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
P36224 UniProt NPD GO	JNM1_YEAST	Nuclear migration protein JNM1	0.72	-	nuc	0		dynactin complex [IDA]			373
P67808 UniProt NPD GO	YBOX1_BOVIN	Nuclease sensitive element-binding protein 1 (Y-box-binding protein 1) (Y-box transcription factor) ...	0.72	+	nuc	0	Cytoplasm. Nucleus. Shuttles between nucleus and cytoplasm. Predominantly cytoplasmic in proliferati ...				323
P67809 UniProt NPD GO	YBOX1_HUMAN	Nuclease sensitive element-binding protein 1 (Y-box-binding protein 1) (Y-box transcription factor) ...	0.72	+	nuc	0	Cytoplasm. Nucleus. Shuttles between nucleus and cytoplasm. Predominantly cytoplasmic in proliferati ...	nucleus [NAS]	154030	1H95	323
P62960 UniProt NPD GO	YBOX1_MOUSE	Nuclease sensitive element-binding protein 1 (Y-box-binding protein 1) (Y-box transcription factor) ...	0.72	+	nuc	0	Cytoplasm. Nucleus. Shuttles between nucleus and cytoplasm. Predominantly cytoplasmic in proliferati ...				321
P62961 UniProt NPD GO	YBOX1_RAT	Nuclease sensitive element-binding protein 1 (Y-box-binding protein 1) (Y-box transcription factor) ...	0.72	+	nuc	0	Cytoplasm. Nucleus. Shuttles between nucleus and cytoplasm. Predominantly cytoplasmic in proliferati ...				321
Q10331 UniProt NPD GO	NU107_SCHPO	Nucleoporin nup107 (Nuclear pore protein nup107)	0.72	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex	nuclear membrane [IDA] Nup107-160 complex [IDA]			794
P18747 UniProt NPD GO	ZO28_XENLA	Oocyte zinc finger protein XLCOF28 (Fragment)	0.72	-	nuc	0	Nucleus (Potential)				439
Q861Q8 UniProt NPD GO	OPTN_MACMU	Optineurin	0.72	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Golgi apparatus (By similarity). Found in the perinuc ...				571
Q9BXB5 UniProt NPD GO	OSB10_HUMAN	Oxysterol-binding protein-related protein 10 (OSBP-related protein 10) (ORP-10)	0.72	-	nuc	0			606738		764
Q64663 UniProt NPD GO	P2RX7_RAT	P2X purinoceptor 7 (ATP receptor) (P2X7) (Purinergic receptor) (P2Z receptor)	0.72	-	cyt	0	Membrane; multi-pass membrane protein	integral to nuclear inner membrane [IDA]			595
P53297 UniProt NPD GO	PBP1_YEAST	PAB1-binding protein 1	0.72	-	nuc	0	Cytoplasm. Nucleus. Mitochondrion	cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA] polysome [IDA]			722
Q6AXW4 UniProt NPD GO	PHF7_RAT	PHD finger protein 7	0.72	-	nuc	0	Nucleus (By similarity)				380
Q4V8C8 UniProt NPD GO	CDC73_RAT	Parafibromin (Cell division cycle protein 73 homolog) (Hyperparathyroidism 2 protein homolog)	0.72	-	nuc	0	Nucleus (By similarity)				531
P27154 UniProt NPD GO	CAPP_TOBAC	Phosphoenolpyruvate carboxylase (EC 4.1.1.31) (PEPCase) (PEPC)	0.72	-	nuc	0	Cytoplasm				964
P29195 UniProt NPD GO	CAPP1_SORBI	Phosphoenolpyruvate carboxylase 1 (EC 4.1.1.31) (PEPCase 1) (PEPC 1) (CP21)	0.72	-	nuc	0	Cytoplasm				960
P46018 UniProt NPD GO	KPB2_RABIT	Phosphorylase b kinase regulatory subunit alpha, liver isoform (Phosphorylase kinase alpha L subunit ...	0.72	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				1235
Q9TLS6 UniProt NPD GO	APCE_CYACA	Phycobilisome linker polypeptide (Anchor polypeptide) (PBS-anchor protein)	0.72	-	mit	0	Plastid; chloroplast				870
Q9JMB7 UniProt NPD GO	PIWL1_MOUSE	Piwi-like protein 1	0.72	+	mit	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity)	cytoplasm [IDA]			862
Q9QY23 UniProt NPD GO	PKP3_MOUSE	Plakophilin-3	0.72	-	nuc	0	Nucleus. Cell membrane; cell-cell junction; anchoring junction; desmosome. Nuclear and associated wi ...	desmosome [IDA]			797
O47032 UniProt NPD GO	RR4_PROWI	Plastid 30S ribosomal protein S4	0.72	-	nuc	0	Plastid				207
Q867X0 UniProt NPD GO	PME3_CAEEL	Poly(ADP-ribose) glycohydrolase pme-3 (EC 3.2.1.143) (Poly ADP-ribose metabolism enzyme 3)	0.72	-	nuc	0					781
Q06587 UniProt NPD GO	RING1_HUMAN	Polycomb complex protein RING1 (RING finger protein 1)	0.72	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle	nucleus [IDA]	602045		406
Q8WMN5 UniProt NPD GO	RING1_MACMU	Polycomb complex protein RING1 (RING finger protein 1)	0.72	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				377
