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
Q26519 UniProt NPD GO	TPM_SCHJA	Tropomyosin	0.56	-	nuc	0					284
P12808 UniProt NPD GO	TPM_PICAN	Tropomyosin-like protein (Fragment)	0.56	-	nuc	0					182
Q8CGV2 UniProt NPD GO	TPH2_MOUSE	Tryptophan 5-hydroxylase 2 (EC 1.14.16.4) (Tryptophan 5-monooxygenase 2) (Neuronal tryptophan hydrox ...	0.56	-	cyt	0					488
O93807 UniProt NPD GO	TBG_CANAL	Tubulin gamma chain (Gamma tubulin)	0.56	-	nuc	0					502
Q8VCK3 UniProt NPD GO	TBG2_MOUSE	Tubulin gamma-2 chain (Gamma-2 tubulin)	0.56	-	cyt	0		cytoplasmic microtubule [IDA] pericentriolar material [IDA] spindle microtubule [IDA]			451
O75888 UniProt NPD GO	TNF13_HUMAN	Tumor necrosis factor ligand superfamily member 13 precursor (A proliferation-inducing ligand) (APRI ...	0.56	-	exc	1 *	Secreted protein		604472		250
Q9UBN6 UniProt NPD GO	TR10D_HUMAN	Tumor necrosis factor receptor superfamily member 10D precursor (Decoy receptor 2) (DcR2) (TNF-relat ...	0.56	-	mit	1	Membrane; single-pass type I membrane protein		603614		386
Q32L57 UniProt NPD GO	TUSC3_BOVIN	Tumor suppressor candidate 3	0.56	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				347
Q13454 UniProt NPD GO	TUSC3_HUMAN	Tumor suppressor candidate 3 (Protein N33)	0.56	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)	oligosaccharyl transferase complex [IDA]	601385		348
Q9EPW0 UniProt NPD GO	INP4A_MOUSE	Type I inositol-3,4-bisphosphate 4-phosphatase (EC 3.1.3.66) (Inositol polyphosphate 4-phosphatase t ...	0.56	-	nuc	0					939
Q62784 UniProt NPD GO	INP4A_RAT	Type I inositol-3,4-bisphosphate 4-phosphatase (EC 3.1.3.66) (Inositol polyphosphate 4-phosphatase t ...	0.56	-	nuc	0					939
P42685 UniProt NPD GO	FRK_HUMAN	Tyrosine-protein kinase FRK (EC 2.7.10.2) (Nuclear tyrosine protein kinase RAK)	0.56	-	cyt	0	Cytoplasm (Probable)	intracellular [TAS] nucleus [TAS]	606573		505
P52333 UniProt NPD GO	JAK3_HUMAN	Tyrosine-protein kinase JAK3 (EC 2.7.10.2) (Janus kinase 3) (JAK-3) (Leukocyte janus kinase) (L-JAK) ...	0.56	-	cyt	0	Intracytoplasmic membrane; peripheral membrane protein. Wholly intracellular, possibly membrane asso ...		600173	1YVJ	1124
O35239 UniProt NPD GO	PTN9_MOUSE	Tyrosine-protein phosphatase non-receptor type 9 (EC 3.1.3.48) (Protein-tyrosine phosphatase MEG2) ( ...	0.56	-	cyt	0	Cytoplasm (Probable)				593
Q8K1Z0 UniProt NPD GO	COQ9_MOUSE	Ubiquinone biosynthesis protein COQ9, mitochondrial precursor	0.56	-	mit	0	Mitochondrion	mitochondrion [IDA]			313
P62068 UniProt NPD GO	UBP46_HUMAN	Ubiquitin carboxyl-terminal hydrolase 46 (EC 3.1.2.15) (Ubiquitin thioesterase 46) (Ubiquitin-specif ...	0.56	-	nuc	0					366
P62069 UniProt NPD GO	UBP46_MOUSE	Ubiquitin carboxyl-terminal hydrolase 46 (EC 3.1.2.15) (Ubiquitin thioesterase 46) (Ubiquitin-specif ...	0.56	-	nuc	0					366
Q4R815 UniProt NPD GO	CR054_MACFA	Uncharacterized protein C18orf54 homolog precursor	0.56	-	nuc	0	Secreted protein (Potential)				322
Q96MC9 UniProt NPD GO	CA147_HUMAN	Uncharacterized protein C1orf147	0.56	-	nuc	0					270
Q9D5U8 UniProt NPD GO	CT152_MOUSE	Uncharacterized protein C20orf152 homolog	0.56	-	nuc	0					556
Q9BQP7 UniProt NPD GO	CT072_HUMAN	Uncharacterized protein C20orf72	0.56	-	nuc	0					344
P59383 UniProt NPD GO	CT075_MOUSE	Uncharacterized protein C20orf75 homolog precursor	0.56	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				733
Q8WUT4 UniProt NPD GO	CT075_HUMAN	Uncharacterized protein C20orf75 precursor	0.56	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				740
P32898 UniProt NPD GO	YD430_YEAST	Uncharacterized protein YDR430C	0.56	-	nuc	0		mitochondrial intermembrane space [IDA] mitochondrion [IDA]			989
P53246 UniProt NPD GO	YG2D_YEAST	Uncharacterized protein YGR071C	0.56	-	nuc	0		nucleus [IDA]			860
P38881 UniProt NPD GO	YHZ5_YEAST	Uncharacterized protein YHR195W	0.56	-	nuc	0		nuclear envelope [IDA]			321
