9orf121 homolog	0.05	-	mit	0					156
O62768 UniProt NPD GO	TRXR1_BOVIN	Thioredoxin reductase 1, cytoplasmic (EC 1.8.1.9) (TR) (TR1)	0.05	-	cyt	0	Cytoplasm (By similarity)				499
Q16881 UniProt NPD GO	TRXR1_HUMAN	Thioredoxin reductase 1, cytoplasmic precursor (EC 1.8.1.9) (TR) (TR1)	0.05	-	cyt	0	Cytoplasm (By similarity)		601112	2CFY	499
Q9N2I8 UniProt NPD GO	TRXR2_BOVIN	Thioredoxin reductase 2, mitochondrial precursor (EC 1.8.1.9) (TR3)	0.05	-	mit	0	Mitochondrion	mitochondrion [IEP]			511

You are viewing entries 75751 to 75800 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.