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
P46735 UniProt NPD GO	MYO1B_MOUSE	Myosin Ib (Myosin I alpha) (MMI-alpha) (MMIa) (MIH-L)	0.81	-	cyt	0					1107
P70248 UniProt NPD GO	MYO1F_MOUSE	Myosin If	0.81	-	cyt	0					1099
Q9NRC8 UniProt NPD GO	SIRT7_HUMAN	NAD-dependent deacetylase sirtuin-7 (EC 3.5.1.-) (SIR2-like protein 7)	0.81	-	nuc	0	Cytoplasm. Located under the nuclear membrane		606212		400
Q60867 UniProt NPD GO	NDF1_MOUSE	Neurogenic differentiation factor 1 (NeuroD1)	0.81	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [IDA]			357
Q64289 UniProt NPD GO	NDF1_RAT	Neurogenic differentiation factor 1 (NeuroD1) (Basic helix-loop-helix factor 1) (BHF-1)	0.81	-	nuc	0	Cytoplasm. Nucleus. In pancreatic islet cells, shuttles to the nucleus in response to glucose stimul ...				357
P25435 UniProt NPD GO	NT3_XENLA	Neurotrophin-3 precursor (NT-3) (Neurotrophic factor) (HDNF) (Nerve growth factor 2) (NGF-2)	0.81	-	exc	0	Secreted protein				260
P97432 UniProt NPD GO	NBR1_MOUSE	Next to BRCA1 gene 1 protein (Neighbor of BRCA1 gene 1 protein) (Membrane component, chromosome 17, ...	0.81	-	nuc	0					988
Q28969 UniProt NPD GO	NOS3_PIG	Nitric-oxide synthase, endothelial (EC 1.14.13.39) (EC-NOS) (NOS type III) (NOSIII) (Endothelial NOS ...	0.81	+	cyt	0					1204
P19212 UniProt NPD GO	NIT2_NEUCR	Nitrogen catabolic enzyme regulatory protein	0.81	-	nuc	0	Nucleus				1036
P11633 UniProt NPD GO	NHP6B_YEAST	Nonhistone chromosomal protein 6B	0.81	-	nuc	0	Nucleus	FACT complex [IGI]			99
Q99JX7 UniProt NPD GO	NXF1_MOUSE	Nuclear RNA export factor 1 (Tip-associating protein) (Tip-associated protein) (mRNA export factor T ...	0.81	-	nuc	0	Nucleus; nucleoplasm (By similarity). Cytoplasm (By similarity). Localized predominantly in the nucl ...	nuclear inclusion body [IDA] nuclear pore [IDA] nucleus [IDA]			618
Q9GZY0 UniProt NPD GO	NXF2_HUMAN	Nuclear RNA export factor 2 (TAP-like protein 2) (TAPL-2)	0.81	-	nuc	0	Nucleus; nucleoplasm. Cytoplasm. Localized in the nucleoplasm and at the nuclear envelope. Shuttles ...	cytoplasm [ISS] nuclear RNA export factor complex [NAS] nucleus [ISS]	300315		626
P33244 UniProt NPD GO	FTZF1_DROME	Nuclear hormone receptor FTZ-F1 (FTZ-F1 alpha)	0.81	+	nuc	0	Nucleus	nucleus [IDA]			1027
Q9BJK5 UniProt NPD GO	NHR97_CAEEL	Nuclear hormone receptor family member nhr-97	0.81	-	nuc	0	Nucleus (Potential)				439
P49791 UniProt NPD GO	NU153_RAT	Nuclear pore complex protein Nup153 (Nucleoporin Nup153) (153 kDa nucleoporin)	0.81	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex. Located to the terminal ring structure of the nucle ...				1468
P18745 UniProt NPD GO	ZO22_XENLA	Oocyte zinc finger protein XLCOF22	0.81	-	nuc	0	Nucleus (Potential)				435
Q9UBM4 UniProt NPD GO	OPT_HUMAN	Opticin precursor (Oculoglycan)	0.81	+	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [TAS]	605127		332
