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
P10643 UniProt NPD GO	CO7_HUMAN	Complement component C7 precursor	0.71	-	nuc	0		membrane attack complex [TAS]	217070		843
Q8HXY9 UniProt NPD GO	CFDP1_BOVIN	Craniofacial development protein 1 (Bucentaur) (h-type BCNT protein)	0.71	-	nuc	0					297
P53202 UniProt NPD GO	CUL3_YEAST	Cullin-3 (Cullin-B)	0.71	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			744
Q6AXJ9 UniProt NPD GO	CDKL1_BRARE	Cyclin-dependent kinase-like 1 (EC 2.7.11.22)	0.71	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				350
Q14093 UniProt NPD GO	CYLC2_HUMAN	Cylicin-2 (Cylicin II) (Multiple-band polypeptide II)	0.71	+	nuc	0	Calyx. Sperm head cytoskeletal structure		604035		348
P97696 UniProt NPD GO	CYH3_RAT	Cytohesin-3 (SEC7 homolog C) (msec7-3)	0.71	+	cyt	0					400
Q62871 UniProt NPD GO	DC1I2_RAT	Cytoplasmic dynein 1 intermediate chain 2 (Dynein intermediate chain 2, cytosolic) (DH IC-2) (Cytopl ...	0.71	+	nuc	0		cytoplasmic dynein complex [IPI] dynactin complex [IPI]			638
Q9FLB0 UniProt NPD GO	RH18_ARATH	DEAD-box ATP-dependent RNA helicase 18 (EC 3.6.1.-)	0.71	+	cyt	0					593
Q755A0 UniProt NPD GO	DDC1_ASHGO	DNA damage checkpoint protein 1	0.71	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				543
P49916 UniProt NPD GO	DNL3_HUMAN	DNA ligase 3 (EC 6.5.1.1) (DNA ligase III) (Polydeoxyribonucleotide synthase [ATP] 3)	0.71	-	nuc	0	Nucleus	nucleus [TAS]	600940	1UW0	922
Q12083 UniProt NPD GO	MLH3_YEAST	DNA mismatch repair protein MLH3 (MutL protein homolog 3)	0.71	-	nuc	0	Nucleus (Probable)	nucleus [IPI]			715
O54747 UniProt NPD GO	DPOD1_RAT	DNA polymerase delta catalytic subunit (EC 2.7.7.7)	0.71	+	cyt	0	Nucleus				1103
O42131 UniProt NPD GO	TOP2B_CHICK	DNA topoisomerase 2-beta (EC 5.99.1.3) (DNA topoisomerase II, beta isozyme)	0.71	+	nuc	0	Nucleus; nucleoplasm. Generally located in the nucleoplasm				1627
P22936 UniProt NPD GO	APN1_YEAST	DNA-(apurinic or apyrimidinic site) lyase 1 (EC 4.2.99.18) (AP endonuclease 1) (Apurinic-apyrimidini ...	0.71	+	nuc	0	Nucleus	mitochondrion [IDA] nucleus [IDA]			366
O13089 UniProt NPD GO	IKAR_ONCMY	DNA-binding protein Ikaros	0.71	-	nuc	0	Nucleus				522
O94166 UniProt NPD GO	CREA_ASPAC	DNA-binding protein creA (Carbon catabolite repressor)	0.71	-	nuc	0	Nucleus				431
Q9P889 UniProt NPD GO	CREA_ASPOR	DNA-binding protein creA (Carbon catabolite repressor)	0.71	-	nuc	0	Nucleus				429
Q9HFS2 UniProt NPD GO	CREA_COCCA	DNA-binding protein creA (Carbon catabolite repressor)	0.71	-	nuc	0	Nucleus				430
Q8L6J5 UniProt NPD GO	RPO1B_TOBAC	DNA-directed RNA polymerase 1B, mitochondrial precursor (EC 2.7.7.6) (T7 bacteriophage-type single s ...	0.71	-	mit	0	Mitochondrion				1002
P10964 UniProt NPD GO	RPA1_YEAST	DNA-directed RNA polymerase I 190 kDa polypeptide (EC 2.7.7.6) (A190)	0.71	-	nuc	0	Nucleus	DNA-directed RNA polymerase I complex [TAS]			1664
Q85FM8 UniProt NPD GO	RPOC1_ADICA	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.71	-	mit	0	Plastid; chloroplast				694
Q85WS8 UniProt NPD GO	RPOC1_PINKO	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.71	-	nuc	0	Plastid; chloroplast				696
Q95120 UniProt NPD GO	DMP1_BOVIN	Dentin matrix acidic phosphoprotein 1 precursor (Dentin matrix protein 1) (DMP-1)	0.71	-	exc	0					510
O54908 UniProt NPD GO	DKK1_MOUSE	Dickkopf-related protein 1 precursor (Dkk-1) (Dickkopf-1) (mDkk-1)	0.71	-	exc	1 *	Secreted protein				272
Q9NVM6 UniProt NPD GO	DJC17_HUMAN	DnaJ homolog subfamily C member 17	0.71	-	nuc	0					304
Q91WN1 UniProt NPD GO	DNJC9_MOUSE	DnaJ homolog subfamily C member 9	0.71	-	nuc	0					259
Q9VJ79 UniProt NPD GO	PDE11_DROME	Dual 3',5'-cyclic-AMP and -GMP phosphodiesterase 11 (EC 3.1.4.17) (EC 3.1.4.35) (cAMP and cGMP phosp ...	0.71	-	nuc	0					1451
P39054 UniProt NPD GO	DYN2_MOUSE	Dynamin-2 (EC 3.6.5.5) (Dynamin UDNM)	0.71	-	nuc	0	Cytoplasm (By similarity). Microtubule-associated. Also found in the postsynaptic density of neurona ...				870
