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
Q9TTK7 UniProt NPD GO	OLR1_PIG	Oxidized low-density lipoprotein receptor 1 (Ox-LDL receptor 1) (Lectin-type oxidized LDL receptor 1 ...	0.58	-	nuc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Secreted protein (By similarity ...				274
O70156 UniProt NPD GO	OLR1_RAT	Oxidized low-density lipoprotein receptor 1 (Ox-LDL receptor 1) (Lectin-type oxidized LDL receptor 1 ...	0.58	-	nuc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Secreted protein (By similarity ...				364
Q99572 UniProt NPD GO	P2RX7_HUMAN	P2X purinoceptor 7 (ATP receptor) (P2X7) (Purinergic receptor) (P2Z receptor)	0.58	-	cyt	1 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602566		595
Q8NF64 UniProt NPD GO	ZIMP7_HUMAN	PIAS-like protein Zimp7	0.58	-	nuc	0	Nucleus				920
P55968 UniProt NPD GO	PO4F1_CHICK	POU domain, class 4, transcription factor 1 (Brain-specific homeobox/POU domain protein 3A) (Brn-3A) ...	0.58	+	nuc	0	Nucleus				116
Q01860 UniProt NPD GO	PO5F1_HUMAN	POU domain, class 5, transcription factor 1 (Octamer-binding transcription factor 3) (Oct-3) (Oct-4) ...	0.58	+	cyt	0	Nucleus		164177		360
O60810 UniProt NPD GO	PRAM4_HUMAN	PRAME family member 4	0.58	-	cyt	0					478
Q99453 UniProt NPD GO	PHX2B_HUMAN	Paired mesoderm homeobox protein 2B (Paired-like homeobox 2B) (PHOX2B homeodomain protein) (Neurobla ...	0.58	+	nuc	0	Nucleus (By similarity)		603851		314
O35690 UniProt NPD GO	PHX2B_MOUSE	Paired mesoderm homeobox protein 2B (Paired-like homeobox 2B) (PHOX2B homeodomain protein) (Neurobla ...	0.58	+	nuc	0	Nucleus (By similarity)				314
P00439 UniProt NPD GO	PH4H_HUMAN	Phenylalanine-4-hydroxylase (EC 1.14.16.1) (PAH) (Phe-4-monooxygenase)	0.58	-	cyt	0			261600	6PAH	452
P20052 UniProt NPD GO	PHO80_YEAST	Phosphate system cyclin PHO80	0.58	-	nuc	0		cyclin-dependent protein kinase holoenzyme ... [TAS]			293
P78562 UniProt NPD GO	PHEX_HUMAN	Phosphate-regulating neutral endopeptidase (EC 3.4.24.-) (Metalloendopeptidase homolog PEX) (X-linke ...	0.58	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)	integral to plasma membrane [TAS] plasma membrane [TAS]	307800		749
P27608 UniProt NPD GO	AROF_TOBAC	Phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplast precursor (EC 2.5.1.54) (Phospho-2-keto-3 ...	0.58	-	mit	0	Plastid; chloroplast				542
Q8R143 UniProt NPD GO	PTTG_MOUSE	Pituitary tumor-transforming gene 1 protein-interacting protein precursor (Pituitary tumor-transform ...	0.58	-	end	2 *	Cell membrane; single-pass type I membrane protein (By similarity). Cytoplasm (By similarity). Nucle ...				174
P0C191 UniProt NPD GO	GPVI_MOUSE	Platelet glycoprotein VI precursor (GPVI)	0.58	-	exc	1	Membrane; single-pass membrane protein (By similarity)				313
Q9QZA1 UniProt NPD GO	PHLA1_RAT	Pleckstrin homology-like domain family A member 1 (Proline- and glutamine-rich protein) (PQR protein ...	0.58	-	nuc	0	Cytoplasm (By similarity). Colocalizes with intracellular vesicles. Nucleus; nucleolus (By similarit ...				263
Q8WV24 UniProt NPD GO	PHLA1_HUMAN	Pleckstrin homology-like domain family A member 1 (T-cell death-associated gene 51 protein) (Apoptos ...	0.58	-	nuc	0	Cytoplasm. Colocalizes with intracellular vesicles. Nucleus; nucleolus		605335		259
P35227 UniProt NPD GO	PCGF2_HUMAN	Polycomb group RING finger protein 2 (DNA-binding protein Mel-18) (RING finger protein 110) (Zinc fi ...	0.58	-	nuc	0	Nucleus		600346		344
O60828 UniProt NPD GO	PQBP1_HUMAN	Polyglutamine-binding protein 1 (Polyglutamine tract-binding protein 1) (PQBP-1) (38 kDa nuclear pro ...	0.58	+	nuc	0	Nucleus. Co-localized with POU3F2. Co-localized with ATXN1 in nuclear inclusion bodies	nucleus [TAS]	309500		265
Q43082 UniProt NPD GO	HEM3_PEA	Porphobilinogen deaminase, chloroplast precursor (EC 2.5.1.61) (PBG) (Hydroxymethylbilane synthase) ...	0.58	-	mit	0	Plastid; chloroplast				369