Q21037 UniProt NPD GO	ORC2_CAEEL	Origin recognition complex subunit 2 (CeOrc2)	0.81	-	nuc	0	Nucleus				430
Q9QWM1 UniProt NPD GO	NR5A2_RAT	Orphan nuclear receptor NR5A2 (Liver receptor homolog 1) (LRH-1) (FTZ-F1 beta)	0.81	+	nuc	0	Nucleus (Probable)				560
Q8BGT0 UniProt NPD GO	OSTM1_MOUSE	Osteopetrosis-associated transmembrane protein 1 precursor (Gray-lethal protein)	0.81	+	nuc	1	Membrane; single-pass type I membrane protein	cytosol [IDA]			338
Q7RTW8 UniProt NPD GO	OTOAN_HUMAN	Otoancorin precursor	0.81	-	mit	0	Cell membrane; apical cell membrane; lipid-anchor; GPI-anchor; extracellular side (Probable). At the ...		607039		1153
Q9H0X9 UniProt NPD GO	OSBL5_HUMAN	Oxysterol-binding protein-related protein 5 (OSBP-related protein 5) (ORP-5)	0.81	-	nuc	0		cytosol [NAS]	606733		879
P98109 UniProt NPD GO	LYAM3_SHEEP	P-selectin precursor (Granule membrane protein 140) (GMP-140) (PADGEM) (Leukocyte-endothelial cell a ...	0.81	+	nuc	1	Membrane; single-pass type I membrane protein				769
Q90270 UniProt NPD GO	PO5F1_BRARE	POU domain, class 5, transcription factor 1 (POU domain protein 2)	0.81	+	nuc	0	Nucleus				472
P56223 UniProt NPD GO	PO6F1_RAT	POU domain, class 6, transcription factor 1 (Brain-specific homeobox/POU domain protein 5) (Brain-5) ...	0.81	+	nuc	0	Nucleus				301
Q9UKJ1 UniProt NPD GO	PILRA_HUMAN	Paired immunoglobulin-like type 2 receptor alpha precursor (Inhibitory receptor PILR-alpha) (Cell su ...	0.81	-	end	1	Isoform 1, isoform 2: Cell membrane; single-pass type I membrane protein (Potential). Isoform 3, iso ...	integral to plasma membrane [ISS]	605341		303
Q9QX98 UniProt NPD GO	PTF1A_MOUSE	Pancreas transcription factor 1 subunit alpha (Pancreas-specific transcription factor 1a) (bHLH tran ...	0.81	-	nuc	0	Nucleus. Cytoplasm. In the cytoplasm loses its ability to form the PTF1 complex	cytoplasm [ISS] nucleus [ISS] transcription factor complex [ISS]			324
Q9NJA9 UniProt NPD GO	MYSP_ANISI	Paramyosin (Allergen Ani s 2)	0.81	-	nuc	0	Thick filaments of the myofibrils				869
O35973 UniProt NPD GO	PER1_MOUSE	Period circadian protein 1 (Circadian pacemaker protein Rigui) (mPER) (M-Rigui)	0.81	-	nuc	0	Nucleus	nucleus [IDA]			1291
P37233 UniProt NPD GO	PPARB_XENLA	Peroxisome proliferator-activated receptor beta (PPAR-beta)	0.81	+	nuc	0	Nucleus				396
P54674 UniProt NPD GO	PI3K2_DICDI	Phosphatidylinositol 3-kinase 2 (EC 2.7.1.137) (PI3-kinase) (PtdIns-3-kinase) (PI3K)	0.81	-	nuc	0					1858
Q9Y7K2 UniProt NPD GO	TOR2_SCHPO	Phosphatidylinositol 3-kinase tor2 (EC 2.7.1.137) (PtdIns-3-kinase tor2) (PI3-kinase tor2) (PI3K tor ...	0.81	-	nuc	0					2337
O75747 UniProt NPD GO	P3C2G_HUMAN	Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing gamma polypeptide (EC 2.7.1.154) (Pho ...	0.81	-	nuc	0	Membrane; peripheral membrane protein (By similarity)		609001		1448
