NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

We have performed NucPred and PredictNLS predictions for a number of fully sequenced eukaryotic organisms. More precisely, we have used sets of proteins from the EBI which are thought to be complete proteomes (but may not be, of course). We also include the pseudo-proteome of all 98716 eukaryotic sequences in UniProt Knowledgebase - for which quality functional annotations are often available. This is a simple interface to view and analyse the results. With it you can answer questions such as: "Which proteins are confidently predicted to have a nuclear function by NucPred but are not currently known to be nuclear?" You can also focus your interests on proteins associated with human diseases. When you click on the link in the NucPred score column you can see the NucPred prediction in detail and can then easily send the sequence to other prediction servers (PredictNLS and PSORT II).

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)

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
P51826 UniProt NPD GO	AFF3_HUMAN	AF4/FMR2 family member 3 (Protein LAF-4) (Lymphoid nuclear protein related to AF4)	1.00	-	nuc	0	Nucleus	nucleus [TAS]	601464		1227
P35187 UniProt NPD GO	SGS1_YEAST	ATP-dependent helicase SGS1 (EC 3.6.1.-) (Helicase TPS1)	1.00	-	nuc	0	Nucleus	nucleolus [IDA] RecQ helicase-Topo III complex [IPI]		1D8B	1447
Q6PL18 UniProt NPD GO	ATAD2_HUMAN	ATPase family AAA domain-containing protein 2	1.00	+	nuc	0					1390
Q61315 UniProt NPD GO	APC_MOUSE	Adenomatous polyposis coli protein (Protein APC) (mAPC)	1.00	-	nuc	0		cytoplasm [IDA] nucleus [IDA]		1VJ6	2845
P55196 UniProt NPD GO	AFAD_HUMAN	Afadin (Protein AF-6)	1.00	+	nuc	0	Cell membrane; cell-cell junction; adherens junction. Not found at cell-matrix AJs	intercellular junction [TAS]	159559	1XZ9	1816
O35889 UniProt NPD GO	AFAD_RAT	Afadin (Protein Af-6)	1.00	+	nuc	0	Cell membrane; cell-cell junction; adherens junction. Not found at cell-matrix AJs				1829
Q5U312 UniProt NPD GO	RAI14_RAT	Ankycorbin (Ankyrin repeat and coiled-coil structure-containing protein) (Retinoic acid-induced prot ...	1.00	-	nuc	0	Cytoplasm. Associated with the cortical actin cytoskeleton structures in terminal web and cell-cell ...				978
Q9P0K7 UniProt NPD GO	RAI14_HUMAN	Ankycorbin (Ankyrin repeat and coiled-coil structure-containing protein) (Retinoic acid-induced prot ...	1.00	-	nuc	0	Cytoplasm. Associated with the cortical actin cytoskeleton structures in terminal web and cell-cell ...		606586		980
Q9EP71 UniProt NPD GO	RAI14_MOUSE	Ankycorbin (Ankyrin repeat and coiled-coil structure-containing protein) (Retinoic acid-induced prot ...	1.00	-	nuc	0	Cytoplasm (By similarity). Associated with the cortical actin cytoskeleton structures in terminal we ...	mitochondrion [IDA]			979
P46013 UniProt NPD GO	KI67_HUMAN	Antigen KI-67	1.00	+	nuc	0	Nucleus. Predominantly localized in the G1 phase in the perinucleolar region, in the later phases it ...		176741	2AFF	3256
Q8R4I1 UniProt NPD GO	ATX7_MOUSE	Ataxin-7 (Spinocerebellar ataxia type 7 protein homolog)	1.00	-	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). Nucleus; nuclear matrix (By similarity) ...	cytoplasm [IDA] nucleus [IDA]			867
