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
Q68S16 UniProt NPD GO	RPOC2_PANGI	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.83	-	nuc	0	Plastid; chloroplast				1387
Q9ESZ0 UniProt NPD GO	XRCC1_RAT	DNA-repair protein XRCC1 (X-ray repair cross-complementing protein 1)	0.83	+	nuc	0	Nucleus (Probable)				631
Q9UI36 UniProt NPD GO	DACH1_HUMAN	Dachshund homolog 1 (Dach1)	0.83	-	mit	0	Nucleus		603803	1L8R	758
Q6Y2X3 UniProt NPD GO	DCJ14_HUMAN	DnaJ homolog subfamily C member 14 (Dopamine receptor-interacting protein of 78 kDa) (DRiP78)	0.83	+	nuc	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				702
Q9IAM7 UniProt NPD GO	MRE11_CHICK	Double-strand break repair protein MRE11	0.83	+	nuc	0	Nucleus (By similarity). Localizes to discrete nuclear foci after treatment with genotoxic agents (B ...				700
Q91ZS8 UniProt NPD GO	RED1_MOUSE	Double-stranded RNA-specific editase 1 (EC 3.5.-.-) (dsRNA adenosine deaminase) (RNA-editing deamina ...	0.83	+	nuc	0		nucleus [ISS]			711
Q9BY84 UniProt NPD GO	DUS16_HUMAN	Dual specificity protein phosphatase 16 (EC 3.1.3.48) (EC 3.1.3.16) (Mitogen-activated protein kinas ...	0.83	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [TAS]	607175		665
P45444 UniProt NPD GO	DYHC_EMENI	Dynein heavy chain, cytosolic (DYHC)	0.83	-	nuc	0	Cytoplasm				4344
Q92462 UniProt NPD GO	PUB1_SCHPO	E3 ubiquitin--protein ligase pub1 (EC 6.3.2.-)	0.83	-	nuc	0	Membrane; peripheral membrane protein. Cytoplasm	cytoplasm [IDA]			767
Q8K4S7 UniProt NPD GO	CBLB_RAT	E3 ubiquitin-protein ligase CBL-B (EC 6.3.2.-) (Signal transduction protein CBL-B) (SH3-binding prot ...	0.83	-	nuc	0	Cytoplasm. In mast cells, translocates to lipid raft upon FCER1 engagement				938
Q9V853 UniProt NPD GO	SMUF1_DROME	E3 ubiquitin-protein ligase Smurf1 (EC 6.3.2.-) (Smad ubiquitination regulatory factor 1 homolog) (D ...	0.83	-	nuc	0		ubiquitin ligase complex [ISS]			1061
Q8R4Z4 UniProt NPD GO	ETV3_MOUSE	ETS translocation variant 3 (ETS-domain transcriptional repressor PE1) (PE-1) (Mitogenic Ets transcr ...	0.83	+	nuc	0	Nucleus (By similarity)	transcriptional repressor complex [IDA]			513
P29551 UniProt NPD GO	EF3_PNECA	Elongation factor 3 (EF-3)	0.83	+	nuc	0					1042
Q01068 UniProt NPD GO	ESM3_DROME	Enhancer of split m3 protein (E(spl)m3) (HLH-m3)	0.83	-	nuc	0	Nucleus (Probable)				224
P06212 UniProt NPD GO	ESR1_CHICK	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.83	+	nuc	0	Nucleus	chromatin remodeling complex [ISS] membrane [ISS]			589
P81559 UniProt NPD GO	ESR1_XENLA	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.83	+	nuc	0	Nucleus	chromatin remodeling complex [ISS] membrane [ISS]			586
Q9YH32 UniProt NPD GO	ESR2_ORENI	Estrogen receptor beta (ER-beta)	0.83	+	nuc	0	Nucleus				557
Q9TU15 UniProt NPD GO	ESR2_SHEEP	Estrogen receptor beta (ER-beta)	0.83	+	nuc	0	Nucleus	nucleus [ISS]			527
Q4WM32 UniProt NPD GO	EXO84_ASPFU	Exocyst complex component exo84	0.83	-	nuc	0	Secretory vesicle (By similarity). Cell periphery. The polarization of EXO84 requires actin cables ( ...				683
P31976 UniProt NPD GO	EZRI_BOVIN	Ezrin (p81) (Cytovillin) (Villin-2)	0.83	-	nuc	0	Membrane. Localization to the apical membrane of parietal cells depends on the interaction with MPP5 ...	actin cytoskeleton [ISS]			580
Q4P2U5 UniProt NPD GO	SPT16_USTMA	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16)	0.83	+	cyt	0	Nucleus (By similarity)				1032
P41848 UniProt NPD GO	SSP1A_CAEEL	FACT complex subunit SSRP1-A (Facilitates chromatin transcription complex subunit ssrp1-A) (Structur ...	0.83	+	nuc	0	Nucleus (By similarity)				697
Q24669 UniProt NPD GO	TRSF_DROSI	Female-specific protein transformer	0.83	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Speckled subnuclear compartment (By similarit ...				184
P42128 UniProt NPD GO	FOXK1_MOUSE	Forkhead box protein K1 (Myocyte nuclear factor) (MNF)	0.83	-	nuc	0	Nucleus				617
