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
O16130 UniProt NPD GO	RL39_DROME	60S ribosomal protein L39 (Ribosomal protein 46)	0.52	-	mit	0					51
P18101 UniProt NPD GO	RL40_DROME	60S ribosomal protein L40 (CEP52)	0.52	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [IDA]			52
P46575 UniProt NPD GO	RL40_EIMBO	60S ribosomal protein L40 (CEP52) (CEP53)	0.52	-	nuc	0					53
P02405 UniProt NPD GO	RL44_YEAST	60S ribosomal protein L42 (L44) (YL27) (YP44) (L41) (Maintenance of killer protein 18)	0.52	+	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	105
Q9UVB8 UniProt NPD GO	RL44_PICCI	60S ribosomal protein L44 (60S ribosomal protein L41)	0.52	-	nuc	0					105
Q00477 UniProt NPD GO	RL44P_CANMA	60S ribosomal protein L44 P (L41) (L41 P-type)	0.52	-	nuc	0					105
P22451 UniProt NPD GO	RL5_CHICK	60S ribosomal protein L5	0.52	-	mit	0	Cytoplasm				296
O65353 UniProt NPD GO	RL5_HELAN	60S ribosomal protein L5	0.52	-	nuc	0					297
O59953 UniProt NPD GO	RL5_NEUCR	60S ribosomal protein L5 (CPR4)	0.52	-	mit	0					301
P15125 UniProt NPD GO	RL5A_XENLA	60S ribosomal protein L5-A	0.52	-	mit	0	Cytoplasm				295
O19004 UniProt NPD GO	ARAF_PIG	A-Raf proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1) (A-Raf-1)	0.52	-	nuc	0					606
O43184 UniProt NPD GO	ADA12_HUMAN	ADAM 12 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 12) (Meltrin alpha)	0.52	-	nuc	1	Isoform 12L: Cell membrane; single-pass type I membrane protein. Isoform 12S: Secreted protein	plasma membrane [TAS]	602714		909
O95782 UniProt NPD GO	AP2A1_HUMAN	AP-2 complex subunit alpha-1 (Adapter-related protein complex 2 alpha-1 subunit) (Alpha-adaptin A) ( ...	0.52	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	AP-2 adaptor complex [NAS] clathrin coat of trans-Golgi network vesicle [NAS]	601026		977
Q08211 UniProt NPD GO	DHX9_HUMAN	ATP-dependent RNA helicase A (EC 3.6.1.-) (Nuclear DNA helicase II) (NDH II) (DEAH box protein 9)	0.52	-	mit	0	Cytoplasm. Nucleus; nucleolus. Can shuttle between nucleus and cytoplasm	cytoplasm [TAS] nucleus [TAS]	603115		1270
Q5R874 UniProt NPD GO	DHX9_PONPY	ATP-dependent RNA helicase A (EC 3.6.1.-) (Nuclear DNA helicase II) (NDH II) (DEAH box protein 9)	0.52	-	mit	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity). Can shuttle between nucleus and cytop ...				1269
Q4PDT1 UniProt NPD GO	DBP3_USTMA	ATP-dependent RNA helicase DBP3 (EC 3.6.1.-)	0.52	+	nuc	0	Nucleus; nucleolus (By similarity)				585
Q6C799 UniProt NPD GO	DBP8_YARLI	ATP-dependent RNA helicase DBP8 (EC 3.6.1.-)	0.52	-	cyt	0	Nucleus; nucleolus (By similarity)				442
Q6FUA6 UniProt NPD GO	DBP9_CANGA	ATP-dependent RNA helicase DBP9 (EC 3.6.1.-)	0.52	-	cyt	0	Nucleus; nucleolus (By similarity)				595
Q62167 UniProt NPD GO	DDX3X_MOUSE	ATP-dependent RNA helicase DDX3X (EC 3.6.1.-) (DEAD box protein 3, X-chromosomal) (DEAD box RNA heli ...	0.52	-	cyt	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Cytoplasm (By similarity). Located predominan ...	cytoplasm [ISS] nucleus [ISS]			661
O00571 UniProt NPD GO	DDX3X_HUMAN	ATP-dependent RNA helicase DDX3X (EC 3.6.1.-) (DEAD box protein 3, X-chromosomal) (Helicase-like pro ...	0.52	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Cytoplasm. Located predominantly in nuclear speckles and, at ...	cytoplasm [IDA] nucleus [IDA]	300160		661
Q6FQU5 UniProt NPD GO	DHH1_CANGA	ATP-dependent RNA helicase DHH1 (EC 3.6.1.-)	0.52	-	cyt	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				507
P47047 UniProt NPD GO	MTR4_YEAST	ATP-dependent RNA helicase DOB1 (EC 3.6.1.-) (mRNA transport regulator MTR4)	0.52	+	cyt	0	Nucleus	nucleolus [TAS] nucleus [IDA] TRAMP complex [IDA]			1073
Q58Z64 UniProt NPD GO	DHH1_CRYNV	ATP-dependent RNA helicase VAD1 (EC 3.6.1.-) (Virulence-associated DEAD box protein 1)	0.52	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				616
Q4IFI0 UniProt NPD GO	RRP3_GIBZE	ATP-dependent rRNA helicase RRP3 (EC 3.6.1.-)	0.52	-	mit	0	Nucleus (Probable)				486
Q6PAF6 UniProt NPD GO	AN32A_XENLA	Acidic leucine-rich nuclear phosphoprotein 32 family member A	0.52	-	nuc	0	Nucleus. Cytoplasm. Shuttles between nucleus and cytoplasm (By similarity)				244
