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
Q99569 UniProt NPD GO	PKP4_HUMAN	Plakophilin-4 (p0071)	0.90	+	nuc	0	Cell membrane; cell-cell junction; desmosome. Colocalized with desmoplakin at desmosomal junctional ...	intercellular junction [TAS]	604276		1211
Q9UKK3 UniProt NPD GO	PARP4_HUMAN	Poly [ADP-ribose] polymerase 4 (EC 2.4.2.30) (PARP-4) (Vault poly(ADP-ribose) polymerase) (VPARP) (1 ...	0.90	-	cyt	0	Cytoplasm. Nucleus. Also found in the nucleus, associated with mitotic spindles	nucleus [NAS] ribonucleoprotein complex [NAS]	607519		1724
O46043 UniProt NPD GO	PARG_DROME	Poly(ADP-ribose) glycohydrolase (EC 3.2.1.143)	0.90	-	nuc	0					768
Q9ZNT9 UniProt NPD GO	FIS2_ARATH	Polycomb group protein FERTILIZATION-INDEPENDENT SEED 2	0.90	-	nuc	0	Nucleus				632
O17514 UniProt NPD GO	MES2_CAEEL	Polycomb protein mes-2 (Maternal-effect sterile protein 2) (E(z) homolog)	0.90	-	nuc	0	Nucleus				773
Q6BML1 UniProt NPD GO	PRP5_DEBHA	Pre-mRNA-processing ATP-dependent RNA helicase PRP5 (EC 3.6.1.-)	0.90	-	nuc	0	Nucleus (By similarity)				913
Q9Y7T7 UniProt NPD GO	PRP28_SCHPO	Pre-mRNA-splicing ATP-dependent RNA helicase prp28 (EC 3.6.1.-)	0.90	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				662
P49704 UniProt NPD GO	PRP31_YEAST	Pre-mRNA-splicing factor 31	0.90	-	nuc	0	Nucleus	mitochondrion [IDA] U4/U6 x U5 tri-snRNP complex [IDA]			494
P33334 UniProt NPD GO	PRP8_YEAST	Pre-mRNA-splicing factor 8	0.90	+	nuc	0	Nucleus	snRNP U5 [IDA] U4/U6 x U5 tri-snRNP complex [IDA]			2413
Q6CJK2 UniProt NPD GO	CLF1_KLULA	Pre-mRNA-splicing factor CLF1	0.90	-	cyt	0	Nucleus (By similarity)				684
Q59R35 UniProt NPD GO	ISY1_CANAL	Pre-mRNA-splicing factor ISY1	0.90	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				266
P21374 UniProt NPD GO	ISY1_YEAST	Pre-mRNA-splicing factor ISY1 (Interactor of SYF1) (PRP19-associated complex protein 30)	0.90	+	nuc	0	Cytoplasm. Nucleus	spliceosome complex [IDA]			235
Q6FPZ6 UniProt NPD GO	SYF2_CANGA	Pre-mRNA-splicing factor SYF2	0.90	-	nuc	0	Nucleus (By similarity)				200
Q4X1D7 UniProt NPD GO	CWC25_ASPFU	Pre-mRNA-splicing factor cwc25	0.90	+	nuc	0	Nucleus (By similarity)				447
Q4WWR2 UniProt NPD GO	SLU7_ASPFU	Pre-mRNA-splicing factor slu7	0.90	-	nuc	0	Nucleus (By similarity)				536
Q02297 UniProt NPD GO	NRG1_HUMAN	Pro-neuregulin-1, membrane-bound isoform precursor (Pro-NRG1) [Contains: Neuregulin-1 (Neu different ...	0.90	+	nuc	1	Pro-neuregulin-1, membrane-bound isoform: Cell membrane; single-pass type I membrane protein. Neureg ...	extracellular region [NAS] membrane [NAS]	142445	1HRF	639
O13602 UniProt NPD GO	RT28_SCHPO	Probable 40S ribosomal protein S28, mitochondrial precursor	0.90	-	nuc	0	Mitochondrion (By similarity)				288
