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
O70536 UniProt NPD GO	SOAT1_RAT	Sterol O-acyltransferase 1 (EC 2.3.1.26) (Cholesterol acyltransferase 1) (Acyl coenzyme A:cholestero ...	0.31	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				545
Q94225 UniProt NPD GO	SULP3_CAEEL	Sulfate permease family protein 3	0.31	+	end	11 *	Membrane; multi-pass membrane protein (Potential)				782
P52286 UniProt NPD GO	SKP1_YEAST	Suppressor of kinetochore protein 1 (Centromere DNA-binding protein complex CBF3 subunit D) (E3 ubiq ...	0.31	-	nuc	0	Cytoplasm. Nucleus	CBF3 complex [TAS] cytoplasm [IDA] kinetochore [TAS] nuclear ubiquitin ligase complex [TAS] nucleus [IDA] RAVE complex [IPI] SCF ubiquitin ligase complex [IDA]		1NEX	193
O60073 UniProt NPD GO	YKT6_SCHPO	Synaptobrevin homolog ykt6	0.31	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				197
P24505 UniProt NPD GO	SY61_DISOM	Synaptotagmin A (Synaptic vesicle protein O-p65-A)	0.31	-	nuc	1	Synaptic vesicles in neurons				427
P34900 UniProt NPD GO	SDC2_RAT	Syndecan-2 precursor (SYND2) (Fibroglycan) (Heparan sulfate proteoglycan core protein) (HSPG)	0.31	-	end	1	Membrane; single-pass type I membrane protein				201
Q6P4W7 UniProt NPD GO	RIC8A_XENTR	Synembryn-A (Protein Ric-8A)	0.31	-	mit	0	Cytoplasm (By similarity)				539
Q62282 UniProt NPD GO	TAL2_MOUSE	T-cell acute lymphocytic leukemia-2 protein homolog (TAL-2 protein)	0.31	-	nuc	0					108
P30203 UniProt NPD GO	CD6_HUMAN	T-cell differentiation antigen CD6 precursor (T12) (TP120)	0.31	-	nuc	1	Membrane; single-pass type I membrane protein	cell surface [IEP] integral to plasma membrane [TAS]	186720		668
P07725 UniProt NPD GO	CD8A_RAT	T-cell surface glycoprotein CD8 alpha chain precursor (CD8 antigen 32 kDa chain) (OX-8 membrane anti ...	0.31	-	mit	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			236
P01731 UniProt NPD GO	CD8A_MOUSE	T-cell surface glycoprotein CD8 alpha chain precursor (T-cell surface glycoprotein Lyt-2) (CD8a anti ...	0.31	-	cyt	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA] T cell receptor complex [ISS]		2ATP	247
P20937 UniProt NPD GO	LY49A_MOUSE	T-cell surface glycoprotein YE1/48 (T lymphocyte antigen A1) (Ly49-A antigen) (Lymphocyte antigen 49 ...	0.31	-	nuc	1 *	Membrane; single-pass type II membrane protein	external side of plasma membrane [IDA] plasma membrane [TAS]		1QO3	262
P42082 UniProt NPD GO	CD86_MOUSE	T-lymphocyte activation antigen CD86 precursor (Activation B7-2 antigen) (Early T-cell costimulatory ...	0.31	-	nuc	2 *	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			309
P37173 UniProt NPD GO	TGFR2_HUMAN	TGF-beta receptor type-2 precursor (EC 2.7.11.30) (TGF-beta receptor type II) (TGFR-2) (TGF-beta typ ...	0.31	-	nuc	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS]	133239	1PLO	567
