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
Q6DDW4 UniProt NPD GO	CPSF6_XENLA	Cleavage and polyadenylation specificity factor 6	0.73	+	nuc	0	Nucleus (By similarity)				548
Q9XSC5 UniProt NPD GO	CLUS_RABIT	Clusterin precursor (Apolipoprotein J) (Apo-J) [Contains: Clusterin beta chain; Clusterin alpha chai ...	0.73	-	exc	0	Present in chromaffin granules				447
P10909 UniProt NPD GO	CLUS_HUMAN	Clusterin precursor (Complement-associated protein SP-40,40) (Complement cytolysis inhibitor) (CLI) ...	0.73	-	exc	0	Secreted protein	extracellular space [NAS]	185430		449
Q9PVW7 UniProt NPD GO	CO8B_PAROL	Complement component C8 beta chain precursor (Complement component 8 subunit beta)	0.73	-	exc	0					588
Q75UQ2 UniProt NPD GO	CFDP1_RAT	Craniofacial development protein 1 (Bucentaur)	0.73	-	nuc	0					295
P48130 UniProt NPD GO	RK34_CYAPA	Cyanelle 50S ribosomal protein L34	0.73	-	nuc	0	Plastid; cyanelle				46
O65717 UniProt NPD GO	CNGC1_ARATH	Cyclic nucleotide-gated ion channel 1 (AtCNGC1) (Cyclic nucleotide-and calmodulin-regulated ion chan ...	0.73	-	end	5	Cell membrane; multi-pass membrane protein (Potential)				716
P34425 UniProt NPD GO	CCNT1_CAEEL	Cyclin-T1.1	0.73	-	nuc	0					468
O19001 UniProt NPD GO	CDN1B_FELCA	Cyclin-dependent kinase inhibitor 1B (Cyclin-dependent kinase inhibitor p27) (p27Kip1)	0.73	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear and cytoplasmic in quiescent cells. Upon ...				198
Q28092 UniProt NPD GO	CYLC2_BOVIN	Cylicin-2 (Cylicin II) (Multiple-band polypeptide II)	0.73	+	nuc	0	Calyx. Sperm head cytoskeletal structure				488
P51870 UniProt NPD GO	CP4F5_RAT	Cytochrome P450 4F5 (EC 1.14.14.1) (CYPIVF5)	0.73	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				526
P51813 UniProt NPD GO	BMX_HUMAN	Cytoplasmic tyrosine-protein kinase BMX (EC 2.7.10.2) (Bone marrow tyrosine kinase gene in chromosom ...	0.73	-	nuc	0	Cytoplasm (Probable)		300101		675
Q75DE8 UniProt NPD GO	ASK1_ASHGO	DASH complex subunit ASK1 (Outer kinetochore protein ASK1) (Associated with spindles and kinetochore ...	0.73	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				181
Q6FLI2 UniProt NPD GO	SPC34_CANGA	DASH complex subunit SPC34 (Outer kinetochore protein SPC34)	0.73	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				307
Q6CJ49 UniProt NPD GO	SPC34_KLULA	DASH complex subunit SPC34 (Outer kinetochore protein SPC34)	0.73	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				275
P52496 UniProt NPD GO	DNLI_CANAL	DNA ligase (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])	0.73	-	cyt	0	Nucleus				928
P52431 UniProt NPD GO	DPOD1_MOUSE	DNA polymerase delta catalytic subunit (EC 2.7.7.7)	0.73	+	cyt	0	Nucleus				1105
Q9DG67 UniProt NPD GO	RA54B_CHICK	DNA repair and recombination protein RAD54B (EC 3.6.1.-) (RAD54 homolog B)	0.73	-	nuc	0	Nucleus (Probable)				918
