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
P00927 UniProt NPD GO	THDH_YEAST	Threonine dehydratase, mitochondrial precursor (EC 4.3.1.19) (Threonine deaminase)	0.07	-	nuc	0	Mitochondrion	mitochondrion [IDA]			576
P30987 UniProt NPD GO	TA2R_MOUSE	Thromboxane A2 receptor (TXA2-R) (Prostanoid TP receptor)	0.07	-	end	6 *	Membrane; multi-pass membrane protein				341
O46639 UniProt NPD GO	TRFR_BOVIN	Thyrotropin-releasing hormone receptor (TRH-R) (Thyroliberin receptor)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				398
Q28596 UniProt NPD GO	TRFR_SHEEP	Thyrotropin-releasing hormone receptor (TRH-R) (Thyroliberin receptor)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				398
Q9JLU8 UniProt NPD GO	TF_CAVPO	Tissue factor precursor (TF) (Coagulation factor III) (CD142 antigen)	0.07	-	end	1	Membrane; single-pass type I membrane protein				289
P25682 UniProt NPD GO	TX66_DENJA	Toxin S6C6	0.07	-	nuc	0	Secreted protein				63
Q5QD10 UniProt NPD GO	TAA7D_MOUSE	Trace amine-associated receptor 7d	0.07	-	end	7 *	Membrane; multi-pass membrane protein				358
Q923X5 UniProt NPD GO	TAA7D_RAT	Trace amine-associated receptor 7d (Trace amine receptor 15) (TaR-15)	0.07	-	end	6 *	Membrane; multi-pass membrane protein				358
Q9TZ93 UniProt NPD GO	SPT4H_CAEEL	Transcription elongation factor SPT4 (DRB sensitivity-inducing factor small subunit) (DSIF small sub ...	0.07	-	nuc	0	Nucleus (By similarity)				120
P83946 UniProt NPD GO	ATRY_MACEU	Transcriptional regulator ATRY (EC 3.6.1.-) (ATP-dependent helicase ATRY) (Fragments)	0.07	-	nuc	0	Nucleus (By similarity)				96
Q2V905 UniProt NPD GO	TFR1_HORSE	Transferrin receptor protein 1 (TfR1) (TR) (TfR) (Trfr) (CD71 antigen)	0.07	-	mit	1	Cell membrane; single-pass type II membrane (By similarity)				767
P31232 UniProt NPD GO	TAGL_RAT	Transgelin (Smooth muscle protein 22-alpha) (SM22-alpha)	0.07	-	nuc	0	Cytoplasm (Probable)				200
P37804 UniProt NPD GO	TAGL_MOUSE	Transgelin (Smooth muscle protein 22-alpha) (SM22-alpha) (Actin-associated protein p27)	0.07	-	nuc	0	Cytoplasm (Probable)			1UJO	200
P34736 UniProt NPD GO	TKT_PICST	Transketolase (EC 2.2.1.1) (TK)	0.07	-	cyt	1					695
P84540 UniProt NPD GO	TKT_POPEU	Transketolase (EC 2.2.1.1) (TK) (Fragment)	0.07	-		0					15
P23254 UniProt NPD GO	TKT1_YEAST	Transketolase 1 (EC 2.2.1.1) (TK 1)	0.07	-	cyt	0				1TRK	679
Q7SIC9 UniProt NPD GO	TKTC_MAIZE	Transketolase, chloroplast (EC 2.2.1.1) (TK)	0.07	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane (By similarity)			1ITZ	675
Q5SD15 UniProt NPD GO	IF1C_HUPLU	Translation initiation factor IF-1, chloroplast	0.07	-	nuc	0	Plastid; chloroplast				78
Q9DBU0 UniProt NPD GO	TM9S1_MOUSE	Transmembrane 9 superfamily protein member 1 precursor	0.07	-	end	9	Membrane; multi-pass membrane protein (Probable)				606
Q5R8F1 UniProt NPD GO	TM9S1_PONPY	Transmembrane 9 superfamily protein member 1 precursor	0.07	-	end	9	Membrane; multi-pass membrane protein (Probable)				606
Q90515 UniProt NPD GO	TMEDA_FUGRU	Transmembrane emp24 domain-containing protein 10 precursor (Transmembrane protein Tmp21) (S31III125) ...	0.07	-	end	2 *	Golgi apparatus; Golgi membrane; single-pass type I membrane protein; lumenal side (By similarity)				213
Q9BVC6 UniProt NPD GO	TM109_HUMAN	Transmembrane protein 109 precursor (Mitsugumin-23) (Mg23)	0.07	+	end	5 *	Nucleus; nuclear outer membrane; multi-pass membrane protein (By similarity). Endoplasmic reticulum; ...				243
O77751 UniProt NPD GO	TM109_RABIT	Transmembrane protein 109 precursor (Mitsugumin-23) (Mg23)	0.07	+	end	5 *	Nucleus; nuclear outer membrane; multi-pass membrane protein. Endoplasmic reticulum; endoplasmic ret ...				243
