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
Q9Y4I5 UniProt NPD GO	MTL5_HUMAN	Tesmin (Metallothionein-like 5, testis-specific) (Testis-specific metallothionein-like protein)	0.43	-	nuc	0			604374		299
Q9H6P5 UniProt NPD GO	TASP1_HUMAN	Threonine aspartase 1 (EC 3.4.25.-) (Taspase-1) [Contains: Threonine aspartase subunit alpha; Threon ...	0.43	+	cyt	0			608270	2A8M	420
Q08351 UniProt NPD GO	TPOR_MOUSE	Thrombopoietin receptor precursor (TPO-R) (Myeloproliferative leukemia protein) (C-mpl) (CD110 antig ...	0.43	-	exc	1	Membrane; single-pass type I membrane protein				625
O22773 UniProt NPD GO	TL16_ARATH	Thylakoid lumenal 16.5 kDa protein, chloroplast precursor	0.43	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				216
Q9QX05 UniProt NPD GO	TLR4_RAT	Toll-like receptor 4 precursor (Toll4) (CD284 antigen)	0.43	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]			835
O00206 UniProt NPD GO	TLR4_HUMAN	Toll-like receptor 4 precursor (hToll) (CD284 antigen)	0.43	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] lipopolysaccharide receptor complex [NAS]	603030		839
Q8BGW8 UniProt NPD GO	VGLL2_MOUSE	Transcription cofactor vestigial-like protein 2 (Vgl-2) (Protein VITO1)	0.43	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			322
P49373 UniProt NPD GO	TFS2_SCHPO	Transcription elongation factor S-II (TFIIS)	0.43	-	nuc	0	Nucleus (By similarity)				293
Q90595 UniProt NPD GO	MAFF_CHICK	Transcription factor MafF (V-maf musculoaponeurotic fibrosarcoma oncogene homolog F)	0.43	-	nuc	0	Nucleus				149
Q8VI67 UniProt NPD GO	SP7_MOUSE	Transcription factor Sp7 (Zinc finger protein osterix) (C22)	0.43	-	nuc	0	Nucleus	nucleus [IDA]			428
P48513 UniProt NPD GO	TF2B_SOYBN	Transcription initiation factor IIB (General transcription factor TFIIB)	0.43	-	nuc	0	Nucleus				313
P29083 UniProt NPD GO	T2EA_HUMAN	Transcription initiation factor IIE subunit alpha (TFIIE-alpha) (General transcription factor IIE 56 ...	0.43	-	cyt	0	Nucleus		189962	1VD4	439
Q09869 UniProt NPD GO	TAF9_SCHPO	Transcription initiation factor TFIID subunit 9 (TBP-associated factor 9)	0.43	-	nuc	0	Nucleus (By similarity)				163
O75762 UniProt NPD GO	TRPA1_HUMAN	Transient receptor potential cation channel subfamily A member 1 (Ankyrin-like with transmembrane do ...	0.43	-	end	5	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS]	604775		1119
Q9WTR1 UniProt NPD GO	TRPV2_MOUSE	Transient receptor potential cation channel subfamily V member 2 (TrpV2) (osm-9-like TRP channel 2) ...	0.43	-	end	6	Cell membrane; multi-pass membrane protein. Cytoplasm. Translocates from the cytoplasm to the plasma ...	plasma membrane [IDA]			756
P39742 UniProt NPD GO	SEC72_YEAST	Translocation protein SEC72 (Sec62/63 complex 23 kDa subunit) (p23)	0.43	-	cyt	0	Cytoplasm (Potential)	endoplasmic reticulum membrane [TAS] Sec62/Sec63 complex [IPI]			192
Q8R4P5 UniProt NPD GO	TMC1_MOUSE	Transmembrane cochlear-expressed protein 1 (Beethoven protein) (Deafness protein)	0.43	+	end	6	Membrane; multi-pass membrane protein (Potential)				757
Q9NQ90 UniProt NPD GO	TM16B_HUMAN	Transmembrane protein 16B	0.43	-	end	7	Membrane; multi-pass membrane protein (Probable)				999
P12258 UniProt NPD GO	HOBOT_DROME	Transposable element Hobo transposase	0.43	-	nuc	0	Nucleus				644
Q5TM55 UniProt NPD GO	TRI15_MACMU	Tripartite motif-containing protein 15	0.43	-	cyt	0					465
Q5REJ9 UniProt NPD GO	TRI54_PONPY	Tripartite motif-containing protein 54	0.43	-	nuc	0	Cytoplasm (By similarity). Associates with microtubules. Localizes to the Z-lines in skeletal muscle ...				358
Q9BYV2 UniProt NPD GO	TRI54_HUMAN	Tripartite motif-containing protein 54 (Muscle-specific RING finger protein 3) (MuRF3) (MURF-3) (Mus ...	0.43	-	nuc	0	Cytoplasm (By similarity). Associates with microtubules. Localizes to the Z-lines in skeletal muscle ...		606474		358