Q8IVH2 UniProt NPD GO	FOXP4_HUMAN	Forkhead box protein P4 (Fork head-related protein-like A)	0.83	-	nuc	0	Nucleus (Potential)		608924		680
O95466 UniProt NPD GO	FMNL_HUMAN	Formin-like 1 protein (Formin-like protein) (Leukocyte formin) (CLL-associated antigen KW-13)	0.83	-	nuc	0	Cytoplasm (By similarity)		604656		1100
Q8LG10 UniProt NPD GO	GAT16_ARATH	GATA transcription factor 16	0.83	+	nuc	0	Nucleus (Probable)				149
P70005 UniProt NPD GO	GAT6B_XENLA	GATA-binding factor 6-B (Transcription factor xGATA-6B)	0.83	-	nuc	0	Nucleus				391
Q9QYY0 UniProt NPD GO	GAB1_MOUSE	GRB2-associated-binding protein 1 (GRB2-associated binder 1)	0.83	-	nuc	0		cytoplasm [IDA]			695
P53258 UniProt NPD GO	GYP2_YEAST	GTPase-activating protein GYP2 (MAC1-dependent regulator) (Protein MIC1)	0.83	-	cyt	0		cytoplasm [IDA] soluble fraction [TAS]			950
Q96RT7 UniProt NPD GO	GCP6_HUMAN	Gamma-tubulin complex component 6 (GCP-6)	0.83	-	nuc	0	Centrosome	gamma-tubulin ring complex [IDA]			1819
P24322 UniProt NPD GO	GGPPS_NEUCR	Geranylgeranyl pyrophosphate synthetase (GGPP synthetase) (GGPPSase) (Geranylgeranyl diphosphate syn ...	0.83	-	nuc	0	Cytoplasm	soluble fraction [ISS]			428
Q9NZM4 UniProt NPD GO	GSCR1_HUMAN	Glioma tumor suppressor candidate region gene 1 protein	0.83	-	nuc	0			605690		1509
P79269 UniProt NPD GO	GCR_SAGOE	Glucocorticoid receptor (GR)	0.83	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in the absence of ligand; nuclear af ...				777
O94744 UniProt NPD GO	GIT3_SCHPO	Glucose receptor protein git3 (Glucose insensitive transcription protein 3)	0.83	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				466
P13816 UniProt NPD GO	GARP_PLAFF	Glutamic acid-rich protein precursor	0.83	+	nuc	1 *					678
Q7TNY6 UniProt NPD GO	GCP60_RAT	Golgi resident protein GCP60 (Acyl-CoA-binding domain-containing protein 3) (Golgi phosphoprotein 1) ...	0.83	+	nuc	0	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Mito ...				525
Q9Y7B7 UniProt NPD GO	GPA1_KLULA	Guanine nucleotide-binding protein alpha-1 subunit (GP1-alpha)	0.83	-	cyt	0					446
Q6P4W5 UniProt NPD GO	GNL3_XENTR	Guanine nucleotide-binding protein-like 3 (Nucleostemin-like protein)	0.83	+	nuc	0	Nucleus (By similarity)	nucleolus [ISS] nucleus [ISS]			548
P97832 UniProt NPD GO	HAND1_RAT	Heart- and neural crest derivatives-expressed protein 1 (Extraembryonic tissues, heart, autonomic ne ...	0.83	+	nuc	0					216
P10961 UniProt NPD GO	HSF_YEAST	Heat shock factor protein (HSF) (Heat shock transcription factor) (HSTF)	0.83	-	nuc	0	Nucleus	mitochondrion [IDA] nucleus [NAS]			833
P36016 UniProt NPD GO	LHS1_YEAST	Heat shock protein 70 homolog LHS1 precursor	0.83	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum lumen [IDA]			881
P06146 UniProt NPD GO	H2BS2_LYTPI	Histone H2B.2, sperm	0.83	+	mit	0	Nucleus				142
P02292 UniProt NPD GO	H2BS3_PARAN	Histone H2B.3, sperm	0.83	+	mit	0	Nucleus				148
Q99N13 UniProt NPD GO	HDAC9_MOUSE	Histone deacetylase 9 (HD9) (HD7B) (Histone deacetylase-related protein) (MEF2-interacting transcrip ...	0.83	-	nuc	0	Nucleus (By similarity)	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]		1TQE	588
Q8GZ42 UniProt NPD GO	ATX5_ARATH	Histone-lysine N-methyltransferase ATX5 (EC 2.1.1.43) (Trithorax-homolog protein 5) (TRX-homolog pro ...	0.83	+	nuc	0	Nucleus (By similarity)				1043
P48731 UniProt NPD GO	ATH1_ARATH	Homeobox protein ATH1	0.83	-	nuc	0	Nucleus (Probable)				473
Q9PWD4 UniProt NPD GO	HXA7_MORSA	Homeobox protein Hox-A7	0.83	+	nuc	0	Nucleus (By similarity)				225
P24342 UniProt NPD GO	HXD11_CHICK	Homeobox protein Hox-D11 (Chox-4.6) (GHOX-4.6) (Chox-4E)	0.83	+	nuc	0	Nucleus				280
Q9PVR2 UniProt NPD GO	HXD9_ORYLA	Homeobox protein Hox-D9	0.83	+	nuc	0	Nucleus (By similarity)				271

You are viewing entries 7351 to 7400 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.