Q9Y6G1 UniProt NPD GO	TM14A_HUMAN	Transmembrane protein 14A	0.07	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				99
Q58CR4 UniProt NPD GO	TMM15_BOVIN	Transmembrane protein 15	0.07	-	end	14 *	Membrane; multi-pass membrane protein (Potential)				538
Q6PFT6 UniProt NPD GO	TMM47_BRARE	Transmembrane protein 47 (Transmembrane 4 superfamily member 10)	0.07	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				181
P17261 UniProt NPD GO	ERS1_YEAST	Transmembrane protein ERS1 (ERD suppressor)	0.07	-	end	6 *	Membrane; multi-pass membrane protein	endosome [IDA] vacuole [IDA]			260
P52875 UniProt NPD GO	TPARL_MOUSE	Transmembrane protein TPARL (TPA-regulated locus protein) (Transmembrane protein PFT27)	0.07	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				323
Q27173 UniProt NPD GO	T2A_PARTE	Trichocyst matrix protein T2-A (Secretory granule protein T2-A) (TMP 2-A) (Fragment)	0.07	-	nuc	0	Trichocyst. These are architecturally complex secretory storage granules-docked at the plasma membra ...				23
O13489 UniProt NPD GO	TRI5_MYRRO	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.07	-	cyt	0					385
P04828 UniProt NPD GO	TPIS_EMENI	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.07	-	cyt	0					249
Q96VN5 UniProt NPD GO	TPIS_PARBR	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.07	-	mit	0					249
P48501 UniProt NPD GO	TPIS_SCHMA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.07	-	mit	0	Cytoplasm (Probable)				253
P15159 UniProt NPD GO	TNNC_TACTR	Troponin C	0.07	-	cyt	0					153
P06707 UniProt NPD GO	TNNC1_PONLE	Troponin C, isotype alpha	0.07	-	cyt	0					150
P02588 UniProt NPD GO	TNNC2_CHICK	Troponin C, skeletal muscle	0.07	-	cyt	0				4TNC	162
P10246 UniProt NPD GO	TNNC2_MELGA	Troponin C, skeletal muscle	0.07	-	cyt	0				5TNC	162
P54626 UniProt NPD GO	TRYDG_DROER	Trypsin delta/gamma precursor (EC 3.4.21.4)	0.07	-	exc	0	Secreted protein; extracellular space				253
P10295 UniProt NPD GO	ITR2_MOMCH	Trypsin inhibitor 2 (Trypsin inhibitor II) (MCTI-II) (MCTI-A)	0.07	-	nuc	0	Secreted protein			1F2S	28
P35046 UniProt NPD GO	TRYB_MANSE	Trypsin, alkaline B precursor (EC 3.4.21.4)	0.07	-	exc	0	Secreted protein; extracellular space				256
P35047 UniProt NPD GO	TRYC_MANSE	Trypsin, alkaline C precursor (EC 3.4.21.4)	0.07	-	exc	0	Secreted protein; extracellular space				256
Q1XDA5 UniProt NPD GO	TRPA_PORYE	Tryptophan synthase alpha chain (EC 4.2.1.20)	0.07	-	nuc	0	Plastid; chloroplast				263
O50046 UniProt NPD GO	TRPB_CAMAC	Tryptophan synthase beta chain 2, chloroplast precursor (EC 4.2.1.20)	0.07	-	mit	0	Plastid; chloroplast (Probable)				466
Q9C413 UniProt NPD GO	TBA_GLOLA	Tubulin alpha chain (Alpha-tubulin)	0.07	-	cyt	0					454
P09733 UniProt NPD GO	TBA1_YEAST	Tubulin alpha-1 chain	0.07	-	cyt	0		cytoplasmic microtubule [TAS] kinetochore microtubule [TAS] nuclear microtubule [TAS] polar microtubule [TAS] spindle pole body [IDA]			447
P09643 UniProt NPD GO	TBA4_CHICK	Tubulin alpha-4 chain (Fragment)	0.07	-	cyt	0					322
Q52NY7 UniProt NPD GO	TBB_METAN	Tubulin beta chain (Beta tubulin)	0.07	-	cyt	0					448
P41388 UniProt NPD GO	TBB_VENIN	Tubulin beta chain (Beta tubulin)	0.07	-	cyt	0					447
P32971 UniProt NPD GO	TNFL8_HUMAN	Tumor necrosis factor ligand superfamily member 8 (CD30 ligand) (CD30-L) (CD153 antigen)	0.07	-	mit	1 *	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS]	603875		234
P41274 UniProt NPD GO	TNFL9_MOUSE	Tumor necrosis factor ligand superfamily member 9 (4-1BB ligand) (4-1BBL)	0.07	-	mit	1	Membrane; single-pass type II membrane protein				309

You are viewing entries 71151 to 71200 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.