Q75EN0 UniProt NPD GO	RAD18_ASHGO	Postreplication repair ubiquitin-protein ligase E3 RAD18 (EC 6.-.-.-)	0.58	-	nuc	0	Nucleus (By similarity)				443
P59111 UniProt NPD GO	KCNH8_MOUSE	Potassium voltage-gated channel subfamily H member 8 (Voltage-gated potassium channel subunit Kv12.1 ...	0.58	-	end	4 *	Membrane; multi-pass membrane protein				876
Q09801 UniProt NPD GO	FIP1X_SCHPO	Pre-mRNA polyadenylation factor fip1	0.58	-	nuc	0	Nucleus (By similarity)				344
Q756C3 UniProt NPD GO	CEF1_ASHGO	Pre-mRNA-splicing factor CEF1	0.58	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				477
Q51TF7 UniProt NPD GO	CWC2_MAGGR	Pre-mRNA-splicing factor CWC2	0.58	+	cyt	0	Nucleus (By similarity)				580
Q6CJ08 UniProt NPD GO	CWC26_KLULA	Pre-mRNA-splicing factor CWC26	0.58	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				268
O22315 UniProt NPD GO	SFRS1_ARATH	Pre-mRNA-splicing factor SF2 (SR1 protein)	0.58	+	nuc	0	Nucleus (Potential)				303
P38919 UniProt NPD GO	DDX48_HUMAN	Probable ATP-dependent RNA helicase DDX48 (EC 3.6.1.-) (DEAD box protein 48) (Eukaryotic initiation ...	0.58	-	cyt	0	Nucleus		608546		410
Q9Y6V7 UniProt NPD GO	DDX49_HUMAN	Probable ATP-dependent RNA helicase DDX49 (EC 3.6.1.-) (DEAD box protein 49)	0.58	-	cyt	0					483
Q01529 UniProt NPD GO	DPOM_PODAN	Probable DNA polymerase (EC 2.7.7.7)	0.58	-	mit	0					1197
Q8IZF6 UniProt NPD GO	GP112_HUMAN	Probable G-protein coupled receptor 112	0.58	-	end	6	Membrane; multi-pass membrane protein	integral to membrane [TAS]			2799
Q9LZV6 UniProt NPD GO	WRK62_ARATH	Probable WRKY transcription factor 62 (WRKY DNA-binding protein 62)	0.58	-	nuc	0	Nucleus (Probable)				263
Q9VXN4 UniProt NPD GO	SYR_DROME	Probable arginyl-tRNA synthetase (EC 6.1.1.19) (Arginine--tRNA ligase) (ArgRS)	0.58	-	cyt	0	Cytoplasm (Potential)				665
Q12697 UniProt NPD GO	ATC9_YEAST	Probable cation-transporting ATPase 2 (EC 3.6.3.-)	0.58	-	end	11	Membrane; multi-pass membrane protein				1472
Q9VHP4 UniProt NPD GO	CP313_DROME	Probable cytochrome P450 313b1 (EC 1.14.-.-) (CYPCCCXIIIB1)	0.58	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				502
Q5KGR0 UniProt NPD GO	NDC80_CRYNE	Probable kinetochore protein NDC80	0.58	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				703
Q9V6B9 UniProt NPD GO	NUP54_DROME	Probable nucleoporin Nup54	0.58	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity). Localizes to the nuclear pore compl ...	nuclear pore [ISS]			610
Q8BQQ1 UniProt NPD GO	ZDH14_MOUSE	Probable palmitoyltransferase ZDHHC14 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 14) ( ...	0.58	-	nuc	4	Membrane; multi-pass membrane protein (Potential)				489
Q9P7W9 UniProt NPD GO	RNP1_SCHPO	Probable ribonuclease P protein subunit 1 (EC 3.1.26.5)	0.58	+	nuc	0	Nucleus (Potential)				217
Q8IVL6 UniProt NPD GO	P3H3_HUMAN	Prolyl 3-hydroxylase 3 precursor (EC 1.14.11.7) (Leprecan-like protein 2) (Protein B)	0.58	-	exc	0	Endoplasmic reticulum (By similarity)				736
Q92338 UniProt NPD GO	ABCI_SCHPO	Protein ABC1 homolog, mitochondrial precursor	0.58	-	nuc	0	Mitochondrion (Probable)				610
Q6PQQ4 UniProt NPD GO	BBM_ARATH	Protein BABY BOOM (AtBBM)	0.58	-	nuc	0	Nucleus (Probable)				584
Q06150 UniProt NPD GO	BOP2_YEAST	Protein BOP2 (Bypass of PAM1 protein 2)	0.58	-	cyt	0					570
Q8N326 UniProt NPD GO	CJ111_HUMAN	Protein C10orf111	0.58	-	nuc	1					155
Q5SR76 UniProt NPD GO	CJ093_HUMAN	Protein C10orf93	0.58	-	cyt	0					405
Q2TBC4 UniProt NPD GO	CF049_HUMAN	Protein C6orf49	0.58	-	exc	0					344
Q9NZB2 UniProt NPD GO	CI010_HUMAN	Protein C9orf10	0.58	-	nuc	0					1069
Q9CWD0 UniProt NPD GO	F112A_MOUSE	Protein FAM112A	0.58	-	nuc	0					151
Q5R4R4 UniProt NPD GO	FA61A_PONPY	Protein FAM61A	0.58	+	nuc	0					463
Q14699 UniProt NPD GO	K0084_HUMAN	Protein KIAA0084 (HA2022) (Fragment)	0.58	-	nuc	0					648

You are viewing entries 20351 to 20400 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.