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
Q96GX5 UniProt NPD GO	MASTL_HUMAN	Microtubule-associated serine/threonine-protein kinase-like (EC 2.7.11.1)	0.86	-	nuc	0			608221		879
Q9Y6R4 UniProt NPD GO	M3K4_HUMAN	Mitogen-activated protein kinase kinase kinase 4 (EC 2.7.11.25) (MAPK/ERK kinase kinase 4) (MEK kina ...	0.86	-	nuc	0			602425		1607
O95382 UniProt NPD GO	M3K6_HUMAN	Mitogen-activated protein kinase kinase kinase 6 (EC 2.7.11.25)	0.86	-	nuc	0			604468		1011
Q8IVH8 UniProt NPD GO	M4K3_HUMAN	Mitogen-activated protein kinase kinase kinase kinase 3 (EC 2.7.11.1) (MAPK/ERK kinase kinase kinase ...	0.86	-	nuc	0			604921		894
P38198 UniProt NPD GO	STU1_YEAST	Mitotic spindle protein STU1	0.86	-	nuc	0		spindle pole body [IDA]			1513
P26038 UniProt NPD GO	MOES_HUMAN	Moesin (Membrane-organizing extension spike protein)	0.86	-	nuc	0	Cytoplasm (By similarity). Phosphorylated form is enriched in microvilli-like structures at apical m ...	cytoskeleton [TAS] plasma membrane [TAS]	309845	1SGH	576
Q4WJT7 UniProt NPD GO	MRD1_ASPFU	Multiple RNA-binding domain-containing protein 1	0.86	+	nuc	0	Nucleus (By similarity)				825
Q9N2A3 UniProt NPD GO	ACM3_GORGO	Muscarinic acetylcholine receptor M3	0.86	+	vac	7	Membrane; multi-pass membrane protein				590
O94065 UniProt NPD GO	MSH4_CANAL	MutS protein homolog 4	0.86	-	nuc	0					803
Q02346 UniProt NPD GO	MYOD1_RAT	Myoblast determination protein 1	0.86	+	nuc	0	Nucleus				318
Q02078 UniProt NPD GO	MEF2A_HUMAN	Myocyte-specific enhancer factor 2A (Serum response factor-like protein 1)	0.86	-	nuc	0	Nucleus	nucleus [TAS]	600660	1EGW	507
Q6VNZ9 UniProt NPD GO	MYF6_BRARE	Myogenic factor 6 (Myf-6) (Muscle-specific regulatory factor 4)	0.86	+	nuc	0	Nucleus (By similarity)				239
O94477 UniProt NPD GO	MYO52_SCHPO	Myosin-52 (Myosin type V-2)	0.86	-	nuc	0	Cytoplasm. Localized at the cell poles and septum	cell cortex of cell tip [IDA]			1516
Q9Y4I1 UniProt NPD GO	MYO5A_HUMAN	Myosin-5A (Myosin Va) (Dilute myosin heavy chain, non-muscle) (Myosin heavy chain 12) (Myoxin)	0.86	-	nuc	0		growth cone [NAS] neuron projection [NAS]	609227		1855
Q9ULV0 UniProt NPD GO	MYO5B_HUMAN	Myosin-5B (Myosin Vb)	0.86	-	nuc	0			606540		1849
P53687 UniProt NPD GO	HST3_YEAST	NAD-dependent deacetylase HST3 (EC 3.5.1.-) (Homologous to SIR2 protein 3)	0.86	-	nuc	0	Nucleus (Potential)	nucleus [IC]			447
Q9JLM2 UniProt NPD GO	CD244_RAT	Natural killer cell receptor 2B4 precursor (NKR2B4) (NK cell type I receptor protein 2B4) (CD244 ant ...	0.86	-	exc	0	Membrane; single-pass type I membrane protein (Potential)				311
Q7TNH6 UniProt NPD GO	NPHP3_MOUSE	Nephrocystin-3	0.86	-	cyt	0					1324
P52494 UniProt NPD GO	TREA_CANAL	Neutral trehalase (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.86	-	nuc	0					907
Q03435 UniProt NPD GO	NHP10_YEAST	Non-histone protein 10 (High mobility group protein 2)	0.86	-	nuc	0	Nucleus	INO80 complex [IPI] nucleus [IDA]			203
P40010 UniProt NPD GO	NUG1_YEAST	Nuclear GTP-binding protein NUG1 (Nuclear GTPase 1)	0.86	+	nuc	0	Nucleus	nucleolus [IDA] nucleus [IDA]			520
O13335 UniProt NPD GO	NDE1_NEUCR	Nuclear distribution protein nudE homolog 1 (Nuclear distribution protein ro-11)	0.86	-	nuc	0	Cytoplasm. Localizes to the plus ends of microtubules (By similarity)				697
O88942 UniProt NPD GO	NFAC1_MOUSE	Nuclear factor of activated T-cells, cytoplasmic 1 (NFAT transcription complex cytosolic component) ...	0.86	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic for the phosphorylated form and nucl ...	cytoplasm [IDA] nucleus [IDA]			717
Q94407 UniProt NPD GO	NHR48_CAEEL	Nuclear hormone receptor family member nhr-48	0.86	-	nuc	0	Nucleus (Potential)				780
Q8NI08 UniProt NPD GO	NCOA7_HUMAN	Nuclear receptor coactivator 7 (140 kDa estrogen receptor-associated protein) (Estrogen nuclear rece ...	0.86	+	nuc	0	Nucleus (Probable)		609752		942
O77645 UniProt NPD GO	STP2_CANFA	Nuclear transition protein 2 (TP-2) (TP2)	0.86	-	mit	0	Nucleus (By similarity)				129
O13874 UniProt NPD GO	NOC2_SCHPO	Nucleolar complex protein 2 homolog	0.86	-	nuc	0	Nucleus (Probable)				528
