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
Q8VE65 UniProt NPD GO	TAF12_MOUSE	Transcription initiation factor TFIID subunit 12 (Transcription initiation factor TFIID 20 kDa subun ...	0.47	-	nuc	0	Nucleus (By similarity)				161
Q9HBM6 UniProt NPD GO	TAF9B_HUMAN	Transcription initiation factor TFIID subunit 9B (Transcription initiation factor TFIID subunit 9-li ...	0.47	-	nuc	0	Nucleus (By similarity)				251
Q8BTH6 UniProt NPD GO	SCRT2_MOUSE	Transcriptional repressor scratch 2 (Scratch homolog 2 zinc finger protein)	0.47	-	nuc	0	Nucleus (Potential)				311
Q91WD2 UniProt NPD GO	TRPV6_MOUSE	Transient receptor potential cation channel subfamily V member 6 (TrpV6) (Epithelial calcium channel ...	0.47	-	end	6	Cell membrane; multi-pass membrane protein				727
Q9N6P4 UniProt NPD GO	FZO_DROSI	Transmembrane GTPase fzo (EC 3.6.5.-) (Protein fuzzy onions) (Fragment)	0.47	-	nuc	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)	mitochondrial envelope [ISS]			454
Q9C030 UniProt NPD GO	TRIM6_HUMAN	Tripartite motif-containing protein 6 (RING finger protein 89)	0.47	-	nuc	0			607564		488
P26651 UniProt NPD GO	TTP_HUMAN	Tristetraproline (TTP) (Zinc finger protein 36 homolog) (Zfp-36) (TIS11A protein) (TIS11) (Growth fa ...	0.47	-	nuc	0	Nucleus	cytoplasm [TAS] cytosol [IDA]	190700		326
Q12816 UniProt NPD GO	TROP_HUMAN	Trophinin (MAGE-D3 antigen)	0.47	-	nuc	0		integral to plasma membrane [TAS] plasma membrane [TAS]	300132		1387
P42636 UniProt NPD GO	TPM1_BIOGL	Tropomyosin 1 (TMI) (Bg 39)	0.47	-	nuc	0					284
Q6IRU2 UniProt NPD GO	TPM4_MOUSE	Tropomyosin alpha-4 chain (Tropomyosin-4)	0.47	-	nuc	0					247
Q43723 UniProt NPD GO	IACX1_WHEAT	Trypsin/alpha-amylase inhibitor CMX1/CMX3 precursor (ITRL-1/ITRL-3)	0.47	-	exc	1 *	Secreted protein (Potential)				121
Q10197 UniProt NPD GO	ALP1_SCHPO	Tubulin-folding cofactor D (Altered polarity protein 1)	0.47	-	nuc	0	Membrane; multi-pass membrane protein (Potential)	astral microtubule [IDA]			1121
Q9JLL3 UniProt NPD GO	TNR19_MOUSE	Tumor necrosis factor receptor superfamily member 19 precursor (Toxicity and JNK inducer) (TRADE)	0.47	-	exc	1	Isoform 1, isoform 3, isoform 4: Cell membrane; single-pass type I membrane protein (Probable). Isof ...				416
P25118 UniProt NPD GO	TNR1A_MOUSE	Tumor necrosis factor receptor superfamily member 1A precursor (p60) (TNF-R1) (TNF-RI) (TNFR-I) (p55 ...	0.47	-	exc	2 *	Membrane; single-pass type I membrane protein	extracellular region [ISS] plasma membrane [TAS]			454
Q9HAV5 UniProt NPD GO	TNR27_HUMAN	Tumor necrosis factor receptor superfamily member 27 (X-linked ectodysplasin-A2 receptor) (EDA-A2 re ...	0.47	-	nuc	1	Membrane; single-pass type III membrane protein	integral to membrane [IC]	300276		297
Q68F50 UniProt NPD GO	TWF1_XENLA	Twinfilin-1	0.47	-	cyt	0					350
P90986 UniProt NPD GO	TY3H_CAEEL	Tyrosine 3-monooxygenase (EC 1.14.16.2) (Tyrosine 3-hydroxylase) (TH)	0.47	-	cyt	0		axon [IDA]			454
O73791 UniProt NPD GO	TIE2_BRARE	Tyrosine-protein kinase receptor Tie-2 precursor (EC 2.7.10.1)	0.47	-	nuc	1	Membrane; single-pass type I membrane protein				1116
P34137 UniProt NPD GO	PTP1_DICDI	Tyrosine-protein phosphatase 1 (EC 3.1.3.48) (Protein-tyrosine-phosphate phosphohydrolase 1)	0.47	-	nuc	0	Cytoplasm. Cell membrane (Probable). Might be tethered to the plasma membrane				521
Q9P7H1 UniProt NPD GO	FLP1_SCHPO	Tyrosine-protein phosphatase CDC14 homolog (EC 3.1.3.48) (CDC fourteen-like phosphatase 1)	0.47	-	nuc	0	Nucleus; nucleolus. Until mitosis and the spindle pole body through to late anaphase	cytoplasm [IDA] nucleolus [IDA] spindle pole body [IDA]			537
Q05946 UniProt NPD GO	UTP13_YEAST	U3 small nucleolar RNA-associated protein 13 (U3 snoRNA-associated protein 13)	0.47	-	mit	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [IPI]			817
O43172 UniProt NPD GO	PRP4_HUMAN	U4/U6 small nuclear ribonucleoprotein Prp4 (U4/U6 snRNP 60 kDa protein) (WD splicing factor Prp4) (h ...	0.47	-	mit	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Colocalizes with spliceosomal snRNPs (By simi ...	nucleus [TAS] spliceosome complex [NAS]	607795	1MZW	522
Q5ABE5 UniProt NPD GO	ALG13_CANAL	UDP-N-acetylglucosamine transferase subunit ALG13 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.47	-	nuc	0	Endoplasmic reticulum (By similarity)				293