Q8WXX7 UniProt NPD GO	AUTS2_HUMAN	Autism susceptibility gene 2 protein	1.00	+	nuc	0			607270		1259
O54952 UniProt NPD GO	BRCA1_RAT	Breast cancer type 1 susceptibility protein homolog	1.00	-	nuc	0	Nucleus (Potential)			1L0B	1817
Q9NRL2 UniProt NPD GO	BAZ1A_HUMAN	Bromodomain adjacent to zinc finger domain protein 1A (ATP-utilizing chromatin assembly and remodeli ...	1.00	+	nuc	0	Nucleus. May target the CHRAC complex to heterochromatin		605680		1556
Q921C3 UniProt NPD GO	BRWD1_MOUSE	Bromodomain and WD repeat domain-containing protein 1 (WD repeat protein 9)	1.00	+	nuc	0	Cytoplasm. Nucleus	nucleus [IDA]			2304
Q4R8Y1 UniProt NPD GO	BRDT_MACFA	Bromodomain testis-specific protein	1.00	+	nuc	0	Nucleus (Probable)				947
Q58F21 UniProt NPD GO	BRDT_HUMAN	Bromodomain testis-specific protein (RING3-like protein)	1.00	+	nuc	0	Nucleus (Probable)		602144		947
Q91Y44 UniProt NPD GO	BRDT_MOUSE	Bromodomain testis-specific protein (RING3-like protein) (Bromodomain-containing female sterile home ...	1.00	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			956
Q32S26 UniProt NPD GO	BRD2_BOVIN	Bromodomain-containing protein 2	1.00	+	nuc	0	Nucleus (Potential)				803
Q5TJG6 UniProt NPD GO	BRD2_CANFA	Bromodomain-containing protein 2	1.00	+	nuc	0	Nucleus (Potential)				803
P25440 UniProt NPD GO	BRD2_HUMAN	Bromodomain-containing protein 2 (Protein RING3) (O27.1.1)	1.00	+	nuc	0	Nucleus (Potential)		601540	1X0J	801
O60885 UniProt NPD GO	BRD4_HUMAN	Bromodomain-containing protein 4 (HUNK1 protein)	1.00	+	nuc	0	Nucleus (By similarity)		608749		1362
Q9ESU6 UniProt NPD GO	BRD4_MOUSE	Bromodomain-containing protein 4 (Mitotic chromosome-associated protein) (MCAP)	1.00	+	nuc	0	Nucleus				1400
Q6NXW6 UniProt NPD GO	RAD17_MOUSE	Cell cycle checkpoint protein RAD17	1.00	-	nuc	0	Nucleus. Phosphorylated form redistributes to discrete nuclear foci upon DNA damage (By similarity)				688
Q69ZA1 UniProt NPD GO	CD2L5_MOUSE	Cell division cycle 2-like protein kinase 5 (EC 2.7.11.22) (CDC2-related protein kinase 5)	1.00	+	nuc	0					1511
Q14004 UniProt NPD GO	CD2L5_HUMAN	Cell division cycle 2-like protein kinase 5 (EC 2.7.11.22) (CDC2-related protein kinase 5) (Cholines ...	1.00	+	nuc	0			603309		1512
Q9NYV4 UniProt NPD GO	CD2L7_HUMAN	Cell division cycle 2-related protein kinase 7 (EC 2.7.11.22) (CDC2-related protein kinase 7) (Cdc2- ...	1.00	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			1490
Q8IX12 UniProt NPD GO	CCAR1_HUMAN	Cell division cycle and apoptosis regulator protein 1 (Cell cycle and apoptosis regulatory protein 1 ...	1.00	+	nuc	0	Cytoplasm; perinuclear region				1150
Q03188 UniProt NPD GO	CENPC_HUMAN	Centromere protein C 1 (CENP-C) (Centromere autoantigen C)	1.00	+	nuc	0	Nucleus	kinetochore [TAS]	117141		943
P49452 UniProt NPD GO	CENPC_MOUSE	Centromere protein C 1 (CENP-C) (Centromere autoantigen C)	1.00	+	nuc	0	Nucleus				906
Q5VT06 UniProt NPD GO	CEP35_HUMAN	Centrosome-associated protein 350 (Centrosome-associated protein of 350 kDa)	1.00	+	nuc	0	Centrosome. Spindle. Associated with mitotic spindles. Nucleus. Nuclear, in discrete foci. Associate ...			2COZ	3117
