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
P11483 UniProt NPD GO	ACM3_PIG	Muscarinic acetylcholine receptor M3	0.88	+	vac	7	Membrane; multi-pass membrane protein				590
P08483 UniProt NPD GO	ACM3_RAT	Muscarinic acetylcholine receptor M3	0.88	+	vac	7	Membrane; multi-pass membrane protein				589
P21572 UniProt NPD GO	MYOD1_COTJA	Myoblast determination protein 1 homolog (Myogenic factor 1)	0.88	+	nuc	0	Nucleus				297
P13904 UniProt NPD GO	MYODA_XENLA	Myoblast determination protein 1 homolog A (Myogenic factor 1)	0.88	+	nuc	0	Nucleus				289
Q91154 UniProt NPD GO	MYF5_NOTVI	Myogenic factor 5 (Myf-5)	0.88	+	nuc	0	Nucleus				256
P24700 UniProt NPD GO	MYF5_XENLA	Myogenic factor 5 (Myf-5)	0.88	+	nuc	0	Nucleus				255
Q05000 UniProt NPD GO	MYS_PODCA	Myosin heavy chain (Fragment)	0.88	-	nuc	0	Thick filaments of the myofibrils				692
P42527 UniProt NPD GO	KMHA_DICDI	Myosin heavy chain kinase A (EC 2.7.11.7) (MHCK A)	0.88	-	nuc	0					1146
Q90339 UniProt NPD GO	MYSS_CYPCA	Myosin heavy chain, fast skeletal muscle	0.88	+	nuc	0	Thick filaments of the myofibrils				1935
Q9Y7Z8 UniProt NPD GO	MYO1_SCHPO	Myosin-1	0.88	-	nuc	0	Cytoplasm; cell cortex. Localizes to cortical patches at the tips of growing cells and at sites of c ...	actin cortical patch [IDA] cell tip [IDA] contractile ring (sensu Fungi) [TAS] lipid raft [IDA] myosin [TAS]			1217
O74805 UniProt NPD GO	MYO51_SCHPO	Myosin-51 (Myosin type V-1)	0.88	-	end	0	Cytoplasm. Component of the cytokinetic actin ring (CAR)	contractile ring (sensu Fungi) [IDA]			1471
P70569 UniProt NPD GO	MYO5B_RAT	Myosin-5B (Myosin Vb) (Myosin heavy chain myr 6)	0.88	-	nuc	0					1846
Q13615 UniProt NPD GO	MTMR3_HUMAN	Myotubularin-related protein 3 (EC 3.1.3.48) (FYVE domain-containing dual specificity protein phosph ...	0.88	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	cytoplasm [IDA] membrane fraction [IDA]	603558		1198
O75113 UniProt NPD GO	N4BP1_HUMAN	NEDD4-binding protein 1 (N4BP1) (Fragment)	0.88	+	nuc	0	Nucleus. In discrete circular structures (By similarity)				943
Q9H0M0 UniProt NPD GO	WWP1_HUMAN	NEDD4-like E3 ubiquitin-protein ligase WWP1 (EC 6.3.2.-) (WW domain-containing protein 1) (Atropin-1 ...	0.88	-	nuc	0		ubiquitin ligase complex [NAS]	602307	1ND7	922
P56183 UniProt NPD GO	NNP1_MOUSE	NNP-1 protein (Novel nuclear protein 1) (Nop52)	0.88	+	nuc	0	Nucleus; nucleolus (By similarity)				494
Q95107 UniProt NPD GO	WASL_BOVIN	Neural Wiskott-Aldrich syndrome protein (N-WASP)	0.88	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Preferentially localized in the cytoplasm when p ...				505
Q91YD9 UniProt NPD GO	WASL_MOUSE	Neural Wiskott-Aldrich syndrome protein (N-WASP)	0.88	-	nuc	0	Cytoplasm. Nucleus. Preferentially localized in the cytoplasm when phosphorylated and in the nucleus ...	cytoplasm [IC] lamellipodium [IDA]			501
