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
P54842 UniProt NPD GO	MAFB_RAT	Transcription factor MafB (V-maf musculoaponeurotic fibrosarcoma oncogene homolog B) (Transcription ...	0.77	-	nuc	0	Nucleus				323
P54841 UniProt NPD GO	MAFB_MOUSE	Transcription factor MafB (V-maf musculoaponeurotic fibrosarcoma oncogene homolog B) (Transcription ...	0.77	-	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			323
Q2Z1R2 UniProt NPD GO	SOX1B_BRARE	Transcription factor Sox-1b	0.77	+	nuc	0	Nucleus	transcription factor complex [IC]			340
Q93ZE2 UniProt NPD GO	TGA7_ARATH	Transcription factor TGA7 (AtbZIP50)	0.77	-	nuc	0	Nucleus				368
P17535 UniProt NPD GO	JUND_HUMAN	Transcription factor jun-D	0.77	+	nuc	0	Nucleus	chromatin [TAS]	165162		347
Q12753 UniProt NPD GO	HAA1_YEAST	Transcriptional activator HAA1	0.77	-	nuc	0	Nucleus	nucleus [IDA]			694
Q99142 UniProt NPD GO	TAF1_TOBAC	Transcriptional activator TAF-1 (Fragment)	0.77	+	nuc	0	Nucleus				265
P40379 UniProt NPD GO	REC16_SCHPO	Transcriptional activator protein rec16 (Zinc finger protein rep1)	0.77	-	nuc	0	Nucleus (Potential)	MBF transcription complex [TAS]			472
Q09838 UniProt NPD GO	PRZ1_SCHPO	Transcriptional regulator prz1 (Pbp1-responsive zinc finger protein 1)	0.77	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			681
Q8WXI9 UniProt NPD GO	P66B_HUMAN	Transcriptional repressor p66 beta (p66/p68) (GATA zinc finger domain-containing protein 2B)	0.77	-	nuc	0	Nucleus. Nuclear, in discrete foci				593
Q13595 UniProt NPD GO	TRA2A_HUMAN	Transformer-2 protein homolog (TRA-2 alpha)	0.77	+	nuc	0	Nucleus	nucleus [IDA]	602718		282
Q6PFR5 UniProt NPD GO	TRA2A_MOUSE	Transformer-2 protein homolog (TRA-2 alpha)	0.77	+	nuc	0	Nucleus (By similarity)				281
Q8VHE0 UniProt NPD GO	SEC63_MOUSE	Translocation protein SEC63 homolog	0.77	+	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				759
O70472 UniProt NPD GO	TM131_MOUSE	Transmembrane protein 131 (Protein RW1)	0.77	-	end	2	Membrane; multi-pass membrane protein (Potential)				1829
O08712 UniProt NPD GO	TR11B_MOUSE	Tumor necrosis factor receptor superfamily member 11B precursor (Osteoprotegerin) (Osteoclastogenesi ...	0.77	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [IDA]			401
Q96RR1 UniProt NPD GO	PEO1_HUMAN	Twinkle protein, mitochondrial precursor (EC 3.6.1.-) (T7 gp4-like protein with intramitochondrial n ...	0.77	-	mit	0	Mitochondrion. Colocalizes with mtDNA in mitochondrial nucleoids, a nucleoproteins complex consistin ...		609286		684
Q04372 UniProt NPD GO	TAP42_YEAST	Type 2A phosphatase-associated protein 42	0.77	-	nuc	0					366
Q6P1Y8 UniProt NPD GO	INP4B_MOUSE	Type II inositol-3,4-bisphosphate 4-phosphatase (EC 3.1.3.66) (Inositol polyphosphate 4-phosphatase ...	0.77	-	end	1					924
P16620 UniProt NPD GO	PTP69_DROME	Tyrosine-protein phosphatase 69D precursor (EC 3.1.3.48) (Protein-tyrosine-phosphate phosphohydrolas ...	0.77	-	exc	1 *	Membrane; single-pass type I membrane protein				1462
Q10178 UniProt NPD GO	SF3B1_SCHPO	U2 snRNP component prp10	0.77	-	end	0	Nucleus	nucleus [IDA]			1188
Q92738 UniProt NPD GO	US6NL_HUMAN	USP6 N-terminal-like protein (Related to the N-terminus of tre) (RN-tre)	0.77	-	nuc	0			605405		828
Q9Y5T5 UniProt NPD GO	UBP16_HUMAN	Ubiquitin carboxyl-terminal hydrolase 16 (EC 3.1.2.15) (Ubiquitin thioesterase 16) (Ubiquitin-specif ...	0.77	+	nuc	0		cytoplasm [TAS]	604735		823
Q7TPK1 UniProt NPD GO	UHRF1_RAT	Ubiquitin-like PHD and RING finger domain-containing protein 1 (EC 6.3.2.-) (Ubiquitin-like-containi ...	0.77	-	nuc	0	Nucleus (By similarity)				774
Q4I7N9 UniProt NPD GO	BRE1_GIBZE	Ubiquitin-protein ligase BRE1 (EC 6.3.2.-)	0.77	-	nuc	0	Nucleus (By similarity)				703
Q9D518 UniProt NPD GO	CO033_MOUSE	Uncharacterized protein C15orf33 homolog	0.77	-	cyt	0					425
P38278 UniProt NPD GO	YBZ1_YEAST	Uncharacterized protein YBR141C	0.77	-	nuc	0		nucleolus [IDA]			337
P39998 UniProt NPD GO	YEB5_YEAST	Uncharacterized protein YEL015W	0.77	-	nuc	0		cytoplasmic mRNA processing body [IDA]			551
