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
P28025 UniProt NPD GO	EG51_XENLA	Kinesin-related motor protein Eg5 1	0.87	-	nuc	0	Cytoplasm. Concentrated around the polar ends of both meiotic and mitotic spindles				1060
O35738 UniProt NPD GO	KLF12_MOUSE	Krueppel-like factor 12 (Transcriptional repressor AP-2rep)	0.87	-	nuc	0	Nucleus				402
Q9FN11 UniProt NPD GO	LBD37_ARATH	LOB domain-containing protein 37	0.87	-	nuc	0					250
Q71RC2 UniProt NPD GO	LARP4_HUMAN	La-related protein 4 (La ribonucleoprotein domain family member 4)	0.87	-	nuc	0				2CQK	723
Q96NI6 UniProt NPD GO	LRFN5_HUMAN	Leucine-rich repeat and fibronectin type-III domain-containing protein 5 precursor	0.87	-	end	1	Membrane; single-pass type I membrane protein (Potential)				719
Q8BXA0 UniProt NPD GO	LRFN5_MOUSE	Leucine-rich repeat and fibronectin type-III domain-containing protein 5 precursor	0.87	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				719
Q8IUZ0 UniProt NPD GO	LRC49_HUMAN	Leucine-rich repeat-containing protein 49	0.87	-	nuc	0					685
Q10077 UniProt NPD GO	SNT2_SCHPO	Lid2 complex component snt2 (Lid2C component snt2)	0.87	-	nuc	0	Nucleus (Probable)	Lid2 complex [IDA]			1131
Q99PI5 UniProt NPD GO	LPIN2_MOUSE	Lipin-2	0.87	+	nuc	0	Nucleus (Potential)				893
Q9QXN1 UniProt NPD GO	LEF1_RAT	Lymphoid enhancer-binding factor 1 (LEF-1)	0.87	+	nuc	0	Nucleus (By similarity). Found in nuclear bodies upon PIASG binding (By similarity)				397
Q9HG12 UniProt NPD GO	MATA1_KLULA	Mating-type protein A1 (A1 transcription factor) (MATa1 protein)	0.87	-	nuc	0	Nucleus (By similarity)				228
Q5GGR6 UniProt NPD GO	MATK_CUBDO	Maturase K (Intron maturase)	0.87	-	cyt	0	Plastid; chloroplast				505
Q8SM14 UniProt NPD GO	MATK_KECCO	Maturase K (Intron maturase)	0.87	-	nuc	0	Plastid; chloroplast				513
Q507Y2 UniProt NPD GO	MATK_RANTR	Maturase K (Intron maturase)	0.87	-	cyt	0	Plastid; chloroplast				508
P20050 UniProt NPD GO	HOP1_YEAST	Meiosis-specific protein HOP1	0.87	-	nuc	0	Synapsis of meiotic chromosomes	synaptonemal complex [TAS]			605
Q9Y7J9 UniProt NPD GO	MCP5_SCHPO	Meiotic coiled-coil protein 5 (Nuclear migration protein num1) (Meiotically up-regulated protein 21) ...	0.87	-	nuc	0	Cytoplasm. Cell cortex. Localizes to the cell cortex during the 'horsetail' phase of mitosis				968
Q09772 UniProt NPD GO	RDH54_SCHPO	Meiotic recombination protein rdh54 (EC 3.6.1.-) (ATP-dependent helicase rdh54) (RAD54 protein homol ...	0.87	-	nuc	0	Nucleus				811
Q9BYG8 UniProt NPD GO	MLZE_HUMAN	Melanoma-derived leucine zipper-containing extranuclear factor	0.87	-	cyt	0	Cytoplasm	cytoplasm [IDA] nucleus [NAS]	608384		508
Q03943 UniProt NPD GO	IM30_PEA	Membrane-associated 30 kDa protein, chloroplast precursor (M30)	0.87	-	nuc	0	Plastid; chloroplast; chloroplast inner membrane; peripheral membrane protein. Plastid; chloroplast; ...				323
P59750 UniProt NPD GO	MERL_PAPAN	Merlin (Moesin-ezrin-radixin-like protein) (Neurofibromin-2) (Schwannomin)	0.87	-	mit	0					595
Q63648 UniProt NPD GO	MERL_RAT	Merlin (Moesin-ezrin-radixin-like protein) (Neurofibromin-2) (Schwannomin) (Fragment)	0.87	-	nuc	0					586
Q04716 UniProt NPD GO	RT03_PETHY	Mitochondrial ribosomal protein S3	0.87	-	nuc	0	Mitochondrion				562
P02382 UniProt NPD GO	RMS5_EMENI	Mitochondrial ribosomal protein S5	0.87	+	nuc	0	Mitochondrion				410
Q99558 UniProt NPD GO	M3K14_HUMAN	Mitogen-activated protein kinase kinase kinase 14 (EC 2.7.11.25) (NF-kappa beta-inducing kinase) (Se ...	0.87	+	nuc	0	Cytoplasm		604655		947
P30290 UniProt NPD GO	MIK1_SCHPO	Mitosis inhibitor protein kinase mik1 (EC 2.7.11.1)	0.87	-	nuc	0					581
P26042 UniProt NPD GO	MOES_PIG	Moesin (Membrane-organizing extension spike protein)	0.87	-	nuc	0	Cytoplasm (By similarity). Phosphorylated form is enriched in microvilli-like structures at apical m ...				576
P41984 UniProt NPD GO	ACM3_BOVIN	Muscarinic acetylcholine receptor M3	0.87	+	vac	7	Membrane; multi-pass membrane protein				590
