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
P58397 UniProt NPD GO	ATS12_HUMAN	ADAMTS-12 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 12 ...	0.88	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		606184		1593
Q4VC17 UniProt NPD GO	ATS18_MOUSE	ADAMTS-18 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 18 ...	0.88	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				1219
Q9D8S3 UniProt NPD GO	ARFG3_MOUSE	ADP-ribosylation factor GTPase-activating protein 3 (ARF GAP 3)	0.88	-	nuc	0	Cytoplasm; perinuclear region (By similarity)	cytosol [ISS]			525
P40535 UniProt NPD GO	ACA2_YEAST	ATF/CREB activator 2 (Chromosome stability protein CST6)	0.88	-	nuc	0	Nucleus	nucleus [IPI]			587
Q75NR7 UniProt NPD GO	RECQ4_MOUSE	ATP-dependent DNA helicase Q4 (EC 3.6.1.-) (RecQ protein-like 4)	0.88	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1216
Q5AF95 UniProt NPD GO	DBP4_CANAL	ATP-dependent RNA helicase DBP4 (EC 3.6.1.-)	0.88	+	nuc	0	Nucleus; nucleolus (By similarity)				765
Q4IAS1 UniProt NPD GO	DBP4_GIBZE	ATP-dependent RNA helicase DBP4 (EC 3.6.1.-)	0.88	+	nuc	0	Nucleus; nucleolus (By similarity)				793
Q5BFU7 UniProt NPD GO	DBP10_EMENI	ATP-dependent RNA helicase dbp10 (EC 3.6.1.-)	0.88	+	nuc	0	Nucleus; nucleolus (By similarity)				936
P34400 UniProt NPD GO	MIG10_CAEEL	Abnormal cell migration protein 10	0.88	-	nuc	0					779
P62295 UniProt NPD GO	ASPM_SAGLB	Abnormal spindle-like microcephaly-associated protein homolog (Fragment)	0.88	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...				1527
P53933 UniProt NPD GO	APP1_YEAST	Actin patch protein 1	0.88	-	nuc	0	Cytoplasm	actin cortical patch [IDA] actin cytoskeleton [IPI]			587
Q9JKL8 UniProt NPD GO	ADNP_RAT	Activity-dependent neuroprotector (Activity-dependent neuroprotective protein)	0.88	+	nuc	0	Nucleus (Potential)				823
Q8VC66 UniProt NPD GO	ADIP_MOUSE	Afadin- and alpha-actinin-binding protein (ADIP) (Afadin DIL domain-interacting protein)	0.88	-	nuc	0	Cell membrane; cell-cell junction; adherens junction. Not found at cell-matrix AJs				615
Q8CGZ2 UniProt NPD GO	ADIP_RAT	Afadin- and alpha-actinin-binding protein (ADIP) (Afadin DIL domain-interacting protein)	0.88	-	nuc	0	Cell membrane; cell-cell junction; adherens junction. Not found at cell-matrix AJs				613
Q38840 UniProt NPD GO	AGL17_ARATH	Agamous-like MADS-box protein AGL17	0.88	-	nuc	0	Nucleus (By similarity)				227
Q6GPB5 UniProt NPD GO	ALKB5_XENLA	Alkylated repair protein alkB homolog 5	0.88	+	nuc	0					360
Q90WY6 UniProt NPD GO	ADA2C_BRARE	Alpha-2C adrenergic receptor (Alpha-2C adrenoceptor) (Alpha-2C adrenoreceptor) (Alpha(2C)AR)	0.88	+	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IC]			432
P49641 UniProt NPD GO	MA2A2_HUMAN	Alpha-mannosidase IIx (EC 3.2.1.114) (Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase) (MAN IIx) ...	0.88	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi membrane [NAS]	600988		1139
Q8BXQ6 UniProt NPD GO	AMPO_MOUSE	Aminopeptidase O (EC 3.4.11.-) (AP-O)	0.88	+	cyt	0	Cytoplasm (Potential)				817
Q09994 UniProt NPD GO	ANI2_CAEEL	Anillin-like protein 2	0.88	-	nuc	0					1009
Q8IVF6 UniProt NPD GO	ANR18_HUMAN	Ankyrin repeat domain-containing protein 18A	0.88	-	nuc	0					992
Q90369 UniProt NPD GO	KALM_COTJA	Anosmin-1 precursor (Kallmann syndrome protein homolog)	0.88	+	mit	0	Cell surface (By similarity)				674
P92966 UniProt NPD GO	RSP41_ARATH	Arginine/serine-rich-splicing factor RSP41	0.88	-	nuc	0	Nucleus (Potential)				356
P27540 UniProt NPD GO	ARNT_HUMAN	Aryl hydrocarbon receptor nuclear translocator (ARNT protein) (Dioxin receptor, nuclear translocator ...	0.88	+	nuc	0	Nucleus	nucleus [TAS]	126110	2ARN	789
O02748 UniProt NPD GO	ARNT_RABIT	Aryl hydrocarbon receptor nuclear translocator (ARNT protein) (Dioxin receptor, nuclear translocator ...	0.88	+	nuc	0	Nucleus				790