P40026 UniProt NPD GO	KRE29_YEAST	DNA repair protein KRE29 (Killer toxin-resistance protein 29)	0.73	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA] Smc5-Smc6 complex [IPI]			464
P06838 UniProt NPD GO	RAD10_YEAST	DNA repair protein RAD10	0.73	-	nuc	0	Nucleus	nucleotide-excision repair factor 1 complex [IPI] nucleus [IDA]			210
O42130 UniProt NPD GO	TOP2A_CHICK	DNA topoisomerase 2-alpha (EC 5.99.1.3) (DNA topoisomerase II, alpha isozyme)	0.73	+	nuc	0	Nucleus; nucleoplasm. Generally located in the nucleoplasm				1553
Q6ENI4 UniProt NPD GO	RPOB_ORYNI	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.73	-	nuc	0	Plastid; chloroplast				1075
P12091 UniProt NPD GO	RPOB_ORYSA	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.73	-	nuc	0	Plastid; chloroplast				1075
Q5SCX9 UniProt NPD GO	RPOC1_HUPLU	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.73	-	cyt	0	Plastid; chloroplast				676
Q6DI48 UniProt NPD GO	DLLA_BRARE	Delta-like protein A precursor (DeltaA protein)	0.73	-	exc	1 *	Membrane; single-pass type I membrane protein (By similarity)				772
Q8CF97 UniProt NPD GO	VCIP1_RAT	Deubiquitinating protein VCIP135 (EC 3.4.22.-) (Valosin-containing protein p97/p47 complex-interacti ...	0.73	-	nuc	0	Endoplasmic reticulum. Golgi apparatus; Golgi stack. Associated with Golgi stacks and endoplasmic re ...				1221
Q16760 UniProt NPD GO	DGKD_HUMAN	Diacylglycerol kinase delta (EC 2.7.1.107) (Diglyceride kinase delta) (DGK-delta) (DAG kinase delta) ...	0.73	-	nuc	0	Isoform 2: Cytoplasm. Isoform 1: Membrane; peripheral membrane protein	cytoplasm [IDA] plasma membrane [IDA]	601826	1R79	1214
Q12959 UniProt NPD GO	DLG1_HUMAN	Disks large homolog 1 (Synapse-associated protein 97) (SAP-97) (hDlg)	0.73	-	nuc	0	Membrane; peripheral membrane protein (By similarity). Colocalizes with EPB41 at regions of intercel ...	basolateral plasma membrane [IDA] cell-cell adherens junction [ISS] plasma membrane [TAS]	601014	1PDR	904
Q810H6 UniProt NPD GO	DISC1_RAT	Disrupted in schizophrenia 1 homolog	0.73	+	nuc	0	Centrosome (By similarity). Localizes to the centrosome (By similarity). Cytoplasm. Localizes to pun ...				846
Q9D844 UniProt NPD GO	DNJC4_MOUSE	DnaJ homolog subfamily C member 4 (Multiple endocrine neoplasia type 1 candidate protein number 18 h ...	0.73	-	nuc	1	Membrane; single-pass membrane protein (Potential)				244
Q9SEZ3 UniProt NPD GO	DOF1A_ARATH	Dof zinc finger protein DOF1.10 (AtDOF1.10) (H-protein promoter-binding factor 2b)	0.73	-	nuc	0	Nucleus (Probable)				399
P55265 UniProt NPD GO	DSRAD_HUMAN	Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-) (DRADA) (136 kDa double-stranded RNA-b ...	0.73	-	nuc	0	Cytoplasm. Nucleus; nucleolus. Isoform 1 is found predominantly in cytoplasm but appears to shuttle ...	cytoplasm [TAS] nucleus [TAS]	127400	2ACJ	1226