Q5BDC8 UniProt NPD GO	NOP12_EMENI	Nucleolar protein 12	0.86	-	nuc	0	Nucleus; nucleolus (By similarity)				520
Q08208 UniProt NPD GO	NOP12_YEAST	Nucleolar protein 12	0.86	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			459
P53883 UniProt NPD GO	NOP13_YEAST	Nucleolar protein 13	0.86	-	nuc	0	Nucleus; nucleolus. Also found in nucleoplam	nucleolus [IDA] nucleoplasm [IDA]			403
Q9NP64 UniProt NPD GO	NO40_HUMAN	Nucleolar protein of 40 kDa (pNO40) (Zinc finger CCHC domain-containing protein 17) (Putative S1 RNA ...	0.86	+	nuc	0	Nucleus; nucleolus			2CQO	241
P52594 UniProt NPD GO	NUPL_HUMAN	Nucleoporin-like protein RIP (HIV-1 Rev-binding protein) (Rev-interacting protein) (Rev/Rex activati ...	0.86	-	nuc	0	Nucleus. Cytoplasmic vesicle	nuclear pore [TAS]	600862		562
Q5T2D3 UniProt NPD GO	OTUD3_HUMAN	OTU domain-containing protein 3	0.86	-	nuc	0					398
P18748 UniProt NPD GO	ZO29_XENLA	Oocyte zinc finger protein XLCOF29	0.86	-	nuc	0	Nucleus (Potential)				537
P51179 UniProt NPD GO	NR4A3_RAT	Orphan nuclear receptor NR4A3 (Nuclear hormone receptor NOR-1/NOR-2) (Neuron-derived orphan receptor ...	0.86	-	nuc	0	Nucleus (Potential)				628
Q9QZB6 UniProt NPD GO	NR4A3_MOUSE	Orphan nuclear receptor NR4A3 (Orphan nuclear receptor TEC) (Translocated in extraskeletal chondrosa ...	0.86	-	nuc	0	Nucleus (Potential)				627
Q9BZF3 UniProt NPD GO	OSBL6_HUMAN	Oxysterol-binding protein-related protein 6 (OSBP-related protein 6) (ORP-6)	0.86	-	nuc	0			606734		934
Q9BZF1 UniProt NPD GO	OSBL8_HUMAN	Oxysterol-binding protein-related protein 8 (OSBP-related protein 8) (ORP-8)	0.86	-	nuc	1			606736	1V88	889
Q62685 UniProt NPD GO	NR1H3_RAT	Oxysterols receptor LXR-alpha (Liver X receptor alpha) (Nuclear orphan receptor LXR-alpha) (RLD-1)	0.86	-	nuc	0	Nucleus (Potential)				445
O15018 UniProt NPD GO	PDZD2_HUMAN	PDZ domain-containing protein 2 (PDZ domain-containing protein 3) (Activated in prostate cancer prot ...	0.86	+	nuc	0	Nucleus (By similarity). Cytoplasm. Endoplasmic reticulum. At cell-cell contacts in lung epithelial ...	cytoplasm [IDA] endoplasmic reticulum [ISS] extracellular region [ISS] intercellular junction [ISS] nucleus [ISS]			2839
Q8NEN9 UniProt NPD GO	PDZD8_HUMAN	PDZ domain-containing protein 8 (Sarcoma antigen NY-SAR-84/NY-SAR-104)	0.86	-	exc	1 *					1154
Q8BXA7 UniProt NPD GO	PHLPL_MOUSE	PH domain leucine-rich repeat protein phosphatase-like (EC 3.1.3.16)	0.86	-	nuc	0	Cytoplasm (Probable). Membrane; peripheral membrane protein (By similarity). May be membrane-associa ...				1320
O43189 UniProt NPD GO	PHF1_HUMAN	PHD finger protein 1 (Protein PHF1)	0.86	-	nuc	0	Nucleus (Potential)		602881		567
Q8IWS0 UniProt NPD GO	PHF6_HUMAN	PHD finger protein 6 (PHD-like zinc finger protein)	0.86	+	nuc	0	Nucleus. Nucleus; nucleolus. Nuclear, it particularly localizes to the nucleolus		301900		365
Q9HAZ2 UniProt NPD GO	PRD16_HUMAN	PR domain zinc finger protein 16 (PR domain-containing protein 16) (Transcription factor MEL1)	0.86	-	nuc	0	Nucleus (Potential)	nucleus [IC]	605557		1276
Q96ST3 UniProt NPD GO	SIN3A_HUMAN	Paired amphipathic helix protein Sin3a (Transcriptional corepressor Sin3a) (Histone deacetylase comp ...	0.86	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]	607776		1273
Q02171 UniProt NPD GO	MYSP_ONCVO	Paramyosin	0.86	-	nuc	0	Thick filaments of the myofibrils				879
P52211 UniProt NPD GO	PTHR_CANFA	Parathyroid hormone-related protein precursor (PTH-rP) (PTHrP) [Contains: Osteostatin]	0.86	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Secreted protein (By similarity)				177
P0C196 UniProt NPD GO	PPIL4_USTMA	Peptidyl-prolyl cis-trans isomerase-like 4 (EC 5.2.1.8) (PPIase) (Rotamase)	0.86	+	nuc	0	Nucleus (By similarity)				551
O43933 UniProt NPD GO	PEX1_HUMAN	Peroxisome biogenesis factor 1 (Peroxin-1) (Peroxisome biogenesis disorder protein 1)	0.86	-	nuc	0	Cytoplasm. Peroxisome; peroxisomal membrane. Associated with peroxisomal membranes	peroxisome [TAS]	602136		1283

You are viewing entries 6151 to 6200 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.