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
P68417 UniProt NPD GO	NXS1_NAJHA	Short neurotoxin 1 (Neurotoxin alpha)	0.39	-	nuc	0	Secreted protein				61
P68419 UniProt NPD GO	NXS1_NAJNI	Short neurotoxin 1 (Neurotoxin delta)	0.39	-	nuc	0	Secreted protein				61
P68418 UniProt NPD GO	NXS1_NAJHH	Short neurotoxin 1 (Toxin CM-6)	0.39	-	nuc	0	Secreted protein				61
P10458 UniProt NPD GO	NXSC_LATCR	Short neurotoxin C	0.39	-	nuc	0	Secreted protein				62
Q9QZC1 UniProt NPD GO	TRPC3_MOUSE	Short transient receptor potential channel 3 (TrpC3) (Transient receptor protein 3) (Mtrp3) (Recepto ...	0.39	-	end	6	Membrane; multi-pass membrane protein (Probable)				836
O04433 UniProt NPD GO	SRP14_ORYSA	Signal recognition particle 14 kDa protein (SRP14)	0.39	-	nuc	0	Cytoplasm				132
P49968 UniProt NPD GO	SR541_HORVU	Signal recognition particle 54 kDa protein 1 (SRP54)	0.39	-	mit	0	Cytoplasm				497
P38985 UniProt NPD GO	SRP14_YEAST	Signal recognition particle subunit SRP14 (Signal recognition particle 14 kDa protein homolog)	0.39	-	nuc	0	Cytoplasm (By similarity). Nucleus	signal recognition particle (sensu Eukaryota) [IDA]			146
Q80XL1 UniProt NPD GO	CBLC_MOUSE	Signal transduction protein CBL-C (SH3-binding protein CBL-C) (CBL-3)	0.39	-	nuc	0	Nucleus (Potential)				496
Q9HAU4 UniProt NPD GO	SMUF2_HUMAN	Smad ubiquitination regulatory factor 2 (EC 6.3.2.-) (Ubiquitin--protein ligase SMURF2) (Smad-specif ...	0.39	-	mit	0	Nucleus. Cytoplasm. Cytoplasmic in the presence of SMAD7	nucleus [NAS] ubiquitin ligase complex [IDA]	605532	2DJY	748
O89093 UniProt NPD GO	CCL20_MOUSE	Small inducible cytokine A20 precursor (CCL20) (Macrophage inflammatory protein 3 alpha) (MIP-3-alph ...	0.39	-	exc	0	Secreted protein			1HA6	97
Q4PR21 UniProt NPD GO	CCL25_PIG	Small inducible cytokine A25 precursor (CCL25) (Chemokine ligand 25)	0.39	-	exc	0	Secreted protein (By similarity)				151
P51670 UniProt NPD GO	CCL9_MOUSE	Small inducible cytokine A9 precursor (CCL9) (Macrophage inflammatory protein 1-gamma) (MIP-1-gamma) ...	0.39	-	exc	0	Secreted protein				122
P48973 UniProt NPD GO	SCYBA_RAT	Small inducible cytokine B10 precursor (CXCL10) (Interferon-inducible protein 10) (Gamma-IP10) (IP-1 ...	0.39	-	exc	1 *	Secreted protein	extracellular region [TAS]			98
Q9DC77 UniProt NPD GO	SMPX_MOUSE	Small muscular protein (Stretch-responsive skeletal muscle protein) (Chisel protein)	0.39	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			85
P48763 UniProt NPD GO	SL9A2_RAT	Sodium/hydrogen exchanger 2 (Na(+)/H(+) exchanger 2) (NHE-2) (Solute carrier family 9 member 2) (H7) ...	0.39	-	end	11 *	Membrane; multi-pass membrane protein	apical plasma membrane [TAS]			813
Q9JJL3 UniProt NPD GO	SO1B2_MOUSE	Solute carrier organic anion transporter family member 1B2 (Solute carrier family 21 member 10) (Liv ...	0.39	-	end	12 *	Membrane; multi-pass membrane protein				689
Q9GMB3 UniProt NPD GO	SOMA_CALJA	Somatotropin precursor (Growth hormone)	0.39	-	vac	0	Secreted protein				217
P10298 UniProt NPD GO	SOMA_CYPCA	Somatotropin precursor (Growth hormone)	0.39	-	nuc	0	Secreted protein				210
Q05163 UniProt NPD GO	SOMA_DICLA	Somatotropin precursor (Growth hormone)	0.39	-	exc	0	Secreted protein				204
O12980 UniProt NPD GO	SOMA_FUGRU	Somatotropin precursor (Growth hormone)	0.39	-	exc	0	Secreted protein				196
P08591 UniProt NPD GO	SOMA_PAGMA	Somatotropin precursor (Growth hormone)	0.39	-	exc	0	Secreted protein				203
P58343 UniProt NPD GO	SOMA_SAIBB	Somatotropin precursor (Growth hormone)	0.39	-	mit	0	Secreted protein				217
P01241 UniProt NPD GO	SOMA_HUMAN	Somatotropin precursor (Growth hormone) (GH) (GH-N) (Pituitary growth hormone) (Growth hormone 1)	0.39	-	exc	0	Secreted protein		139250	3HHR	217
P33093 UniProt NPD GO	SOMA_MACMU	Somatotropin precursor (Growth hormone) (GH) (GH-N) (Pituitary growth hormone) (Growth hormone 1)	0.39	-	exc	0	Secreted protein				217
P58756 UniProt NPD GO	SOMA_PANTR	Somatotropin precursor (Growth hormone) (GH) (GH-N) (Pituitary growth hormone) (Growth hormone 1)	0.39	-	exc	0	Secreted protein				217