Q24246 UniProt NPD GO	DYIN_DROME	Dynein intermediate chain, cytosolic (DH IC) (Cytoplasmic dynein intermediate chain) (Protein short ...	0.71	+	nuc	0	Isoform 2c: Lysosome; lysosomal membrane; peripheral membrane protein; cytoplasmic side. Isoform 2a, ...				663
P46935 UniProt NPD GO	NEDD4_MOUSE	E3 ubiquitin-protein ligase NEDD4 (EC 6.3.2.-) (Neural precursor cell expressed developmentally down ...	0.71	-	cyt	0	Cytoplasm	cytosol [IDA] ubiquitin ligase complex [IPI]			887
Q05787 UniProt NPD GO	HRD3_YEAST	ERAD-associated E3 ubiquitin-protein ligase component HRD3 precursor (HMG-CoA reductase degradation ...	0.71	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)	endoplasmic reticulum [TAS]			833
O73692 UniProt NPD GO	EGR1_COTJA	Early growth response protein 1 (EGR-1) (Zinc finger protein ZENK) (Fragment)	0.71	-	nuc	0	Nucleus				194
P08152 UniProt NPD GO	EGR2_MOUSE	Early growth response protein 2 (EGR-2) (Krox-20 protein)	0.71	-	nuc	0	Nucleus	nucleus [IDA]			470
P49882 UniProt NPD GO	ECR_CHITE	Ecdysone receptor (Ecdysteroid receptor) (20-hydroxy-ecdysone receptor) (20E receptor) (EcRH)	0.71	-	nuc	0	Nucleus				536
O97939 UniProt NPD GO	ENAM_PIG	Enamelin precursor [Contains: 89 kDa enamelin; 142 kDa enamelin; 155 kDa enamelin; 56 kDa enamelin; ...	0.71	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [ISS]			1142
Q28949 UniProt NPD GO	MA2B2_PIG	Epididymis-specific alpha-mannosidase precursor (EC 3.2.1.24) (Mannosidase alpha class 2B member 2) ...	0.71	-	cyt	0	Secreted protein. Found at the sperm surface as a 27 kDa fragment				995
Q9TV98 UniProt NPD GO	ESR1_HORSE	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.71	+	nuc	0	Nucleus	chromatin remodeling complex [ISS] membrane [ISS]			594
P50242 UniProt NPD GO	ESR1_SALSA	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha) (Fragment)	0.71	-	nuc	0	Nucleus				535
Q9XTM1 UniProt NPD GO	EXOC5_DROME	Exocyst complex component 5 (Exocyst complex component Sec10)	0.71	-	nuc	0		exocyst [NAS]			710
Q6CK11 UniProt NPD GO	EXO70_KLULA	Exocyst complex protein EXO70	0.71	-	nuc	0	Bud (By similarity). Bud neck (By similarity)				619
Q9BQS8 UniProt NPD GO	FYCO1_HUMAN	FYVE and coiled-coil domain-containing protein 1 (Zinc finger FYVE domain-containing protein 7)	0.71	-	nuc	0			607182		1478
Q6IV68 UniProt NPD GO	FACD2_RAT	Fanconi anemia group D2 protein homolog (Protein FACD2) (FanCD2)	0.71	-	nuc	0	Nucleus (By similarity). Concentrates in nuclear foci during S phase and upon genotoxic stress (By s ...				1451
Q09312 UniProt NPD GO	FBF2_CAEEL	Fem-3 mRNA-binding factor 2	0.71	-	nuc	0	Cytoplasm (By similarity)				632
P35555 UniProt NPD GO	FBN1_HUMAN	Fibrillin-1 precursor	0.71	-	nuc	0		basement membrane [IDA] extracellular space [IDA] microfibril [IDA]	129600	1UZQ	2871
P98133 UniProt NPD GO	FBN1_BOVIN	Fibrillin-1 precursor (MP340)	0.71	-	nuc	0					2871
Q12934 UniProt NPD GO	BFSP1_HUMAN	Filensin (Beaded filament structural protein 1) (Lens fiber cell beaded-filament structural protein ...	0.71	-	nuc	0	Membrane. Cytoplasm. Membrane- and cytoskeleton-associated	intermediate filament [TAS]	603307		665
Q06637 UniProt NPD GO	BFSP1_CHICK	Filensin (Beaded filament structural protein 1) (Lens fiber cell beaded-filament structural protein ...	0.71	-	nuc	0	Membrane. Cytoplasm. Membrane- and cytoskeleton-associated				657
Q9WVH3 UniProt NPD GO	FOXO4_MOUSE	Fork head domain transcription factor AFX1 (Afxh) (Forkhead box protein O4)	0.71	-	nuc	0	Cytoplasm. Nucleus. When phosphorylated, translocated from nucleus to cytoplasm. Dephosphorylation t ...				505
P32030 UniProt NPD GO	SLP1_DROME	Fork head domain transcription factor slp1 (Sloppy paired locus protein 1)	0.71	+	nuc	0	Nucleus				322
Q16676 UniProt NPD GO	FOXD1_HUMAN	Forkhead box protein D1 (Forkhead-related protein FKHL8) (Forkhead-related transcription factor 4) ( ...	0.71	+	nuc	0	Nucleus		601091		465

You are viewing entries 13201 to 13250 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.