Q04690 UniProt NPD GO	NF1_MOUSE	Neurofibromin (Neurofibromatosis-related protein NF-1)	0.88	-	mit	0					2841
P97460 UniProt NPD GO	NPAS2_MOUSE	Neuronal PAS domain-containing protein 2 (Neuronal PAS2)	0.88	+	nuc	0	Nucleus (Potential)				816
Q9TST2 UniProt NPD GO	NT3_FELCA	Neurotrophin-3 precursor (NT-3) (Neurotrophic factor) (HDNF) (Nerve growth factor 2) (NGF-2)	0.88	-	nuc	0	Secreted protein				257
P70313 UniProt NPD GO	NOS3_MOUSE	Nitric-oxide synthase, endothelial (EC 1.14.13.39) (EC-NOS) (NOS type III) (NOSIII) (Endothelial NOS ...	0.88	+	cyt	0					1201
Q62600 UniProt NPD GO	NOS3_RAT	Nitric-oxide synthase, endothelial (EC 1.14.13.39) (EC-NOS) (NOS type III) (NOSIII) (Endothelial NOS ...	0.88	+	cyt	0					1201
Q9Y7U4 UniProt NPD GO	NSE3_SCHPO	Non-structural maintenance of chromosome element 3 (Non-SMC element 3)	0.88	+	nuc	0	Nucleus	nucleus [TAS] Smc5-Smc6 complex [IPI]			328
Q9N4M4 UniProt NPD GO	ANC1_CAEEL	Nuclear anchorage protein 1 (Anchorage 1 protein) (Nesprin homolog)	0.88	+	nuc	0	Nucleus; nuclear membrane; single-pass type IV membrane protein (Potential). The largest part of the ...	cytoplasm [IDA]			8545
P97305 UniProt NPD GO	NFAC3_MOUSE	Nuclear factor of activated T-cells, cytoplasmic 3 (NF-ATc3) (NFATc3) (T cell transcription factor N ...	0.88	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic for the phosphorylated form and nuclear after activation that is con ...	cytoplasm [IDA] nucleus [IDA]			1075
Q6PIJ4 UniProt NPD GO	NFRKB_MOUSE	Nuclear factor related to kappa-B-binding protein (DNA-binding protein R kappa-B)	0.88	+	nuc	0	Nucleus (Probable)				1296
Q05670 UniProt NPD GO	FUS2_YEAST	Nuclear fusion protein FUS2	0.88	-	nuc	0	Localizes near the site of cell fusion	mating projection tip [IDA] mitochondrion [IDA]			677
P21330 UniProt NPD GO	GAGJ_DROME	Nucleic-acid-binding protein from mobile element jockey (ORF1)	0.88	-	nuc	0					568
Q99ME9 UniProt NPD GO	NOG1_MOUSE	Nucleolar GTP-binding protein 1 (Chronic renal failure gene protein) (GTP-binding protein NGB)	0.88	+	nuc	0	Nucleus; nucleolus (By similarity)				633
Q5SY16 UniProt NPD GO	NOL9_HUMAN	Nucleolar protein 9	0.88	+	nuc	0	Nucleus; nucleolus				702
Q3ZBK7 UniProt NPD GO	GLE1_BOVIN	Nucleoporin GLE1 (GLE1-like protein)	0.88	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Shuttles between the nucleus and the cytoplasm. ...				698
O95948 UniProt NPD GO	ONEC2_HUMAN	One cut domain family member 2 (Transcription factor ONECUT-2) (OC-2)	0.88	-	nuc	0	Nucleus		604894		485
Q6XBJ3 UniProt NPD GO	ONEC2_MOUSE	One cut domain family member 2 (Transcription factor ONECUT-2) (OC-2)	0.88	-	nuc	0	Nucleus				486