Q9ULK2 UniProt NPD GO	AT7L1_HUMAN	Ataxin-7-like protein 1 (Fragment)	0.88	+	nuc	0					864
Q6FQT7 UniProt NPD GO	ATG9_CANGA	Autophagy-related protein 9	0.88	-	end	4	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				928
Q8IWQ3 UniProt NPD GO	BRSK2_HUMAN	BR serine/threonine-protein kinase 2 (EC 2.7.11.1) (Serine/threonine-protein kinase 29) (SAD1B)	0.88	-	nuc	0			609236		736
Q8IY92 UniProt NPD GO	BTBDC_HUMAN	BTB/POZ domain-containing protein 12	0.88	-	nuc	0					1151
Q5RBS5 UniProt NPD GO	BOREA_PONPY	Borealin (Cell division cycle-associated protein 8)	0.88	-	nuc	0	Nucleus; nucleolus. Cytoplasm. Localizes on chromosome arms and inner centromeres from prophase thro ...				280
Q53HL2 UniProt NPD GO	BOREA_HUMAN	Borealin (Dasra-B) (hDasra-B) (Cell division cycle-associated protein 8) (Pluripotent embryonic stem ...	0.88	-	nuc	0	Nucleus; nucleolus. Cytoplasm. Localizes on chromosome arms and inner centromeres from prophase thro ...		609977		280
Q04787 UniProt NPD GO	BSH_DROME	Brain-specific homeobox protein	0.88	+	nuc	0	Nucleus	nucleus [NAS]			429
Q6R3Q6 UniProt NPD GO	BSH_BRARE	Brain-specific homeobox protein homolog	0.88	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			227
Q9BTV7 UniProt NPD GO	CABL2_HUMAN	CDK5 and ABL1 enzyme substrate 2 (Interactor with CDK3 2) (Ik3-2)	0.88	-	mit	0					478
Q6NYW6 UniProt NPD GO	CLAP2_BRARE	CLIP-associating protein 2 (Cytoplasmic linker-associated protein 2)	0.88	-	nuc	0	Cytoplasm. Localizes to microtubule tips (By similarity)				1288
O60244 UniProt NPD GO	CRSP2_HUMAN	CRSP complex subunit 2 (Cofactor required for Sp1 transcriptional activation subunit 2) (Transcripti ...	0.88	-	nuc	0	Nucleus	mediator complex [IDA] nucleus [IDA]	300182		1454
Q96JQ2 UniProt NPD GO	CLMN_HUMAN	Calmin	0.88	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)				1002
Q8C8B0 UniProt NPD GO	CART1_MOUSE	Cartilage homeoprotein 1 (CART-1)	0.88	+	nuc	0	Nucleus (Probable)				326
Q63087 UniProt NPD GO	CART1_RAT	Cartilage homeoprotein 1 (CART-1)	0.88	+	nuc	0	Nucleus (Probable)	nucleus [IMP]			326
Q09822 UniProt NPD GO	CDC15_SCHPO	Cell division control protein 15	0.88	-	nuc	0		contractile ring (sensu Fungi) [IDA] cytoplasm [IDA]			927
Q08288 UniProt NPD GO	LYAR_MOUSE	Cell growth-regulating nucleolar protein	0.88	+	nuc	0	Nucleus; nucleolus			1WJV	388
P36011 UniProt NPD GO	STUA_EMENI	Cell pattern formation-associated protein stuA	0.88	-	nuc	0	Nucleus (Potential)				622
Q8CB62 UniProt NPD GO	CNTRB_MOUSE	Centrobin (LYST-interacting protein 8)	0.88	-	nuc	0	Centrosome. Centriole-associated, asymmetrically localizes to the daughter centriole (By similarity) ...	centriole [ISS]			887
Q9CPQ5 UniProt NPD GO	CENPQ_MOUSE	Centromere protein Q (CENP-Q)	0.88	-	nuc	0					269
Q66H02 UniProt NPD GO	CENPQ_RAT	Centromere protein Q (CENP-Q)	0.88	-	nuc	0					270
Q9P209 UniProt NPD GO	CEP72_HUMAN	Centrosomal protein of 72 kDa (Cep72 protein)	0.88	-	nuc	0	Centrosome				647
P54623 UniProt NPD GO	CNN_DROME	Centrosomin (Protein arrow)	0.88	-	nuc	0	Cytoplasm. Centrosome. Localized to the centrosomes through complete nuclear cycles in mitotic and m ...	pericentriolar material [NAS]			1320
O94486 UniProt NPD GO	CHR2_SCHPO	Chitin synthase regulatory factor 2 (Chs four homolog 2)	0.88	+	nuc	0	Membrane; lipid-anchor				512
Q6CXN0 UniProt NPD GO	YNG2_KLULA	Chromatin modification-related protein YNG2 (ING1 homolog 2)	0.88	-	nuc	0	Nucleus (By similarity)				295
Q24368 UniProt NPD GO	ISWI_DROME	Chromatin remodelling complex ATPase chain Iswi (EC 3.6.1.-) (Protein imitation swi) (Nucleosome rem ...	0.88	+	nuc	0	Nucleus (Potential)	ACF complex [IDA] chromatin accessibility complex [IDA] NURF complex [IDA] transcription factor complex [IPI]		1OFC	1027

You are viewing entries 5001 to 5050 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.)

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