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
P48018 UniProt NPD GO	SYT1_BOVIN	Synaptotagmin-1 (Synaptotagmin I) (SytI) (p65)	0.30	-	nuc	1	Synaptic vesicles and chromaffin granules				422
P47191 UniProt NPD GO	SYT1_CHICK	Synaptotagmin-1 (Synaptotagmin I) (SytI) (p65)	0.30	-	nuc	1	Synaptic vesicles and chromaffin granules				424
P21579 UniProt NPD GO	SYT1_HUMAN	Synaptotagmin-1 (Synaptotagmin I) (SytI) (p65)	0.30	-	nuc	1	Synaptic vesicles and chromaffin granules	synaptic vesicle [TAS]	185605		422
Q642H7 UniProt NPD GO	RIC8A_BRARE	Synembryn-A (Protein Ric-8A)	0.30	-	cyt	0	Cytoplasm (By similarity)				548
Q9ZQZ8 UniProt NPD GO	SY123_ARATH	Syntaxin-123 (AtSYP123)	0.30	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				305
Q8VZU2 UniProt NPD GO	SY132_ARATH	Syntaxin-132 (AtSYP132)	0.30	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				304
P50283 UniProt NPD GO	CD7_MOUSE	T-cell antigen CD7 precursor	0.30	-	end	1	Membrane; single-pass type I membrane protein				210
P56280 UniProt NPD GO	TCL1A_MOUSE	T-cell leukemia/lymphoma protein 1A (P14 TCL1 protein) (TCL1 oncogene) (TCL-1 protein)	0.30	-	cyt	0	Microsome (By similarity). Microsomal fraction (By similarity)	cell cortex [IDA] pronucleus [IDA]		1JNP	116
Q9XSM7 UniProt NPD GO	CD8B_SAISC	T-cell surface glycoprotein CD8 beta chain precursor (CD8b antigen)	0.30	-	end	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			209
P39078 UniProt NPD GO	TCPD_YEAST	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta)	0.30	-	nuc	0	Cytoplasm	chaperonin-containing T-complex [IPI] cytoplasm [TAS] cytoskeleton [TAS]			528
Q3T0K2 UniProt NPD GO	TCPG_BOVIN	T-complex protein 1 subunit gamma (TCP-1-gamma) (CCT-gamma)	0.30	-	cyt	0	Cytoplasm (By similarity)				545
P49368 UniProt NPD GO	TCPG_HUMAN	T-complex protein 1 subunit gamma (TCP-1-gamma) (CCT-gamma) (hTRiC5)	0.30	-	cyt	0	Cytoplasm	cytoskeleton [TAS]	600114		545
P46272 UniProt NPD GO	TBP_ACECL	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.30	-	cyt	0	Nucleus				191
Q5U2X7 UniProt NPD GO	TI21L_RAT	TIM21-like protein, mitochondrial precursor	0.30	-	mit	1	Mitochondrion; mitochondrial membrane; single-pass membrane protein (Potential)				245
Q646E8 UniProt NPD GO	TA2R3_PAPHA	Taste receptor type 2 member 3 (T2R3)	0.30	-	end	7 *	Membrane; multi-pass membrane protein				315
P14202 UniProt NPD GO	TEGU_SCHMA	Tegument antigen (I(H)A) (Antigen SmA22.6) (A12)	0.30	-	nuc	0					190
O54863 UniProt NPD GO	TSSK2_MOUSE	Testis-specific serine/threonine-protein kinase 2 (EC 2.7.11.1) (TSSK-2) (Testis-specific kinase 2) ...	0.30	-	nuc	0	Cytoplasm				357
P07996 UniProt NPD GO	TSP1_HUMAN	Thrombospondin-1 precursor	0.30	-	nuc	0		extracellular region [NAS]	188060	2ERF	1170
Q9SW33 UniProt NPD GO	TL1Y_ARATH	Thylakoid lumenal 17.9 kDa protein, chloroplast precursor	0.30	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen				225
Q5REL7 UniProt NPD GO	TCO2_PONPY	Transcobalamin-2 precursor (Transcobalamin II) (TCII) (TC II)	0.30	-	exc	0	Secreted protein				427
P07273 UniProt NPD GO	TFS2_YEAST	Transcription elongation factor S-II (DNA strand transfer protein alpha) (STP-alpha) (DNA strand tra ...	0.30	+	nuc	0	Nucleus	nucleoplasm [IPI]		1Y1Y	309
Q9HAK2 UniProt NPD GO	COE2_HUMAN	Transcription factor COE2 (Early B-cell factor 2) (EBF-2) (Fragment)	0.30	-	nuc	0	Nucleus (Potential)		609934		343
O08792 UniProt NPD GO	COE2_MOUSE	Transcription factor COE2 (Early B-cell factor 2) (EBF-2) (Olf-1/EBF-like 3) (OE-3) (O/E-3) (Metence ...	0.30	-	nuc	0	Nucleus (Potential)				575
Q8C092 UniProt NPD GO	TAF5_MOUSE	Transcription initiation factor TFIID subunit 5 (Transcription initiation factor TFIID 100 kDa subun ...	0.30	+	nuc	0	Nucleus (By similarity)				801
O13282 UniProt NPD GO	TAF5_SCHPO	Transcription initiation factor TFIID subunit 5 (Transcription initiation factor TFIID 72 kDa subuni ...	0.30	-	cyt	0	Nucleus (By similarity)	SLIK (SAGA-like) complex [IDA] transcription factor TFIID complex [IDA]			643
