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
P49956 UniProt NPD GO	CTF18_YEAST	Chromosome transmission fidelity protein 18	0.95	+	nuc	0	Nucleus (Probable)	DNA replication factor C complex [IPI] mitochondrion [IDA]			741
Q80YR7 UniProt NPD GO	CLSPN_MOUSE	Claspin	0.95	-	nuc	0	Nucleus (By similarity)				1315
Q9HAW4 UniProt NPD GO	CLSPN_HUMAN	Claspin (hClaspin) (Hu-Claspin)	0.95	-	nuc	0	Nucleus		605434		1332
Q06194 UniProt NPD GO	FA8_MOUSE	Coagulation factor VIII precursor (Procoagulant component)	0.95	-	nuc	0	Secreted protein; extracellular space				2319
Q6ZU67 UniProt NPD GO	CCDC4_HUMAN	Coiled-coil domain-containing protein 4	0.95	-	nuc	0					530
Q66H89 UniProt NPD GO	CCD41_RAT	Coiled-coil domain-containing protein 41	0.95	-	nuc	0					692
Q5XI03 UniProt NPD GO	CCD45_RAT	Coiled-coil domain-containing protein 45	0.95	-	nuc	0					821
Q66H73 UniProt NPD GO	CCD82_RAT	Coiled-coil domain-containing protein 82	0.95	+	nuc	0					516
P13915 UniProt NPD GO	CVCA_PEA	Convicilin precursor	0.95	-	exc	1 *	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies				571
Q2QLA2 UniProt NPD GO	CTTB2_HORSE	Cortactin-binding protein 2 (CortBP2)	0.95	-	nuc	0					1665
Q8BJW7 UniProt NPD GO	EME1_MOUSE	Crossover junction endonuclease EME1 (EC 3.1.22.-)	0.95	+	nuc	0	Nucleus; nucleolus. Recruited to regions of DNA damage in S-phase cells (By similarity)				570
P29747 UniProt NPD GO	CREBA_DROME	Cyclic AMP response element-binding protein A (Box B-binding factor 2) (BBF-2) (dCREB-A)	0.95	+	nuc	0	Nucleus	nucleus [IDA]			516
Q00969 UniProt NPD GO	ATF2_RAT	Cyclic AMP-dependent transcription factor ATF-2 (Activating transcription factor 2) (cAMP response e ...	0.95	+	nuc	0	Nucleus				487
P15336 UniProt NPD GO	ATF2_HUMAN	Cyclic AMP-dependent transcription factor ATF-2 (Activating transcription factor 2) (cAMP response e ...	0.95	+	nuc	0	Nucleus		123811	1T2K	487
P16951 UniProt NPD GO	ATF2_MOUSE	Cyclic AMP-dependent transcription factor ATF-2 (Activating transcription factor 2) (cAMP response e ...	0.95	+	nuc	0	Nucleus				487
Q9JJA7 UniProt NPD GO	CCNL2_MOUSE	Cyclin-L2 (Cyclin Ania-6b) (Paneth cell-enhanced expression protein) (PCEE)	0.95	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				518
O01835 UniProt NPD GO	CPB3_CAEEL	Cytoplasmic polyadenylation element-binding protein 3	0.95	-	nuc	0					751
Q8C4S8 UniProt NPD GO	DEN2A_MOUSE	DENN domain-containing protein 2A	0.95	+	nuc	0					1000
Q68D51 UniProt NPD GO	DEN2C_HUMAN	DENN domain-containing protein 2C	0.95	-	nuc	0					928
Q6P9P8 UniProt NPD GO	DEN2C_MOUSE	DENN domain-containing protein 2C	0.95	+	nuc	0					914
Q94F87 UniProt NPD GO	CMT2_ARATH	DNA (cytosine-5)-methyltransferase CMT2 (EC 2.1.1.37) (Chromomethylase 2) (Protein CHROMOMETHYLASE2) ...	0.95	+	nuc	0	Nucleus (By similarity)				1244
P18858 UniProt NPD GO	DNL1_HUMAN	DNA ligase 1 (EC 6.5.1.1) (DNA ligase I) (Polydeoxyribonucleotide synthase [ATP] 1)	0.95	-	nuc	0	Nucleus	nucleus [TAS]	126391	1X9N	919
P26019 UniProt NPD GO	DPOLA_DROME	DNA polymerase alpha catalytic subunit (EC 2.7.7.7)	0.95	-	nuc	0	Nucleus	alpha DNA polymerase:primase complex [IDA]			1488
O93845 UniProt NPD GO	DPOE_EMENI	DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A)	0.95	+	nuc	0	Nucleus (By similarity)				2207
P21951 UniProt NPD GO	DPOE_YEAST	DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A)	0.95	+	nuc	0	Nucleus	epsilon DNA polymerase complex [IDA] replication fork [IDA]			2222
P15801 UniProt NPD GO	DPOG_YEAST	DNA polymerase gamma (EC 2.7.7.7) (Mitochondrial DNA polymerase catalytic subunit)	0.95	+	nuc	0	Mitochondrion	mitochondrion [IDA]			1254
Q92698 UniProt NPD GO	RAD54_HUMAN	DNA repair and recombination protein RAD54-like (EC 3.6.1.-) (RAD54 homolog) (hRAD54) (hHR54)	0.95	-	mit	0	Nucleus	nucleus [TAS]	603615		747
P70270 UniProt NPD GO	RAD54_MOUSE	DNA repair and recombination protein RAD54-like (EC 3.6.1.-) (RAD54 homolog) (mRAD54) (mHR54)	0.95	-	mit	0	Nucleus (Probable)				747
Q00578 UniProt NPD GO	RAD25_YEAST	DNA repair helicase RAD25 (EC 3.6.1.-) (General transcription and DNA repair factor IIH subunit RAD2 ...	0.95	-	cyt	0	Nucleus	nucleotide-excision repair factor 3 complex [TAS] transcription factor TFIIH complex [TAS]			843