P25846 UniProt NPD GO	MSH1_YEAST	MutS protein homolog 1	0.87	-	nuc	0		mitochondrion [IDA]			959
Q6DRL5 UniProt NPD GO	MBB1A_BRARE	Myb-binding protein 1A-like protein	0.87	+	nuc	0	Nucleus; nucleolus (By similarity)				1269
Q90477 UniProt NPD GO	MYOD1_BRARE	Myoblast determination protein 1 homolog (Myogenic factor 1)	0.87	+	nuc	0	Nucleus				275
Q03413 UniProt NPD GO	MEF2D_XENLA	Myocyte-specific enhancer factor 2D homolog (Serum response factor-like protein 1) (SL-1)	0.87	-	nuc	0	Nucleus				498
Q6SYV5 UniProt NPD GO	MYF6_FUGRU	Myogenic factor 6 (Myf-6) (Muscle-specific regulatory factor 4)	0.87	+	nuc	0	Nucleus (By similarity)				239
Q8WXR4 UniProt NPD GO	MYO3B_HUMAN	Myosin IIIB (EC 2.7.11.1)	0.87	-	cyt	0					1341
Q05096 UniProt NPD GO	MYO1B_RAT	Myosin Ib (Myosin I alpha) (MMI-alpha) (MMIa) (Myosin heavy chain myr 1)	0.87	-	cyt	0					1136
P04461 UniProt NPD GO	MYH7_RABIT	Myosin heavy chain, cardiac muscle beta isoform (MyHC-beta) (Beta isomyosin) (Fragment)	0.87	+	nuc	0	Thick filaments of the myofibrils				736
P21271 UniProt NPD GO	MYO5B_MOUSE	Myosin-5B (Myosin Vb) (Fragment)	0.87	+	nuc	0					723
Q6NTN5 UniProt NPD GO	MTMRD_XENLA	Myotubularin-related protein 13 (SET-binding factor 2)	0.87	-	nuc	0	Cytoplasm (By similarity). Membrane peripheral membrane protein (By similarity). Associated with mem ...				1873
Q86U44 UniProt NPD GO	MTA70_HUMAN	N6-adenosine-methyltransferase 70 kDa subunit (EC 2.1.1.62) (MT-A70) (Methyltransferase-like protein ...	0.87	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Colocalizes with speckles in interphase nuclei. Suggesting th ...	nucleus [IDA]			580
Q8C3P7 UniProt NPD GO	MTA70_MOUSE	N6-adenosine-methyltransferase 70 kDa subunit (EC 2.1.1.62) (MT-A70) (Methyltransferase-like protein ...	0.87	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Colocalizes with speckles in interphase nucle ...	nucleus [ISS]			580
Q9Y6K9 UniProt NPD GO	NEMO_HUMAN	NF-kappa-B essential modulator (NEMO) (NF-kappa-B essential modifier) (Inhibitor of nuclear factor k ...	0.87	-	nuc	0	Cytoplasm. Nucleus		308300		419
P18615 UniProt NPD GO	NELFE_HUMAN	Negative elongation factor E (NELF-E) (RD protein)	0.87	+	nuc	0	Nucleus	nucleus [NAS]	154040	1X5P	380
Q27571 UniProt NPD GO	NOS_DROME	Nitric-oxide synthase (EC 1.14.13.39) (dNOS)	0.87	-	nuc	0					1349
P29474 UniProt NPD GO	NOS3_HUMAN	Nitric-oxide synthase, endothelial (EC 1.14.13.39) (EC-NOS) (NOS type III) (NOSIII) (Endothelial NOS ...	0.87	+	cyt	0		cytoplasm [TAS]	163729	3NOS	1202
Q6NV18 UniProt NPD GO	NHEJ1_BRARE	Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)	0.87	-	nuc	0	Nucleus (By similarity)				309
Q6C3S1 UniProt NPD GO	NDE1_YARLI	Nuclear distribution protein nudE homolog 1	0.87	-	nuc	0	Cytoplasm. Localizes to the plus ends of microtubules (By similarity)				461
P70255 UniProt NPD GO	NFIC_MOUSE	Nuclear factor 1 C-type (Nuclear factor 1/C) (NF1-C) (NFI-C) (NF-I/C) (CCAAT-box-binding transcripti ...	0.87	-	nuc	0	Nucleus				439
O95644 UniProt NPD GO	NFAC1_HUMAN	Nuclear factor of activated T-cells, cytoplasmic 1 (NFAT transcription complex cytosolic component) ...	0.87	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic for the phosphorylated form and nuclear after activation that is con ...	cytoplasm [TAS]	600489	1NFA	943
Q12968 UniProt NPD GO	NFAC3_HUMAN	Nuclear factor of activated T-cells, cytoplasmic 3 (NF-ATc3) (NFATc3) (T cell transcription factor N ...	0.87	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic for the phosphorylated form and nuclear after activation that is con ...		602698		1075
Q9GTD4 UniProt NPD GO	NHR71_CAEEL	Nuclear hormone receptor family member nhr-71	0.87	-	nuc	0	Nucleus (Potential)				579
Q25604 UniProt NPD GO	NHR1_ONCVO	Nuclear hormone receptor-like 1	0.87	-	nuc	0	Nucleus (By similarity)				367

You are viewing entries 5651 to 5700 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.