Q08968 UniProt NPD GO	YP222_YEAST	UPF0061 protein YPL222W	0.47	-	cyt	0		mitochondrion [IDA]			688
Q8R317 UniProt NPD GO	UBQL1_MOUSE	Ubiquilin-1 (Protein linking IAP with cytoskeleton 1) (PLIC-1)	0.47	-	nuc	0	Nucleus (By similarity). Cytoplasm	cytoplasm [ISS] endoplasmic reticulum [ISS] perinuclear region [ISS]			582
Q9UMX0 UniProt NPD GO	UBQL1_HUMAN	Ubiquilin-1 (Protein linking IAP with cytoskeleton 1) (PLIC-1) (hPLIC-1)	0.47	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] perinuclear region [NAS]	605046		589
Q9CQ69 UniProt NPD GO	UCRQ_MOUSE	Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C (EC 1.10.2.2) (Ubiquinol-cy ...	0.47	-	cyt	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA] mitochondrion [IDA]			81
Q9UUD6 UniProt NPD GO	UBP11_SCHPO	Ubiquitin carboxyl-terminal hydrolase 11 (EC 3.1.2.15) (Ubiquitin thioesterase 11) (Ubiquitin-specif ...	0.47	-	nuc	1 *					350
Q11119 UniProt NPD GO	UBP14_SCHPO	Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.1.2.15) (Ubiquitin thioesterase 14) (Ubiquitin-specif ...	0.47	-	nuc	0					775
P50101 UniProt NPD GO	UBP15_YEAST	Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.1.2.15) (Ubiquitin thioesterase 15) (Ubiquitin-specif ...	0.47	-	cyt	0		cytoplasm [IC]			1230
P50102 UniProt NPD GO	UBP8_YEAST	Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.1.2.15) (Ubiquitin thioesterase 8) (Ubiquitin-specific ...	0.47	-	nuc	0	Nucleus (Probable)	SAGA complex [IDA]			471
Q6GNY1 UniProt NPD GO	MIB1_XENLA	Ubiquitin ligase protein MIB1 (EC 6.3.2.-) (Mind bomb homolog 1)	0.47	-	cyt	0	Cytoplasm (By similarity)				1011
Q9Y385 UniProt NPD GO	UB2J1_HUMAN	Ubiquitin-conjugating enzyme E2 J1 (EC 6.3.2.19) (Non-canonical ubiquitin-conjugating enzyme 1) (NCU ...	0.47	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein				318
Q2M3C6 UniProt NPD GO	CO027_HUMAN	Uncharacterized protein C15orf27	0.47	-	nuc	0					347
Q8BZB3 UniProt NPD GO	CO027_MOUSE	Uncharacterized protein C15orf27 homolog	0.47	-	nuc	0					354
Q2T9Z2 UniProt NPD GO	CT195_BOVIN	Uncharacterized protein C20orf195 homolog	0.47	-	nuc	0					333
P53075 UniProt NPD GO	YGX8_YEAST	Uncharacterized protein YGL228W	0.47	+	cyt	0					577
P40325 UniProt NPD GO	YG5M_YEAST	Uncharacterized protein YGR268C	0.47	-	nuc	0		cytoplasm [IDA]			198
Q08003 UniProt NPD GO	YL073_YEAST	Uncharacterized protein YLR073C	0.47	-	nuc	0	Endosome	endosome [IDA]			200
Q12292 UniProt NPD GO	YO083_YEAST	Uncharacterized protein YOL083W	0.47	-	nuc	0					412
P12887 UniProt NPD GO	UNG_YEAST	Uracil-DNA glycosylase, mitochondrial precursor (EC 3.2.2.-) (UDG)	0.47	+	mit	0	Nucleus. Mitochondrion	mitochondrion [IDA] nucleus [IDA]			359
Q41396 UniProt NPD GO	VATE_SPIOL	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit)	0.47	-	nuc	0					229
Q06696 UniProt NPD GO	VPS36_YEAST	Vacuolar protein sorting protein 36	0.47	-	nuc	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein	ESCRT II complex [IDA]		2CAY	566
O08700 UniProt NPD GO	VPS45_RAT	Vacuolar protein sorting-associated protein 45 (rvps45)	0.47	-	cyt	0	Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity). Endosome; endosomal me ...				570
O13872 UniProt NPD GO	VPS28_SCHPO	Vacuolar protein sorting-associated protein VPS28 homolog	0.47	-	nuc	0					248
P35916 UniProt NPD GO	VGFR3_HUMAN	Vascular endothelial growth factor receptor 3 precursor (EC 2.7.10.1) (VEGFR-3) (Tyrosine-protein ki ...	0.47	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	153100		1298
P25428 UniProt NPD GO	NGFV_VIPLE	Venom nerve growth factor precursor (v-NGF)	0.47	-	exc	0	Secreted protein				244
P35953 UniProt NPD GO	VLDLR_RABIT	Very low-density lipoprotein receptor precursor (VLDL receptor) (VLDL-R)	0.47	-	exc	1	Membrane; single-pass type I membrane protein				873
P98166 UniProt NPD GO	VLDLR_RAT	Very low-density lipoprotein receptor precursor (VLDL receptor) (VLDL-R)	0.47	-	exc	1	Membrane; single-pass type I membrane protein				873
P78768 UniProt NPD GO	VTI1_SCHPO	Vesicle transport v-SNARE protein vti1	0.47	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				214

You are viewing entries 27301 to 27350 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.