P70388 UniProt NPD GO	RAD50_MOUSE	DNA repair protein RAD50 (EC 3.6.-.-) (mRad50)	0.95	-	nuc	0	Nucleus (By similarity). Localizes to discrete nuclear foci after treatment with genotoxic agents (B ...				1312
P06779 UniProt NPD GO	RAD7_YEAST	DNA repair protein RAD7	0.95	+	nuc	0		nucleotide-excision repair factor 4 complex [IDA] repairosome [IDA]			565
Q09761 UniProt NPD GO	SLD3_SCHPO	DNA replication regulator sld3	0.95	-	nuc	0	Nucleus (By similarity)	DNA replication preinitiation complex [IDA]			668
P41511 UniProt NPD GO	TOP1_USTMA	DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I)	0.95	-	nuc	0					1019
Q8WN22 UniProt NPD GO	PRKDC_CANFA	DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) (DNA-PK catalytic subunit) (DNA-PKcs)	0.95	+	nuc	0	Nucleus (By similarity)				4144
Q8QGX4 UniProt NPD GO	PRKDC_CHICK	DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) (DNA-PK catalytic subunit) (DNA-PKcs)	0.95	-	end	0	Nucleus				4134
P78527 UniProt NPD GO	PRKDC_HUMAN	DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) (DNA-PK catalytic subunit) (DNA-PKcs) ( ...	0.95	+	nuc	0	Nucleus		600899		4128
Q01831 UniProt NPD GO	XPC_HUMAN	DNA-repair protein complementing XP-C cells (Xeroderma pigmentosum group C-complementing protein) (p ...	0.95	+	nuc	0	Nucleus (Probable)		278720		939
O18805 UniProt NPD GO	DAXX_CERAE	Death domain-associated protein 6 (Daxx)	0.95	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Translocates from the nucleus to the cytoplasm u ...	nucleus [ISS]			736
Q13574 UniProt NPD GO	DGKZ_HUMAN	Diacylglycerol kinase zeta (EC 2.7.1.107) (Diglyceride kinase zeta) (DGK-zeta) (DAG kinase zeta)	0.95	-	nuc	0	Cytoplasm. Nucleus	nucleus [TAS]	601441		1117
Q80UP3 UniProt NPD GO	DGKZ_MOUSE	Diacylglycerol kinase zeta (EC 2.7.1.107) (Diglyceride kinase zeta) (DGK-zeta) (DAG kinase zeta)	0.95	-	nuc	0	Nucleus (By similarity)				929
P31007 UniProt NPD GO	DLG1_DROME	Discs large 1 tumor suppressor protein	0.95	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoskeleton- and membrane- ...	apical cortex [IDA] apicolateral plasma membrane [IDA] basolateral plasma membrane [TAS] cell cortex [IDA] cytoplasm [NAS] membrane [TAS] septate junction [TAS] synapse [TAS]			970
P78953 UniProt NPD GO	DMF1_SCHPO	Division mal foutue 1 protein	0.95	-	nuc	0	Nucleus. During interphase relocates to medial ring at the cell cortex	medial ring [IDA] nucleus [IDA]			920
Q24025 UniProt NPD GO	SOG_DROME	Dorsal-ventral patterning protein Sog (Short gastrulation protein)	0.95	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)				1038
P36022 UniProt NPD GO	DYHC_YEAST	Dynein heavy chain, cytosolic (DYHC)	0.95	-	nuc	0	Cytoplasm. Probably binds indirectly to the inner plasma membrane	cytoplasmic dynein complex [TAS] cytoplasmic microtubule [IDA]			4092
P11533 UniProt NPD GO	DMD_CHICK	Dystrophin	0.95	-	nuc	0					3660
Q8CHI8 UniProt NPD GO	EP400_MOUSE	E1A-binding protein p400 (EC 3.6.1.-) (p400 kDa SWI2/SNF2-related protein) (Domino homolog) (mDomino ...	0.95	+	nuc	0	Nucleus (By similarity)				3072
Q9H8V3 UniProt NPD GO	ECT2_HUMAN	ECT2 protein (Epithelial cell-transforming sequence 2 oncogene)	0.95	+	nuc	0			600586		883
O15083 UniProt NPD GO	ERC2_HUMAN	ERC protein 2	0.95	-	nuc	0	Cytoplasm. In neurons, localized to synapses, and colocalizes with PCLO. Localized to the active zon ...	endoplasmic reticulum [ISS] growth cone [ISS] presynaptic membrane [ISS] synapse [ISS]			957
Q8K3M6 UniProt NPD GO	ERC2_RAT	ERC protein 2 (CAZ-associated structural protein 1) (CAST1) (Cast) (Cytomatrix protein p110)	0.95	-	nuc	0	Cytoplasm. Localized to the active zone of presynaptic density. Colocalizes with RIMS1 and BSN in ea ...	endoplasmic reticulum [NAS] growth cone [IDA] presynaptic membrane [IDA] synapse [TAS]			957
Q09228 UniProt NPD GO	EGL27_CAEEL	Egg-laying defective protein 27	0.95	-	nuc	0	Nucleus	nucleus [IDA]			1129

You are viewing entries 1801 to 1850 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.