Q8N3T1 UniProt NPD GO	GLTL2_HUMAN	Polypeptide N-acetylgalactosaminyltransferase-like protein 2 (EC 2.4.1.41) (Protein-UDP acetylgalact ...	0.72	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				639
Q8WNY2 UniProt NPD GO	KCNH2_RABIT	Potassium voltage-gated channel subfamily H member 2 (Voltage-gated potassium channel subunit Kv11.1 ...	0.72	-	nuc	4	Membrane; multi-pass membrane protein				1161
Q6BNE1 UniProt NPD GO	CWC25_DEBHA	Pre-mRNA-splicing factor CWC25	0.72	-	nuc	0	Nucleus (By similarity)				244
Q753F1 UniProt NPD GO	ISY1_ASHGO	Pre-mRNA-splicing factor ISY1	0.72	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				240
Q4WU07 UniProt NPD GO	CWC2_ASPFU	Pre-mRNA-splicing factor cwc2	0.72	+	nuc	0	Nucleus (By similarity)				414
Q9VXX8 UniProt NPD GO	RL371_DROME	Probable 60S ribosomal protein L37-A	0.72	-	mit	0					93
P26802 UniProt NPD GO	DBP73_DROME	Probable ATP-dependent RNA helicase Dbp73D (EC 3.6.1.-) (DEAD box protein 73D)	0.72	-	cyt	0	Nucleus; nucleolus (By similarity)				687
Q8I4V5 UniProt NPD GO	UTP11_PLAF7	Probable U3 small nucleolar RNA-associated protein 11 (U3 snoRNA-associated protein 11)	0.72	+	nuc	0	Nucleus; nucleolus (By similarity)				212
Q9Y3A2 UniProt NPD GO	UTP11_HUMAN	Probable U3 small nucleolar RNA-associated protein 11 (U3 snoRNA-associated protein 11) (UTP11-like ...	0.72	-	nuc	0	Nucleus; nucleolus (By similarity)	cytoplasm [IDA] extracellular space [IDA] nucleus [IDA]	609440		253
Q8R5K5 UniProt NPD GO	UTP11_RAT	Probable U3 small nucleolar RNA-associated protein 11 (U3 snoRNA-associated protein 11) (UTP11-like ...	0.72	-	nuc	0	Nucleus; nucleolus				253
Q8RWS9 UniProt NPD GO	CNGC5_ARATH	Probable cyclic nucleotide-gated ion channel 5 (AtCNGC5) (Cyclic nucleotide- and calmodulin-regulate ...	0.72	+	end	3	Cell membrane; multi-pass membrane protein (Potential)				717
Q7KR10 UniProt NPD GO	CCD1D_DROME	Probable cytochrome P450 12d1 distal, mitochondrial precursor (EC 1.14.-.-) (CYPXIID1)	0.72	-	nuc	0	Mitochondrion (Potential)	mitochondrion [ISS]			521
Q9FKZ0 UniProt NPD GO	DRL43_ARATH	Probable disease resistance protein At5g66910	0.72	-	cyt	0					815
O97655 UniProt NPD GO	GON2_MACMU	Progonadoliberin-2 precursor (Progonadoliberin II) [Contains: Gonadoliberin-2 (Gonadoliberin II) (Lu ...	0.72	-	exc	0	Secreted protein (By similarity)				114
O43586 UniProt NPD GO	PPIP1_HUMAN	Proline-serine-threonine phosphatase-interacting protein 1 (PEST phosphatase-interacting protein 1) ...	0.72	-	nuc	0	Cytoplasm (By similarity). Colocalized with the cortical actin cytoskeleton during interphase, lamel ...		606347		416
P38928 UniProt NPD GO	AXL2_YEAST	Protein AXL2 precursor (Suppressor of RHO3 protein 4)	0.72	-	exc	1	Cell membrane; single-pass type I membrane protein. In small, buds localizes to incipient bud sites, ...	bud neck [IDA] integral to plasma membrane [TAS] septin ring [TAS]			823
Q74ZM2 UniProt NPD GO	BUR2_ASHGO	Protein BUR2	0.72	-	cyt	0	Nucleus (By similarity)				381
Q751B2 UniProt NPD GO	EBS1_ASHGO	Protein EBS1	0.72	-	mit	0	Nucleus (Probable)				775
P40546 UniProt NPD GO	FAF1_YEAST	Protein FAF1 (Forty S assembly factor)	0.72	-	nuc	0	Nucleus; nucleolus	cytoplasm [IDA] nucleolus [IDA] nucleus [IDA]			346
O95990 UniProt NPD GO	F107A_HUMAN	Protein FAM107A (Down-regulated in renal cell carcinoma 1) (Protein TU3A)	0.72	-	nuc	0	Nucleus	nucleus [IDA]	608295		144
Q3TGF2 UniProt NPD GO	F107B_MOUSE	Protein FAM107B	0.72	-	nuc	0					131
Q9CR80 UniProt NPD GO	FA32A_MOUSE	Protein FAM32A	0.72	+	nuc	0					112
Q9BX40 UniProt NPD GO	FA61B_HUMAN	Protein FAM61B	0.72	-	nuc	0					385
Q92622 UniProt NPD GO	K0226_HUMAN	Protein KIAA0226	0.72	-	nuc	0					972
Q6ZNE5 UniProt NPD GO	K0831_HUMAN	Protein KIAA0831	0.72	-	nuc	0					492
Q12342 UniProt NPD GO	LDB17_YEAST	Protein LDB17 (Low dye-binding protein 17)	0.72	-	nuc	0	Cytoplasm. Bud. Bud neck	bud neck [IDA] cytoplasm [IDA]			491
Q08904 UniProt NPD GO	RDR1_YEAST	Protein RDR1 (Repressor of drug resistance protein 1)	0.72	-	nuc	0	Nucleus (Probable)	nucleus [TAS]			546

You are viewing entries 12901 to 12950 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.