Q03640 UniProt NPD GO	YMH2_YEAST	Uncharacterized protein YML072C	0.56	-	nuc	1	Membrane; multi-pass membrane protein (Potential)	bud [IDA] mitochondrion [IDA]			1545
Q03559 UniProt NPD GO	YM8V_YEAST	Uncharacterized protein YMR295C	0.56	+	nuc	0		bud [IDA]			197
Q15853 UniProt NPD GO	USF2_HUMAN	Upstream stimulatory factor 2 (Upstream transcription factor 2) (FOS-interacting protein) (FIP) (Maj ...	0.56	+	nuc	0	Nucleus		600390		346
Q64705 UniProt NPD GO	USF2_MOUSE	Upstream stimulatory factor 2 (Upstream transcription factor 2) (Major late transcription factor 2)	0.56	+	nuc	0	Nucleus	nucleus [IDA]			346
Q63665 UniProt NPD GO	USF2_RAT	Upstream stimulatory factor 2 (Upstream transcription factor 2) (Major late transcription factor 2)	0.56	+	nuc	0	Nucleus				346
Q9QYG8 UniProt NPD GO	UCK2_RAT	Uridine-cytidine kinase 2 (EC 2.7.1.48) (UCK 2) (Uridine monophosphokinase 2) (Cytidine monophosphok ...	0.56	-	nuc	0					105
O13034 UniProt NPD GO	RAG2_BRARE	V(D)J recombination-activating protein 2 (RAG-2)	0.56	-	nuc	0	Nucleus				530
P48143 UniProt NPD GO	VIP_CHICK	VIP peptides precursor [Contains: Intestinal peptide PHI-27-like; Vasoactive intestinal peptide (VIP ...	0.56	-	exc	0	Secreted protein				200
Q9EPR5 UniProt NPD GO	SORC2_MOUSE	VPS10 domain-containing receptor SorCS2 precursor	0.56	-	end	1	Membrane; single-pass type I membrane protein				1159
Q6XPR4 UniProt NPD GO	BRO1_EMENI	Vacuolar protein-sorting protein bro1 (BRO domain-containing protein 1)	0.56	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity)				1000
P35968 UniProt NPD GO	VGFR2_HUMAN	Vascular endothelial growth factor receptor 2 precursor (EC 2.7.10.1) (VEGFR-2) (Kinase insert domai ...	0.56	-	end	2	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	191306	1YWN	1356
O08775 UniProt NPD GO	VGFR2_RAT	Vascular endothelial growth factor receptor 2 precursor (EC 2.7.10.1) (VEGFR-2) (Protein-tyrosine ki ...	0.56	-	end	2	Membrane; single-pass type I membrane protein				1343
Q3HXZ1 UniProt NPD GO	NGFV1_OXYMI	Venom nerve growth factor 1 precursor (vNGF-1)	0.56	-	exc	0	Secreted protein				243
P01124 UniProt NPD GO	BLYM_HUMAN	Very hypothetical BLYM-1 proto-oncogene	0.56	+	nuc	0					58
P48674 UniProt NPD GO	VIME_ONCMY	Vimentin	0.56	-	mit	0					461
P24789 UniProt NPD GO	VIM1_XENLA	Vimentin-1/2	0.56	-	mit	0					458
Q9GLP2 UniProt NPD GO	PROC_PIG	Vitamin K-dependent protein C precursor (EC 3.4.21.69) (Autoprothrombin IIA) (Anticoagulant protein ...	0.56	-	end	0		extracellular region [ISS]			459
P54284 UniProt NPD GO	CACB3_HUMAN	Voltage-dependent L-type calcium channel subunit beta-3 (CAB3) (Calcium channel voltage-dependent su ...	0.56	-	nuc	0		voltage-gated calcium channel complex [TAS]	601958		484
P54286 UniProt NPD GO	CACB3_RABIT	Voltage-dependent L-type calcium channel subunit beta-3 (CAB3) (Calcium channel voltage-dependent su ...	0.56	-	nuc	0					477
P54285 UniProt NPD GO	CACB3_MOUSE	Voltage-dependent L-type calcium channel subunit beta-3 (CAB3) (Calcium channel voltage-dependent su ...	0.56	-	nuc	0		voltage-gated calcium channel complex [TAS]			484
Q8N5D0 UniProt NPD GO	WDTC1_HUMAN	WD and tetratricopeptide repeats protein 1	0.56	-	nuc	0					677
Q9SI37 UniProt NPD GO	WRKY1_ARATH	WRKY transcription factor 1 (WRKY DNA-binding protein 1) (Zinc-dependent activator protein 1) (Trans ...	0.56	-	nuc	0	Nucleus (Probable)				487
Q9SIB4 UniProt NPD GO	WOX3_ARATH	WUSCHEL-related homeobox 3 (Protein PRESSED FLOWER)	0.56	-	nuc	0	Nucleus (Probable)				244
Q5QQ56 UniProt NPD GO	XYLT1_CANFA	Xylosyltransferase 1 (EC 2.4.2.26) (Xylosyltransferase I) (Peptide O-xylosyltransferase 1)	0.56	+	mit	0	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...				950

You are viewing entries 21701 to 21750 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.