P53289 UniProt NPD GO	YG3S_YEAST	Uncharacterized protein YGR161C	0.77	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			263
Q8K3K1 UniProt NPD GO	USH2A_RAT	Usherin precursor (Usher syndrome type-2A protein homolog) (Usher syndrome type IIa protein homolog) ...	0.77	-	nuc	0	Secreted protein (By similarity)	extracellular matrix (sensu Metazoa) [NAS]			1512
Q9WTT4 UniProt NPD GO	VATG2_MOUSE	Vacuolar ATP synthase subunit G 2 (EC 3.6.3.14) (V-ATPase G subunit 2) (Vacuolar proton pump G subun ...	0.77	-	nuc	0		hydrogen-translocating V-type ATPase complex [IPI] integral to synaptic vesicle membrane [IDA]			118
P39904 UniProt NPD GO	VPS52_YEAST	Vacuolar protein sorting protein 52 (Suppressor of actin mutation protein 2)	0.77	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein. End ...	GARP complex [IPI] Golgi apparatus [IDA]			641
Q01668 UniProt NPD GO	CAC1D_HUMAN	Voltage-dependent L-type calcium channel subunit alpha-1D (Voltage-gated calcium channel subunit alp ...	0.77	+	end	19	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]	114206		2161
O75132 UniProt NPD GO	ZBED4_HUMAN	Zinc finger BED domain-containing protein 4	0.77	-	nuc	0					1171
Q5ZL36 UniProt NPD GO	ZFY27_CHICK	Zinc finger FYVE domain-containing protein 27	0.77	-	end	3	Membrane; multi-pass membrane protein (Potential)				406
O15231 UniProt NPD GO	ZN185_HUMAN	Zinc finger protein 185 (LIM-domain protein ZNF185) (P1-A)	0.77	-	nuc	0	Nucleus (Potential)		300381		457
P10078 UniProt NPD GO	ZFP28_MOUSE	Zinc finger protein 28 (Zfp-28) (Protein mKR5)	0.77	-	nuc	0	Nucleus (Potential)				825
Q6P9Y7 UniProt NPD GO	ZN545_MOUSE	Zinc finger protein 545 (Zinc finger protein 82)	0.77	-	nuc	0	Nucleus (Probable)				530
Q8N9Z0 UniProt NPD GO	ZN610_HUMAN	Zinc finger protein 610	0.77	-	nuc	0	Nucleus (Probable)				462
P51523 UniProt NPD GO	ZNF84_HUMAN	Zinc finger protein 84 (Zinc finger protein HPF2)	0.77	-	nuc	0	Nucleus (Probable)	nucleus [NAS]			738
O50055 UniProt NPD GO	COL1_ARATH	Zinc finger protein CONSTANS-LIKE 1	0.77	+	nuc	0	Nucleus (Probable)				355
P10070 UniProt NPD GO	GLI2_HUMAN	Zinc finger protein GLI2 (Tax helper protein)	0.77	-	nuc	0	Nucleus (Potential)		165230		1258
P14373 UniProt NPD GO	TRI27_HUMAN	Zinc finger protein RFP (Ret finger protein) (Tripartite motif-containing protein 27) (RING finger p ...	0.77	-	nuc	0	Or: Nucleus (By similarity). Or: Cytoplasm (By similarity). Nuclear or cytoplasmic depending on the ...	integral to plasma membrane [TAS] membrane fraction [TAS]	602165		513
P32338 UniProt NPD GO	RME1_YEAST	Zinc finger protein RME1	0.77	+	nuc	0	Nucleus	nucleus [IDA]			300
P40962 UniProt NPD GO	RTS2_YEAST	Zinc finger protein RTS2	0.77	-	nuc	0	Nucleus (Potential)	cytoplasm [IDA] nucleus [IDA]			232
P07278 UniProt NPD GO	KAPR_YEAST	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.77	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			415
P12252 UniProt NPD GO	PDE4B_DROME	cAMP-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) (Learning/memory process protein) (Protei ...	0.77	-	nuc	0					1070
Q7S1Y0 UniProt NPD GO	RNA14_NEUCR	mRNA 3'-end-processing protein rna-14	0.77	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleus and/or cytoplasm (By similarity)				1167
Q8IU60 UniProt NPD GO	DCP2_HUMAN	mRNA decapping enzyme 2 (EC 3.-.-.-) (hDpc) (Nucleoside diphosphate-linked moiety X motif 20) (Nudix ...	0.77	-	nuc	0	Cytoplasm. Nucleus. Predominantly cytoplasmic, in processing bodies (PB). A minor amount is nuclear		609844		420
Q9HFB3 UniProt NPD GO	PACC_ASPOR	pH-response transcription factor pacC/RIM101	0.77	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				662
P15711 UniProt NPD GO	104K_THEPA	104 kDa microneme-rhoptry antigen precursor (p104)	0.76	+	exc	1	Cell membrane; lipid-anchor; GPI-anchor (Potential). In microneme/rhoptry complexes				924

You are viewing entries 10651 to 10700 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.