Q86V81 UniProt NPD GO	THOC4_HUMAN	THO complex subunit 4 (Tho4) (Ally of AML-1 and LEF-1) (Transcriptional coactivator Aly/REF) (bZIP-e ...	0.31	+	nuc	0	Nucleus. Cytoplasm. Travels to the cytoplasm as part of the exon junction complex (EJC) bound to mRN ...		604171		256
O08583 UniProt NPD GO	THOC4_MOUSE	THO complex subunit 4 (Tho4) (RNA and export factor-binding protein 1) (REF1-I) (Ally of AML-1 and L ...	0.31	+	nuc	0	Nucleus. Cytoplasm. Travels to the cytoplasm as part of the exon junction complex (EJC) bound to mRN ...	nucleus [TAS]		1NO8	254
Q9BTF0 UniProt NPD GO	THUM2_HUMAN	THUMP domain-containing protein 2	0.31	+	mit	0					473
Q9BVV7 UniProt NPD GO	TI21L_HUMAN	TIM21-like protein, mitochondrial precursor	0.31	-	nuc	1	Mitochondrion; mitochondrial membrane; single-pass membrane protein (Potential)				248
P39428 UniProt NPD GO	TRAF1_MOUSE	TNF receptor-associated factor 1	0.31	-	nuc	0	Cytoplasm				409
Q9V6G5 UniProt NPD GO	TAZ_DROME	Tafazzin homolog	0.31	-	nuc	1	Membrane; single-pass membrane anchor (By similarity). Isoforms with hydrophobic N-terminus are thou ...	integral to membrane [NAS]			378
Q80Z71 UniProt NPD GO	TENN_MOUSE	Tenascin-N precursor (TN-N)	0.31	-	vac	0		cell surface [IDA] extracellular matrix (sensu Metazoa) [IDA]			1560
P49744 UniProt NPD GO	TSP4_RAT	Thrombospondin-4 precursor	0.31	-	nuc	0		extracellular matrix (sensu Metazoa) [IDA]			980
P81834 UniProt NPD GO	TL16_SPIOL	Thylakoid lumenal 13.3 kDa protein (P16.5) (Fragment)	0.31	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen				30
Q9N0C5 UniProt NPD GO	KITM_MACFA	Thymidine kinase 2, mitochondrial precursor (EC 2.7.1.21) (Mt-TK)	0.31	-	mit	0	Mitochondrion (By similarity)				265
P60979 UniProt NPD GO	TX13_KUKHI	Toxin DW13.3	0.31	-	nuc	0	Secreted protein				74
Q8N8G2 UniProt NPD GO	VGLL2_HUMAN	Transcription cofactor vestigial-like protein 2 (Vgl-2) (Protein VITO1)	0.31	-	nuc	0	Nucleus (By similarity)				317
Q8LCQ3 UniProt NPD GO	SPT41_ARATH	Transcription elongation factor SPT4 homolog 1	0.31	-	cyt	0	Nucleus (By similarity)				116
O73741 UniProt NPD GO	COE2_XENLA	Transcription factor COE2 (xCOE2) (Olf-1/EBF-like 3) (OE-3) (xOE-3)	0.31	-	nuc	0	Nucleus (Potential)				574
Q9Y603 UniProt NPD GO	ETV7_HUMAN	Transcription factor ETV7 (Transcription factor Tel-2) (ETS-related protein Tel2) (Tel-related Ets f ...	0.31	-	nuc	0	Nucleus	nucleus [TAS]	605255		341
P29052 UniProt NPD GO	TF2B_DROME	Transcription initiation factor IIB (General transcription factor TFIIB)	0.31	-	nuc	0	Nucleus				315
O35295 UniProt NPD GO	PURB_MOUSE	Transcriptional activator protein Pur-beta (Purine-rich element-binding protein B) (Vascular actin s ...	0.31	-	cyt	0	Nucleus	DNA replication factor A complex [IDA] nuclear chromosome, telomeric region [ISS] nucleus [ISS]			323
Q9WVA4 UniProt NPD GO	TAGL2_MOUSE	Transgelin-2	0.31	-	nuc	0					211