Q29016 UniProt NPD GO	ACRBP_PIG	Acrosin-binding protein precursor (Proacrosin-binding protein sp32) (Fragment)	0.52	-	exc	0	Secreted protein. Acrosome. Colocalizes with proacrosin in the acrosome of sperm				537
P80428 UniProt NPD GO	ARP4_YEAST	Actin-like protein ARP4	0.52	-	nuc	0	Nucleus	H4/H2A histone acetyltransferase complex [IPI] INO80 complex [IPI] nuclear chromatin [IDA] nucleus [IDA] SWR1 complex [IPI]			489
Q8HYL8 UniProt NPD GO	ACOX1_PHACI	Acyl-coenzyme A oxidase 1, peroxisomal (EC 1.3.3.6) (Palmitoyl-CoA oxidase) (AOX)	0.52	-	pox	0	Peroxisome				661
P36953 UniProt NPD GO	AFAM_RAT	Afamin precursor (Alpha-albumin) (Alpha-Alb)	0.52	-	exc	0	Secreted protein	extracellular space [IDA]			608
Q8R4G6 UniProt NPD GO	MGAT5_MOUSE	Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V (EC 2.4.1.155) (Mannoside ac ...	0.52	+	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				740
Q3SZ57 UniProt NPD GO	FETA_BOVIN	Alpha-fetoprotein precursor (Alpha-fetoglobulin) (Alpha-1-fetoprotein)	0.52	-	exc	0	Secreted protein (By similarity)				610
Q8MJU5 UniProt NPD GO	FETA_CANFA	Alpha-fetoprotein precursor (Alpha-fetoglobulin) (Alpha-1-fetoprotein)	0.52	-	nuc	0	Secreted protein (By similarity)				609
P46660 UniProt NPD GO	AINX_MOUSE	Alpha-internexin (Alpha-Inx) (66 kDa neurofilament protein) (Neurofilament-66) (NF-66)	0.52	-	nuc	0					504
Q708S4 UniProt NPD GO	ACC4A_BRARE	Amiloride-sensitive cation channel 4-A (Acid-sensing ion channel 4.1) (ZASIC4.1)	0.52	-	nuc	0	Cell membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [IDA]			539
Q9GLN7 UniProt NPD GO	ACE_PANTR	Angiotensin-converting enzyme, somatic isoform precursor (EC 3.4.15.1) (Dipeptidyl carboxypeptidase ...	0.52	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				1304
P48746 UniProt NPD GO	B3A2_RABIT	Anion exchange protein 2 (Non-erythroid band 3-like protein) (AE2 anion exchanger) (Solute carrier f ...	0.52	-	end	11	Membrane; multi-pass membrane protein				1237
P51901 UniProt NPD GO	ANXA6_CHICK	Annexin A6 (Annexin VI) (Lipocortin VI) (P68) (P70) (Protein III) (Chromobindin-20) (67 kDa calelect ...	0.52	-	cyt	0	Stress fibers (By similarity)				671
P13492 UniProt NPD GO	A103_SCHMA	Antigen 10-3 precursor	0.52	-	exc	0					263
P11682 UniProt NPD GO	APOB_CHICK	Apolipoprotein B (Fragment)	0.52	-	nuc	0	Secreted protein				433
O95236 UniProt NPD GO	APOL3_HUMAN	Apolipoprotein-L3 (Apolipoprotein L-III) (ApoL-III) (TNF-inducible protein CG12-1) (CG12_1)	0.52	-	nuc	0	Cytoplasm (Probable)		607253		402
Q8K4H4 UniProt NPD GO	APTX_RAT	Aprataxin homolog (Forkhead-associated domain histidine triad-like protein) (FHA-HIT)	0.52	-	nuc	0	Nucleus (By similarity). Upon genotoxic stress, it colocalizes with XRCC1 at sites of DNA damage (By ...				329
P38316 UniProt NPD GO	ATG12_YEAST	Autophagy-related protein 12 (Autophagy-related ubiquitin-like modifier ATG12)	0.52	+	nuc	0	Cytoplasm (Probable)	membrane fraction [IDA]			186
Q6CRH0 UniProt NPD GO	ATG14_KLULA	Autophagy-related protein 14	0.52	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				307
Q6CS99 UniProt NPD GO	ATG17_KLULA	Autophagy-related protein 17	0.52	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Cytoplasmic and pu ...				423
O23661 UniProt NPD GO	ARFC_ARATH	Auxin response factor 3 (Protein ETTIN)	0.52	-	nuc	0	Nucleus				608
P28028 UniProt NPD GO	BRAF1_MOUSE	B-Raf proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1) (Fragment)	0.52	-	cyt	0					328
P15530 UniProt NPD GO	CD79B_MOUSE	B-cell antigen receptor complex-associated protein beta-chain precursor (B-cell-specific glycoprotei ...	0.52	-	end	1	Membrane; single-pass type I membrane protein	B cell receptor complex [IDA] external side of plasma membrane [IDA]			228
O95816 UniProt NPD GO	BAG2_HUMAN	BAG family molecular chaperone regulator 2 (BCL2-associated athanogene 2) (BAG-2)	0.52	-	nuc	0			603882		211
P10161 UniProt NPD GO	PRB4M_HUMAN	Basic salivary proline-rich protein 4 allele M (Salivary proline-rich protein Po) (Parotid o protein ...	0.52	-	nuc	0		extracellular region [NAS]	180990		238
P25974 UniProt NPD GO	GLCB_SOYBN	Beta-conglycinin, beta chain precursor	0.52	-	end	0	Embryo axis, and cotyledonary membrane-bound vacuolar protein bodies			1UIJ	439

You are viewing entries 23551 to 23600 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.