Q9Y5X1 UniProt NPD GO	SNX9_HUMAN	Sorting nexin-9 (SH3 and PX domain-containing protein 1) (SDP1 protein)	0.39	-	cyt	0			605952		595
Q8TC36 UniProt NPD GO	SPA4L_HUMAN	Sperm-associated antigen 4-like protein (Testis and spermatogenesis-related gene 4 protein)	0.39	-	nuc	0					379
Q8CFM6 UniProt NPD GO	STAB2_RAT	Stabilin-2 precursor (Hyaluronan receptor for endocytosis) [Contains: 175 kDa stabilin-2 (175 kDa hy ...	0.39	-	nuc	1	Cell membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			1431
P48932 UniProt NPD GO	DHSB_CHOCR	Succinate dehydrogenase [ubiquinone] iron-sulfur protein (EC 1.3.5.1) (IP)	0.39	-	nuc	0	Mitochondrion; mitochondrial inner membrane				250
P21914 UniProt NPD GO	DHSB_DROME	Succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (EC 1.3.5.1) (IP)	0.39	-	nuc	0	Mitochondrion; mitochondrial inner membrane				297
Q9Y2Z0 UniProt NPD GO	SUGT1_HUMAN	Suppressor of G2 allele of SKP1 homolog (Sgt1) (Putative 40-6-3 protein)	0.39	-	nuc	0		kinetochore [TAS] ubiquitin ligase complex [TAS]	604098	1RL1	364
Q5ZL77 UniProt NPD GO	RIC8A_CHICK	Synembryn-A (Protein Ric-8A)	0.39	-	cyt	0	Cytoplasm (By similarity)				539
Q9SF29 UniProt NPD GO	SYP71_ARATH	Syntaxin-71 (AtSYP71)	0.39	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				266
P31783 UniProt NPD GO	CD8A_BOVIN	T-cell surface glycoprotein CD8 alpha chain precursor (CD8a antigen)	0.39	+	end	3 *	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			242
P42071 UniProt NPD GO	CD86_RABIT	T-lymphocyte activation antigen CD86 precursor (Activation B7-2 antigen)	0.39	-	end	2 *	Membrane; single-pass type I membrane protein				330
O08811 UniProt NPD GO	ERCC2_MOUSE	TFIIH basal transcription factor complex helicase subunit (EC 3.6.1.-) (DNA-repair protein complemen ...	0.39	-	cyt	0	Nucleus	nucleus [ISS] transcription factor TFIIH complex [ISS]			760
Q9P2Z0 UniProt NPD GO	THA10_HUMAN	THAP domain-containing protein 10	0.39	-	nuc	0					257
Q645T7 UniProt NPD GO	TA2R7_MACMU	Taste receptor type 2 member 7 (T2R7)	0.39	-	end	7 *	Membrane; multi-pass membrane protein				318
Q645V8 UniProt NPD GO	TA2R7_PONPY	Taste receptor type 2 member 7 (T2R7)	0.39	-	end	7 *	Membrane; multi-pass membrane protein				318
Q9DBG9 UniProt NPD GO	TX1B3_MOUSE	Tax1-binding protein 3 (Tax interaction protein 1) (TIP-1)	0.39	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			124
O14907 UniProt NPD GO	TX1B3_HUMAN	Tax1-binding protein 3 (Tax interaction protein 1) (TIP-1) (Glutaminase-interacting protein 3)	0.39	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [NAS]			124
Q9VMH0 UniProt NPD GO	TECT_DROME	Tectonic precursor (dTectonic)	0.39	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				657
O64628 UniProt NPD GO	TXND9_ARATH	Thioredoxin domain-containing protein 9 homolog	0.39	+	nuc	0					211
O23403 UniProt NPD GO	TL215_ARATH	Thylakoid lumenal 21.5 kDa protein, chloroplast precursor	0.39	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen				287
Q9Y2X0 UniProt NPD GO	TR95_HUMAN	Thyroid hormone receptor-associated protein complex 95 kDa component (Trap95) (Thyroid hormone recep ...	0.39	-	cyt	0	Nucleus	mediator complex [IDA] nucleus [NAS]	604062		877
P35419 UniProt NPD GO	PERT_MOUSE	Thyroid peroxidase precursor (EC 1.11.1.8) (TPO)	0.39	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				914
P14763 UniProt NPD GO	TSHR_CANFA	Thyrotropin receptor precursor (TSH-R) (Thyroid-stimulating hormone receptor)	0.39	-	end	7	Membrane; multi-pass membrane protein				764
Q8SPP9 UniProt NPD GO	TSHR_PIG	Thyrotropin receptor precursor (TSH-R) (Thyroid-stimulating hormone receptor)	0.39	-	end	7	Membrane; multi-pass membrane protein				764
P42533 UniProt NPD GO	TF_RAT	Tissue factor precursor (TF) (Coagulation factor III) (CD142 antigen)	0.39	+	end	2 *	Membrane; single-pass type I membrane protein				295

You are viewing entries 33001 to 33050 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.