Q96QR8 UniProt NPD GO	PURB_HUMAN	Transcriptional activator protein Pur-beta (Purine-rich element-binding protein B)	0.30	-	cyt	0	Nucleus	DNA replication factor A complex [ISS]	608887		311
Q68A21 UniProt NPD GO	PURB_RAT	Transcriptional activator protein Pur-beta (Purine-rich element-binding protein B)	0.30	-	cyt	0	Nucleus (By similarity)	DNA replication factor A complex [ISS]			314
Q95GM9 UniProt NPD GO	IF1C_BREMA	Translation initiation factor IF-1, chloroplast	0.30	-	nuc	0	Plastid; chloroplast				77
Q6L367 UniProt NPD GO	IF1C_SACHY	Translation initiation factor IF-1, chloroplast	0.30	-	nuc	0	Plastid; chloroplast				107
Q6ENS9 UniProt NPD GO	IF1C_SACOF	Translation initiation factor IF-1, chloroplast	0.30	-	nuc	0	Plastid; chloroplast				107
O13787 UniProt NPD GO	SEC62_SCHPO	Translocation protein sec62	0.30	-	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				273
Q8R4Z9 UniProt NPD GO	MFN1_RAT	Transmembrane GTPase MFN1 (EC 3.6.5.-) (Mitofusin-1) (Mitochondrial transmembrane GTPase FZO1B)	0.30	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				741
Q9CZH7 UniProt NPD GO	TMAP1_MOUSE	Transmembrane anchor protein 1	0.30	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				178
Q5XKA6 UniProt NPD GO	TM55B_XENLA	Transmembrane protein 55B (EC 3.1.3.-) (Type I phosphatidylinositol 4,5-bisphosphate 4-phosphatase) ...	0.30	-	nuc	2	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity). Lysos ...				281
Q810I1 UniProt NPD GO	TRI50_RAT	Tripartite motif-containing protein 50	0.30	-	cyt	0					483
Q4R8Y9 UniProt NPD GO	TPBG_MACFA	Trophoblast glycoprotein precursor	0.30	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				420
Q7M3Y8 UniProt NPD GO	TPM_TURCO	Tropomyosin (Major allergen Tur c 1) (Fragments)	0.30	-	nuc	0					146
P09941 UniProt NPD GO	ID5A_ADEPA	Trypsin inhibitor DE5, alpha chain	0.30	-	nuc	0					138
P02556 UniProt NPD GO	TBB_LYTPI	Tubulin beta chain (Beta tubulin) (Fragment)	0.30	-	mit	0					177
P29512 UniProt NPD GO	TBB2_ARATH	Tubulin beta-2/beta-3 chain	0.30	-	cyt	0					450
P48428 UniProt NPD GO	TBCA_MOUSE	Tubulin-specific chaperone A (Tubulin-folding cofactor A) (CFA) (TCP1-chaperonin cofactor A)	0.30	-	nuc	0					107
Q9BTW9 UniProt NPD GO	TBCD_HUMAN	Tubulin-specific chaperone D (Tubulin-folding cofactor D) (Beta-tubulin cofactor D) (tfcD) (SSD-1)	0.30	-	nuc	0			604649		1192
Q99MV1 UniProt NPD GO	TDRD1_MOUSE	Tudor domain-containing protein 1	0.30	-	cyt	0		cytoplasm [IDA] polar granule [IDA]			928
P41047 UniProt NPD GO	TNFL6_MOUSE	Tumor necrosis factor ligand superfamily member 6 (Fas antigen ligand) (Fas ligand) (CD178 antigen) ...	0.30	-	nuc	1	Isoform FASL: Cell membrane; single-pass type II membrane protein. Isoform FASLS, processed isoform ...				279
Q9BDN4 UniProt NPD GO	TNR6_CERTO	Tumor necrosis factor receptor superfamily member 6 precursor (FASLG receptor) (Apoptosis-mediating ...	0.30	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				331
Q6IBS0 UniProt NPD GO	TWF2_HUMAN	Twinfilin-2 (Twinfilin-1-like protein) (A6-related protein) (hA6RP) (Protein tyrosine kinase 9-like) ...	0.30	-	cyt	0	Cytoplasm. Cytoplasm; perinuclear region. Perinuclear and G-actin-rich cortical actin structures sub ...		607433		349
P08631 UniProt NPD GO	HCK_HUMAN	Tyrosine-protein kinase HCK (EC 2.7.10.2) (p59-HCK/p60-HCK) (Hemopoietic cell kinase)	0.30	-	nuc	0	Isoform p60-HCK, isoform p59-HCK: Membrane; lipid-anchor. Isoform p60-HCK: Cytoplasm		142370	5HCK	525
Q00993 UniProt NPD GO	UFO_MOUSE	Tyrosine-protein kinase receptor UFO precursor (EC 2.7.10.1) (Adhesion-related kinase)	0.30	-	end	1	Membrane; single-pass type I membrane protein				888
P49445 UniProt NPD GO	PTN7_RAT	Tyrosine-protein phosphatase non-receptor type 7 (EC 3.1.3.48) (Protein-tyrosine phosphatase LC-PTP) ...	0.30	-	nuc	0	Cytoplasm (By similarity)	cytosol [IDA]			359
O46631 UniProt NPD GO	SHPS1_BOVIN	Tyrosine-protein phosphatase non-receptor type substrate 1 precursor (SHP substrate 1) (SHPS-1) (Inh ...	0.30	-	nuc	1	Membrane; single-pass type I membrane protein				506

You are viewing entries 40801 to 40850 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.