Q13111 UniProt NPD GO	CAF1A_HUMAN	Chromatin assembly factor 1 subunit A (CAF-1 subunit A) (Chromatin assembly factor I p150 subunit) ( ...	1.00	+	nuc	0	Nucleus. DNA replication foci	chromatin assembly complex [TAS]	601246		938
Q6BKL0 UniProt NPD GO	EAF7_DEBHA	Chromatin modification-related protein EAF7	1.00	-	nuc	0	Nucleus (By similarity)				323
Q756L0 UniProt NPD GO	VID21_ASHGO	Chromatin modification-related protein VID21	1.00	-	nuc	0	Nucleus (Probable)				957
O14646 UniProt NPD GO	CHD1_HUMAN	Chromodomain-helicase-DNA-binding protein 1 (EC 3.6.1.-) (ATP-dependent helicase CHD1) (CHD-1)	1.00	-	nuc	0	Nucleus		602118	2B2Y	1709
P40201 UniProt NPD GO	CHD1_MOUSE	Chromodomain-helicase-DNA-binding protein 1 (EC 3.6.1.-) (ATP-dependent helicase CHD1) (CHD-1)	1.00	-	nuc	0	Nucleus	nucleus [NAS]			1711
O14647 UniProt NPD GO	CHD2_HUMAN	Chromodomain-helicase-DNA-binding protein 2 (EC 3.6.1.-) (ATP-dependent helicase CHD2) (CHD-2)	1.00	+	nuc	0	Nucleus (By similarity)		602119		1739
Q3L8U1 UniProt NPD GO	CHD9_HUMAN	Chromodomain-helicase-DNA-binding protein 9 (EC 3.6.1.-) (ATP-dependent helicase CHD9) (CHD-9) (Chro ...	1.00	+	nuc	0	Cytoplasm. Nucleus				2897
Q8BYH8 UniProt NPD GO	CHD9_MOUSE	Chromodomain-helicase-DNA-binding protein 9 (EC 3.6.1.-) (ATP-dependent helicase CHD9) (CHD-9) (Pero ...	1.00	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				2885
Q9DF50 UniProt NPD GO	CLSPN_XENLA	Claspin (xClaspin)	1.00	+	nuc	0	Nucleus (By similarity)				1285
Q9C103 UniProt NPD GO	EME1_SCHPO	Crossover junction endonuclease eme1 (EC 3.1.22.-) (Essential meiotic endonuclease 1)	1.00	+	nuc	0	Nucleus	Holliday junction resolvase complex [TAS]			738
Q05080 UniProt NPD GO	CYK2_YEAST	Cytokinesis 2 protein	1.00	-	nuc	0		contractile ring (sensu Saccharomyces) [IDA]			669
Q9SR66 UniProt NPD GO	DML2_ARATH	DEMETER-like protein 2 (EC 3.2.2.-)	1.00	+	nuc	0	Nucleus (Potential)				1309
Q9JIC3 UniProt NPD GO	DCR1A_MOUSE	DNA cross-link repair 1A protein	1.00	-	nuc	0	Nucleus (By similarity). In some cells it may be found in typically 1 or 2 discrete nuclear aggregat ...				1026
P51892 UniProt NPD GO	DNL1_XENLA	DNA ligase 1 (EC 6.5.1.1) (DNA ligase I) (Polydeoxyribonucleotide synthase [ATP] 1)	1.00	-	nuc	0	Nucleus				1070
Q61493 UniProt NPD GO	DPOLZ_MOUSE	DNA polymerase zeta catalytic subunit (EC 2.7.7.7) (Seizure-related protein 4)	1.00	+	nuc	0	Nucleus (Potential)				3122
O60673 UniProt NPD GO	DPOLZ_HUMAN	DNA polymerase zeta catalytic subunit (EC 2.7.7.7) (hREV3)	1.00	+	nuc	0	Nucleus (Potential)		602776		3130
Q8TDM6 UniProt NPD GO	DLG5_HUMAN	Discs large homolog 5 (Placenta and prostate DLG) (Discs large protein P-dlg)	1.00	-	nuc	0	Cell membrane; cell-cell junction; peripheral membrane protein. Localized at sites of cell-cell cont ...	cytoplasm [TAS] plasma membrane [NAS]	604090	1UIT	1809
Q752Q3 UniProt NPD GO	EPL1_ASHGO	Enhancer of polycomb-like protein 1	1.00	-	nuc	0	Nucleus (By similarity)				742
Q6FLZ0 UniProt NPD GO	EPL1_CANGA	Enhancer of polycomb-like protein 1	1.00	+	nuc	0	Nucleus (By similarity)				821

You are viewing entries 1 to 50 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.