Q9UNH5 UniProt NPD GO	CC14A_HUMAN	Dual specificity protein phosphatase CDC14A (EC 3.1.3.48) (EC 3.1.3.16) (CDC14 cell division cycle 1 ...	0.73	-	nuc	0	Nucleus. Centrosomal during interphase; released into the cytoplasm at the onset of mitosis. Subsequ ...	nucleus [TAS]	603504		594
Q92630 UniProt NPD GO	DYRK2_HUMAN	Dual specificity tyrosine-phosphorylation-regulated kinase 2 (EC 2.7.12.1)	0.73	-	nuc	0	Cytoplasm	cytoplasm [TAS]	603496		528
P39052 UniProt NPD GO	DYN2_RAT	Dynamin-2 (EC 3.6.5.5)	0.73	-	nuc	0	Cytoplasm (By similarity). Microtubule-associated. Also found in the postsynaptic density of neurona ...	clathrin-coated endocytic vesicle [IDA] postsynaptic membrane [ISS]			870
P17322 UniProt NPD GO	EDN1_BOVIN	Endothelin-1 precursor (ET-1) (Preproendothelin-1) (PPET1)	0.73	-	nuc	0	Secreted protein				202
P11678 UniProt NPD GO	PERE_HUMAN	Eosinophil peroxidase precursor (EC 1.11.1.7) (EPO) [Contains: Eosinophil peroxidase light chain; Eo ...	0.73	-	exc	0	Cytoplasmic granule. Cytoplasmic granules of eosinophils		261500		715
Q8VYM0 UniProt NPD GO	ERF15_ARATH	Ethylene-responsive transcription factor 15 (Ethylene-responsive element-binding factor 15) (EREBP-1 ...	0.73	-	nuc	0	Nucleus (Probable)				243
Q8LDC8 UniProt NPD GO	ERF1B_ARATH	Ethylene-responsive transcription factor 1B (Ethylene-responsive element-binding factor 1B) (EREBP-1 ...	0.73	-	nuc	0	Nucleus (Probable)				218
Q06245 UniProt NPD GO	SEC10_YEAST	Exocyst complex component SEC10	0.73	-	mit	0		exocyst [IPI]			871
Q8VEG4 UniProt NPD GO	EXDL2_MOUSE	Exonuclease 3'-5' domain-like-containing protein 2	0.73	-	nuc	0					496
P34686 UniProt NPD GO	CAPZB_CAEEL	F-actin capping protein subunit beta	0.73	-	nuc	0		cytoplasm [IDA]			270
Q96NE9 UniProt NPD GO	FRMD6_HUMAN	FERM domain-containing protein 6	0.73	-	nuc	0					622
O75494 UniProt NPD GO	FUSIP_HUMAN	FUS-interacting serine-arginine-rich protein 1 (TLS-associated protein with Ser-Arg repeats) (TLS-as ...	0.73	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Cytoplasm	cytoplasm [NAS] nucleoplasm [IDA] nucleus [IC]	605221		262
Q9R0U0 UniProt NPD GO	FUSIP_MOUSE	FUS-interacting serine-arginine-rich protein 1 (TLS-associated protein with Ser-Arg repeats) (TLS-as ...	0.73	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle	cytoplasm [IC] nucleoplasm [IDA] nucleus [IC]			262
Q9UHY8 UniProt NPD GO	FEZ2_HUMAN	Fasciculation and elongation protein zeta 2 (Zygin-2) (Zygin II)	0.73	-	nuc	0			604826		353
Q40872 UniProt NPD GO	AG_PANGI	Floral homeotic protein AGAMOUS (GAG2)	0.73	-	nuc	0	Nucleus (By similarity)				242
Q03488 UniProt NPD GO	FBP1_PETHY	Floral homeotic protein FBP1 (Floral-binding protein 1)	0.73	-	nuc	0	Nucleus				210
P32031 UniProt NPD GO	SLP2_DROME	Fork head domain transcription factor slp2 (Sloppy paired locus protein 2)	0.73	-	nuc	0	Nucleus				445
Q3BJS0 UniProt NPD GO	FOXN5_XENLA	Forkhead box protein N5	0.73	-	nuc	0	Nucleus (Potential)				295

You are viewing entries 12251 to 12300 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.