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
P26871 UniProt NPD GO	RT12_MARPO	Mitochondrial ribosomal protein S12	0.66	-	nuc	0	Mitochondrion				126
P27070 UniProt NPD GO	RT12_PANGI	Mitochondrial ribosomal protein S12	0.66	-	nuc	0	Mitochondrion				125
P68535 UniProt NPD GO	RT12_PETHY	Mitochondrial ribosomal protein S12	0.66	-	nuc	0	Mitochondrion				125
P68536 UniProt NPD GO	RT12_PETPA	Mitochondrial ribosomal protein S12	0.66	-	nuc	0	Mitochondrion				125
P05716 UniProt NPD GO	RT14_VICFA	Mitochondrial ribosomal protein S14	0.66	-	nuc	0	Mitochondrion				100
P27527 UniProt NPD GO	RT19_PETHY	Mitochondrial ribosomal protein S19	0.66	-	mit	0	Mitochondrion				94
P46755 UniProt NPD GO	RT04_ACACA	Mitochondrial ribosomal protein S4	0.66	-	cyt	0	Mitochondrion				374
Q60700 UniProt NPD GO	M3K12_MOUSE	Mitogen-activated protein kinase kinase kinase 12 (EC 2.7.11.25) (Mixed lineage kinase) (Leucine-zip ...	0.66	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	cytosol [IDA] plasma membrane [IDA]			888
Q63796 UniProt NPD GO	M3K12_RAT	Mitogen-activated protein kinase kinase kinase 12 (EC 2.7.11.25) (Mixed lineage kinase) (Leucine-zip ...	0.66	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	cytosol [ISS] plasma membrane [ISS]			888
P70218 UniProt NPD GO	M4K1_MOUSE	Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) (MAPK/ERK kinase kinase kinase ...	0.66	-	nuc	0				1UTI	827
Q8IZK6 UniProt NPD GO	MCLN2_HUMAN	Mucolipin-2	0.66	-	end	5	Membrane; multi-pass membrane protein (Potential)		607399		538
Q03372 UniProt NPD GO	HMSH_DROME	Muscle segmentation homeobox (Protein drop) (Protein msh)	0.66	+	mit	0	Nucleus				515
O15457 UniProt NPD GO	MSH4_HUMAN	MutS protein homolog 4	0.66	-	nuc	0		nucleus [TAS]	602105		936
P58340 UniProt NPD GO	MLF1_HUMAN	Myeloid leukemia factor 1 (Myelodysplasia-myeloid leukemia factor 1)	0.66	-	nuc	0	Cytoplasm. Nucleus; nucleolus. Found in the nucleolus, when fused to NPM	centrosome [ISS] cytoplasm [ISS]	601402		268
Q2KJ24 UniProt NPD GO	MTMR9_BOVIN	Myotubularin-related protein 9	0.66	-	cyt	0					543
Q8SQ24 UniProt NPD GO	MYOZ1_BOVIN	Myozenin-1 (Calsarcin-2)	0.66	-	nuc	0	Localized to the nucleus and pseudopodia of undifferentiated cells and detected throughout the myotu ...				297
Q9DBH0 UniProt NPD GO	WWP2_MOUSE	NEDD4-like E3 ubiquitin-protein ligase WWP2 (EC 6.3.2.-) (WW domain-containing protein 2)	0.66	-	nuc	0					870
Q15742 UniProt NPD GO	NAB2_HUMAN	NGFI-A-binding protein 2 (EGR-1-binding protein 2) (Melanoma-associated delayed early response prote ...	0.66	+	nuc	0	Nucleus (By similarity). Isoform 2 is not localized to the nucleus (By similarity)		602381		525
Q9H093 UniProt NPD GO	NUAK2_HUMAN	NUAK family SNF1-like kinase 2 (EC 2.7.11.1) (SNF1/AMP kinase-related kinase) (SNARK)	0.66	-	nuc	0					628
Q02916 UniProt NPD GO	NFL_COTJA	Neurofilament triplet L protein (Neurofilament light polypeptide) (NF-L)	0.66	-	nuc	0					555
O02316 UniProt NPD GO	NHR77_CAEEL	Nuclear hormone receptor family member nhr-77	0.66	-	cyt	0	Nucleus (Potential)				362
Q9VKJ3 UniProt NPD GO	NU160_DROME	Nuclear pore complex protein Nup160 homolog	0.66	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex				1411
Q5E9S2 UniProt NPD GO	NFYA_BOVIN	Nuclear transcription factor Y subunit alpha (Nuclear transcription factor Y subunit A) (NF-YA) (CAA ...	0.66	+	nuc	0	Nucleus (By similarity)				341
P23511 UniProt NPD GO	NFYA_HUMAN	Nuclear transcription factor Y subunit alpha (Nuclear transcription factor Y subunit A) (NF-YA) (CAA ...	0.66	+	cyt	0	Nucleus	CCAAT-binding factor complex [IDA] nucleus [IDA]	189903		347
P23708 UniProt NPD GO	NFYA_MOUSE	Nuclear transcription factor Y subunit alpha (Nuclear transcription factor Y subunit A) (NF-YA) (CAA ...	0.66	+	cyt	0	Nucleus	nucleus [IDA]			346
P18576 UniProt NPD GO	NFYA_RAT	Nuclear transcription factor Y subunit alpha (Nuclear transcription factor Y subunit A) (NF-YA) (CAA ...	0.66	+	nuc	0	Nucleus				341