Q5XIH6 UniProt NPD GO	TRI54_RAT	Tripartite motif-containing protein 54 (RING finger protein 30)	0.43	-	nuc	0	Cytoplasm (By similarity). Associates with microtubules. Localizes to the Z-lines in skeletal muscle ...				364
Q9BRZ2 UniProt NPD GO	TRI56_HUMAN	Tripartite motif-containing protein 56 (RING finger protein 109)	0.43	-	nuc	0					755
O01673 UniProt NPD GO	TPM_ACAVI	Tropomyosin	0.43	-	nuc	0					284
Q8IT89 UniProt NPD GO	TPM_HAELO	Tropomyosin	0.43	-	nuc	0					284
Q9N2R3 UniProt NPD GO	TPM_CHAFE	Tropomyosin (Allergen Cha f 1) (Cha f I) (Fragment)	0.43	-	nuc	0					264
Q9NFZ4 UniProt NPD GO	TPM_LEPDS	Tropomyosin (Allergen Lep d 10)	0.43	-	nuc	0					284
Q25456 UniProt NPD GO	TPM_METEN	Tropomyosin (Allergen Met e 1) (Met e I)	0.43	-	nuc	0					274
P04268 UniProt NPD GO	TPM1_CHICK	Tropomyosin 1 alpha chain (Alpha-tropomyosin)	0.43	-	nuc	0				1IC2	284
P58773 UniProt NPD GO	TPM1_COTJA	Tropomyosin 1 alpha chain (Alpha-tropomyosin)	0.43	-	nuc	0					284
P09493 UniProt NPD GO	TPM1_HUMAN	Tropomyosin 1 alpha chain (Alpha-tropomyosin)	0.43	-	nuc	0		cytoskeleton [TAS] muscle thin filament tropomyosin [TAS]	192600		284
P38558 UniProt NPD GO	TBG2_ARATH	Tubulin gamma-2 chain (Gamma-2 tubulin)	0.43	-	nuc	0					474
Q9D777 UniProt NPD GO	TNF13_MOUSE	Tumor necrosis factor ligand superfamily member 13 precursor (A proliferation-inducing ligand) (APRI ...	0.43	-	nuc	1 *	Secreted protein (By similarity)	external side of plasma membrane [IDA]		1XU2	241
Q9BEA8 UniProt NPD GO	TNFL6_PIG	Tumor necrosis factor ligand superfamily member 6 (Fas antigen ligand) (Fas ligand) (CD178 antigen) ...	0.43	-	nuc	1	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				282
Q6IRE4 UniProt NPD GO	TS101_RAT	Tumor susceptibility gene 101 protein	0.43	-	nuc	0	Cytoplasm (By similarity). Mainly. Membrane; peripheral membrane protein (By similarity). Membrane-a ...				391
Q5I082 UniProt NPD GO	TWF1_XENTR	Twinfilin-1	0.43	-	cyt	0					350
P49897 UniProt NPD GO	IOD3_RAT	Type III iodothyronine deiodinase (EC 1.97.1.11) (Type-III 5'deiodinase) (DIOIII) (Type 3 DI) (5DIII ...	0.43	-	nuc	0	Cell membrane; single-pass type II membrane protein (By similarity). Endosome; endosomal membrane; s ...				278
Q6J9G0 UniProt NPD GO	STYK1_HUMAN	Tyrosine protein-kinase STYK1 (EC 2.7.10.2) (Serine/threonine/tyrosine kinase 1) (Novel oncogene wit ...	0.43	-	nuc	1 *	Cytoplasm (By similarity)				422
P41499 UniProt NPD GO	PTN11_RAT	Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) (Protein-tyrosine phosphatase SYP) ( ...	0.43	-	mit	0	Cytoplasm (By similarity)				597
Q4P5F9 UniProt NPD GO	RU2A_USTMA	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.43	-	nuc	0	Nucleus (By similarity)				246
Q3B8B2 UniProt NPD GO	COQ9A_XENLA	Ubiquinone biosynthesis protein COQ9-A, mitochondrial precursor	0.43	-	mit	0	Mitochondrion (By similarity)				317
Q5PPX7 UniProt NPD GO	COQ9B_XENLA	Ubiquinone biosynthesis protein COQ9-B, mitochondrial precursor	0.43	-	nuc	0	Mitochondrion (By similarity)				293
P45974 UniProt NPD GO	UBP5_HUMAN	Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.1.2.15) (Ubiquitin thioesterase 5) (Ubiquitin-specific ...	0.43	-	cyt	0		lysosome [TAS]	601447	2G45	858
P53044 UniProt NPD GO	UFD1_YEAST	Ubiquitin fusion degradation protein 1 (UB fusion protein 1) (Polymerase-interacting protein 3)	0.43	-	nuc	0		endoplasmic reticulum [IDA]		1ZC1	361
Q9I8X5 UniProt NPD GO	SIAH2_XENLA	Ubiquitin ligase SIAH2 (EC 6.3.2.-) (Seven in absentia homolog 2) (Xsiah-2)	0.43	-	nuc	0	Cytoplasm				313
Q80XK6 UniProt NPD GO	CN103_MOUSE	Uncharacterized protein C14orf103 homolog	0.43	-	nuc	0					908
Q8BRE0 UniProt NPD GO	CA036_MOUSE	Uncharacterized protein C1orf36 homolog	0.43	-	mit	0					195
P38177 UniProt NPD GO	YBI6_YEAST	Uncharacterized protein YBL086C	0.43	-	nuc	0					466
Q07349 UniProt NPD GO	YD027_YEAST	Uncharacterized protein YDL027C	0.43	-	end	2	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			420

You are viewing entries 30051 to 30100 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.