P54789 UniProt NPD GO	ORC1_SCHPO	Origin recognition complex subunit 1	0.88	-	mit	0	Nucleus	nuclear chromatin [IDA] nuclear origin of replication recognition c... [IDA]			707
Q06219 UniProt NPD GO	NR4A2_MOUSE	Orphan nuclear receptor NR4A2 (Orphan nuclear receptor NURR1) (NUR-related factor 1)	0.88	-	nuc	0	Nucleus	nucleus [IDA]			598
Q9Z0Y9 UniProt NPD GO	NR1H3_MOUSE	Oxysterols receptor LXR-alpha (Liver X receptor alpha) (Nuclear orphan receptor LXR-alpha)	0.88	-	nuc	0	Nucleus (Potential)	nucleus [IDA]		2ACL	445
Q8WUB8 UniProt NPD GO	PHF10_HUMAN	PHD finger protein 10 (XAP135)	0.88	-	nuc	0	Nucleus (Probable)				410
P20265 UniProt NPD GO	PO3F2_HUMAN	POU domain, class 3, transcription factor 2 (Nervous system-specific octamer-binding transcription f ...	0.88	+	nuc	0	Nucleus		600494		443
P31365 UniProt NPD GO	P3F2A_XENLA	POU domain, class 3, transcription factor 2-A (Transcription factor POU3-A) (XLPOU3)	0.88	+	nuc	0	Nucleus				382
P70030 UniProt NPD GO	P3F2B_XENLA	POU domain, class 3, transcription factor 2-B (Transcription factor POU3-B) (XLPOU3B)	0.88	+	nuc	0	Nucleus				385
Q9CXE0 UniProt NPD GO	PRDM5_MOUSE	PR domain zinc finger protein 5 (PR domain-containing protein 5)	0.88	-	nuc	0	Nucleus (Potential)				599
Q01202 UniProt NPD GO	MYSP_BRUMA	Paramyosin	0.88	-	nuc	0	Thick filaments of the myofibrils				880
Q8T305 UniProt NPD GO	MYSP_TAESA	Paramyosin	0.88	-	nuc	0	Thick filaments of the myofibrils				863
Q9GMB7 UniProt NPD GO	PTHR_HORSE	Parathyroid hormone-related protein (PTH-rP) (PTHrP) [Contains: Osteostatin] (Fragment)	0.88	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Secreted protein (By similarity)				137
P13085 UniProt NPD GO	PTHR_RAT	Parathyroid hormone-related protein precursor (PTH-rP) (PTHrP) (PLP) [Contains: Osteostatin]	0.88	+	mit	0	Cytoplasm (By similarity). Nucleus (By similarity). Secreted protein (By similarity)				177
Q865B7 UniProt NPD GO	PRGC1_BOVIN	Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPAR gamma coactivator 1-alpha ...	0.88	-	nuc	0	Nucleus (By similarity)	DNA-directed RNA polymerase II, core complex [ISS] nucleus [ISS]			796
Q9UW20 UniProt NPD GO	PIK1_CANAL	Phosphatidylinositol 4-kinase PIK1alpha (EC 2.7.1.67) (PI4-kinase) (PtdIns-4-kinase)	0.88	-	nuc	0	Nucleus (By similarity)				977
O13853 UniProt NPD GO	ITS3_SCHPO	Phosphatidylinositol-4-phosphate 5-kinase its3 (EC 2.7.1.68) (1-phosphatidylinositol-4-phosphate kin ...	0.88	-	nuc	0	Nucleus. Membrane; peripheral membrane. The active form of the enzyme is membrane-associated and con ...	cell septum [IDA] plasma membrane [IDA]			742
Q8GVE8 UniProt NPD GO	CAPP4_ARATH	Phosphoenolpyruvate carboxylase 4 (EC 4.1.1.31) (PEPCase 4) (PEPC 4) (AtPPC4)	0.88	-	nuc	0	Cytoplasm (By similarity)				1032

You are viewing entries 5201 to 5250 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.