Q9NQA5 UniProt NPD GO	TRPV5_HUMAN	Transient receptor potential cation channel subfamily V member 5 (TrpV5) (osm-9-like TRP channel 3) ...	0.31	-	end	7	Cell membrane; apical cell membrane; multi-pass membrane protein. Colocalized with S100A10 and ANAX2 ...	integral to plasma membrane [IDA]	606679		729
P46618 UniProt NPD GO	IF1C_MAIZE	Translation initiation factor IF-1, chloroplast	0.31	-	nuc	0	Plastid; chloroplast				107
P58272 UniProt NPD GO	IF1C_WHEAT	Translation initiation factor IF-1, chloroplast	0.31	-	nuc	0	Plastid; chloroplast				113
Q28690 UniProt NPD GO	EI2BB_RABIT	Translation initiation factor eIF-2B subunit beta (eIF-2B GDP-GTP exchange factor subunit beta)	0.31	-	cyt	0					351
Q13144 UniProt NPD GO	EI2BE_HUMAN	Translation initiation factor eIF-2B subunit epsilon (eIF-2B GDP-GTP exchange factor subunit epsilon ...	0.31	-	cyt	0			603945		721
Q9JMG3 UniProt NPD GO	TMUB1_MOUSE	Transmembrane and ubiquitin-like domain-containing protein 1	0.31	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				245
Q5S248 UniProt NPD GO	TM11E_MOUSE	Transmembrane protease, serine 11E precursor (EC 3.4.21.-) (Serine protease DESC1) [Contains: Transm ...	0.31	-	exc	2 *	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein. Activated by ...	integral to plasma membrane [IDA] plasma membrane [IDA]			442
Q6AYA5 UniProt NPD GO	T106B_RAT	Transmembrane protein 106B	0.31	-	mit	1	Membrane; single-pass membrane protein (Potential)				275
Q947R4 UniProt NPD GO	GL1_ARALY	Trichome differentiation protein GL1 (GLABROUS1 protein)	0.31	-	nuc	0	Nucleus (By similarity)				223
Q8IYM9 UniProt NPD GO	TRI22_HUMAN	Tripartite motif-containing protein 22 (RING finger protein 94) (50 kDa-stimulated trans-acting fact ...	0.31	-	nuc	0		nucleus [TAS]	606559		498
Q5RFL1 UniProt NPD GO	TPP1_PONPY	Tripeptidyl-peptidase 1 precursor (EC 3.4.14.9) (Tripeptidyl-peptidase I) (TPP-I) (Tripeptidyl amino ...	0.31	-	vac	0	Lysosome (By similarity)				564
P49455 UniProt NPD GO	TPM4_DROME	Tropomyosin 1, isoforms 33/34 (Tropomyosin II)	0.31	-	nuc	0					518
Q65Z91 UniProt NPD GO	TSK_CHICK	Tsukushi precursor (C-TSK) (Leucine-rich repeat-containing protein 54)	0.31	-	exc	0	Secreted protein (Potential)				369
P54405 UniProt NPD GO	TBG_RETFI	Tubulin gamma chain (Gamma tubulin)	0.31	-	mit	0					478
Q14166 UniProt NPD GO	TTL12_HUMAN	Tubulin--tyrosine ligase-like protein 12	0.31	-	cyt	0					644
Q8MKG8 UniProt NPD GO	TNFA_SAISC	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.31	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
Q95212 UniProt NPD GO	TPD52_RABIT	Tumor protein D52 (28 kDa calcium-dependent phosphoprotein) (pp28)	0.31	-	nuc	0		cytoplasm [ISS] endoplasmic reticulum [ISS] perinuclear region [ISS]			184
Q9CYZ2 UniProt NPD GO	TPD54_MOUSE	Tumor protein D54 (Tumor protein D52-like 2)	0.31	-	nuc	0		cytoplasm [ISS] perinuclear region [ISS]			220

You are viewing entries 39901 to 39950 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.