P53037 UniProt NPD GO	PSD2_YEAST	Phosphatidylserine decarboxylase proenzyme 2 precursor (EC 4.1.1.65) [Contains: Phosphatidylserine d ...	0.81	+	nuc	0	Golgi apparatus; Golgi stack. Vacuole	Golgi membrane [TAS] vacuolar membrane (sensu Fungi) [TAS]			1138
P59114 UniProt NPD GO	PCIF1_MOUSE	Phosphorylated CTD-interacting factor 1	0.81	-	nuc	0	Nucleus (By similarity)				706
Q91VC4 UniProt NPD GO	PLVAP_MOUSE	Plasmalemma vesicle-associated protein (Plasmalemma vesicle protein 1) (PV-1) (MECA-32 antigen)	0.81	-	nuc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Membrane-associated protein of ...				438
P49413 UniProt NPD GO	UAY_EMENI	Positive regulator of purine utilization	0.81	-	mit	2	Nucleus (Probable)				1060
Q9VW97 UniProt NPD GO	LSDA_DROME	Possible lysine-specific histone demethylase 1 (EC 1.-.-.-)	0.81	-	mit	0	Nucleus (By similarity)				890
Q9JK45 UniProt NPD GO	KCNQ5_MOUSE	Potassium voltage-gated channel subfamily KQT member 5 (Voltage-gated potassium channel subunit Kv7. ...	0.81	-	end	5	Membrane; multi-pass membrane protein				878
Q6UN15 UniProt NPD GO	FIP1_HUMAN	Pre-mRNA 3'-end-processing factor FIP1 (FIP1-like 1) (Factor interacting with PAP) (hFip1) (Rearrang ...	0.81	+	nuc	0	Nucleus		607686		594
Q6BLU9 UniProt NPD GO	PRP28_DEBHA	Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 (EC 3.6.1.-)	0.81	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				580
Q4PA86 UniProt NPD GO	CWC2_USTMA	Pre-mRNA-splicing factor CWC2	0.81	+	nuc	0	Nucleus (By similarity)				480
Q5AWZ6 UniProt NPD GO	CWC26_EMENI	Pre-mRNA-splicing factor cwc26	0.81	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				345
O74370 UniProt NPD GO	ISY1_SCHPO	Pre-mRNA-splicing factor isy1 (Complexed with cdc5 protein 12) (Cell cycle control protein cwf12)	0.81	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				217
Q9SF41 UniProt NPD GO	RH45_ARATH	Probable DEAD-box ATP-dependent RNA helicase 45 (EC 3.6.1.-)	0.81	+	nuc	0					989
Q8S8P5 UniProt NPD GO	WRK33_ARATH	Probable WRKY transcription factor 33 (WRKY DNA-binding protein 33)	0.81	-	nuc	0	Nucleus (Probable)				512
Q9VS78 UniProt NPD GO	CP316_DROME	Probable cytochrome P450 316a1 (EC 1.14.-.-) (CYPCCCXVIA1)	0.81	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				478
Q22706 UniProt NPD GO	EXOC2_CAEEL	Probable exocyst complex component 2 (Exocyst complex component Sec5)	0.81	-	nuc	0					884
Q09792 UniProt NPD GO	KAA8_SCHPO	Probable serine/threonine-protein kinase C22G7.08 (EC 2.7.11.1)	0.81	-	nuc	0					513
P31374 UniProt NPD GO	KAB7_YEAST	Probable serine/threonine-protein kinase YAL017W (EC 2.7.11.1)	0.81	-	nuc	0		cytoplasm [IDA]			1356

You are viewing entries 8451 to 8500 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.