Q5R8V9 UniProt NPD GO	NIPA_PONPY	Nuclear-interacting partner of ALK (Nuclear-interacting partner of anaplastic lymphoma kinase) (Zinc ...	0.66	-	nuc	0	Nucleus (By similarity)				502
Q6NRQ2 UniProt NPD GO	NOC41_XENLA	Nucleolar complex protein 4 homolog A (NOC4 protein homolog A) (NOC4-like protein A) (Nucleolar comp ...	0.66	-	end	3	Nucleus; nuclear membrane; multi-pass membrane protein (By similarity). Nucleus; nucleolus (By simil ...				526
O60287 UniProt NPD GO	NPA1P_HUMAN	Nucleolar preribosomal-associated protein 1 (Fragment)	0.66	-	end	0	Nucleus; nucleolus	nucleolus [NAS]	608865		2248
Q5M7P5 UniProt NPD GO	NOL6_XENTR	Nucleolar protein 6	0.66	-	cyt	0	Nucleus; nucleolus (By similarity)				1145
Q5RFS5 UniProt NPD GO	OCLN_PONPY	Occludin	0.66	-	end	5	Membrane; multi-pass membrane protein				522
Q8K3K8 UniProt NPD GO	OPTN_MOUSE	Optineurin	0.66	-	nuc	0	Cytoplasm; perinuclear region. Golgi apparatus. Found in the perinuclear region and associates with ...				584
Q64249 UniProt NPD GO	NR6A1_MOUSE	Orphan nuclear receptor NR6A1 (Germ cell nuclear factor) (GCNF) (Retinoid receptor-related testis-sp ...	0.66	-	nuc	0	Nucleus (Probable)	transcription factor complex [IDA]			495
P22059 UniProt NPD GO	OSBP1_HUMAN	Oxysterol-binding protein 1	0.66	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein. When bound to oxysterols it ...		167040		807
Q925N3 UniProt NPD GO	PEX5R_RAT	PEX5-related protein (Peroxin-5-related protein) (Pex5Rp) (PEX5-like protein) (TPR-containing Rab8b- ...	0.66	-	nuc	0	Cytoplasm. Some fraction is membrane associated via its interaction with RAB8B				602
Q9NQV5 UniProt NPD GO	PRD11_HUMAN	PR domain-containing protein 11	0.66	+	nuc	0					504
O60811 UniProt NPD GO	PRAM2_HUMAN	PRAME family member 2	0.66	-	mit	0					474
Q62798 UniProt NPD GO	PRRXL_RAT	Paired-related homeobox protein-like 1 (Homeobox protein DRG11)	0.66	+	nuc	0	Nucleus (By similarity)				263
Q9R0C0 UniProt NPD GO	PLDN_MOUSE	Pallidin (Pallid protein) (Syntaxin 13-interacting protein)	0.66	-	nuc	0	Cytoplasm. It can exist as a soluble protein as well as a peripheral membrane protein	endosome [IDA]			172
Q13219 UniProt NPD GO	PAPPA_HUMAN	Pappalysin-1 precursor (EC 3.4.24.79) (Pregnancy-associated plasma protein-A) (PAPP-A) (Insulin-like ...	0.66	-	nuc	0	Secreted protein	extracellular region [IDA]	176385		1628
Q8C2E4 UniProt NPD GO	PTCD1_MOUSE	Pentatricopeptide repeat protein 1	0.66	-	cyt	0					695
Q5KNY5 UniProt NPD GO	PPIL4_CRYNE	Peptidyl-prolyl cis-trans isomerase-like 4 (EC 5.2.1.8) (PPIase) (Rotamase)	0.66	+	nuc	0	Nucleus (By similarity)				504
P48676 UniProt NPD GO	PERI_XENLA	Peripherin (Neuronal intermediate filament IF3)	0.66	-	mit	0					456
Q9HG03 UniProt NPD GO	PEX6_PENCH	Peroxisomal biogenesis factor 6 (Peroxin-6)	0.66	+	cyt	0					1459
P34230 UniProt NPD GO	PXA2_YEAST	Peroxisomal long-chain fatty acid import protein 1 (Peroxisomal ABC transporter 2)	0.66	-	nuc	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein	integral to peroxisomal membrane [IDA]			853
O75381 UniProt NPD GO	PEX14_HUMAN	Peroxisomal membrane protein PEX14 (Peroxin-14) (Peroxisomal membrane anchor protein PEX14) (PTS1 re ...	0.66	-	nuc	0	Peroxisome; peroxisomal membrane; peripheral membrane protein; cytoplasmic side	integral to peroxisomal membrane [TAS] peroxisome [TAS]	601791		377
P29194 UniProt NPD GO	CAPP2_SORBI	Phosphoenolpyruvate carboxylase 2 (EC 4.1.1.31) (PEPCase 2) (PEPC 2) (CP28)	0.66	-	nuc	0	Cytoplasm				960
Q8N6C7 UniProt NPD GO	PGSF1_HUMAN	Pituitary gland-specific factor 1	0.66	-	mit	0					128
Q8CGT6 UniProt NPD GO	PIWL4_MOUSE	Piwi-like protein 4 (mAgo5)	0.66	-	mit	0					815
Q9Y446 UniProt NPD GO	PKP3_HUMAN	Plakophilin-3	0.66	-	nuc	0	Nucleus. Cell membrane; cell-cell junction; anchoring junction; desmosome. Nuclear and associated wi ...	intercellular junction [TAS]	605561		797

You are viewing entries 15901 to 15950 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.