Q921N6 UniProt NPD GO	DDX27_MOUSE	Probable ATP-dependent RNA helicase DDX27 (EC 3.6.1.-) (DEAD box protein 27)	0.90	+	nuc	0	Nucleus (Potential)				760
Q9DBV3 UniProt NPD GO	DHX34_MOUSE	Probable ATP-dependent RNA helicase DHX34 (EC 3.6.1.-) (DEAH box protein 34)	0.90	+	nuc	0					1145
Q756G2 UniProt NPD GO	TOM1_ASHGO	Probable E3 ubiquitin protein ligase TOM1 (EC 6.3.2.-)	0.90	-	end	0	Nucleus; nucleolus (By similarity)				3258
Q9M223 UniProt NPD GO	UTP11_ARATH	Probable U3 small nucleolar RNA-associated protein 11 (U3 snoRNA-associated protein 11)	0.90	+	nuc	0	Nucleus; nucleolus (By similarity)				228
Q93WU6 UniProt NPD GO	WRK74_ARATH	Probable WRKY transcription factor 74 (WRKY DNA-binding protein 74)	0.90	-	nuc	0	Nucleus (Probable)				330
O14164 UniProt NPD GO	IF38_SCHPO	Probable eukaryotic translation initiation factor 3 93 kDa subunit (eIF3 p93)	0.90	+	nuc	0					918
Q9VVG4 UniProt NPD GO	EXOC1_DROME	Probable exocyst complex component 1 (Exocyst complex component Sec3)	0.90	-	cyt	0		exocyst [ISS]			889
Q5B3B1 UniProt NPD GO	NDC80_EMENI	Probable kinetochore protein ndc80	0.90	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				738
Q12674 UniProt NPD GO	ATC8_YEAST	Probable phospholipid-transporting ATPase DNF3 (EC 3.6.3.1)	0.90	-	nuc	8	Membrane; multi-pass membrane protein	trans-Golgi network transport vesicle [IDA]			1656
Q38953 UniProt NPD GO	DHX8_ARATH	Probable pre-mRNA-splicing factor ATP-dependent RNA helicase (EC 3.6.1.-)	0.90	+	nuc	0	Nucleus (Probable)				1168
Q9LX30 UniProt NPD GO	GCN2_ARATH	Probable serine/threonine-protein kinase GCN2 (EC 2.7.11.1)	0.90	+	mit	0					1241
P25341 UniProt NPD GO	KIN82_YEAST	Probable serine/threonine-protein kinase KIN82 (EC 2.7.11.1)	0.90	-	nuc	0					720
P56699 UniProt NPD GO	CAC1E_DISOM	Probable voltage-dependent R-type calcium channel subunit alpha-1E (Voltage-gated calcium channel su ...	0.90	-	end	22 *	Membrane; multi-pass membrane protein				2223
P46087 UniProt NPD GO	NOL1_HUMAN	Proliferating-cell nucleolar antigen p120 (Proliferation-associated nucleolar protein p120)	0.90	+	nuc	0	Nucleus; nucleolus	nucleolus [TAS]	164031		855
P06841 UniProt NPD GO	PRTZ2_SCYCA	Protamine Z2 (Scylliorhinine Z2)	0.90	+	nuc	0	Nucleus				45
P35301 UniProt NPD GO	PRM2_PONPY	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.90	+	nuc	0	Nucleus				102
Q09874 UniProt NPD GO	YAGB_SCHPO	Protein C12G12.11c in chromosome I	0.90	-	nuc	0	Cytoplasm				365
Q8K2Y0 UniProt NPD GO	CM007_MOUSE	Protein C13orf7 homolog	0.90	-	nuc	0					722
Q9BGW4 UniProt NPD GO	CN140_MACFA	Protein C14orf140 homolog	0.90	-	nuc	0					531
Q8CGI1 UniProt NPD GO	CD008_MOUSE	Protein C4orf008 homolog (Fragment)	0.90	-	nuc	0					944
Q9D9W6 UniProt NPD GO	CF146_MOUSE	Protein C6orf146 homolog	0.90	-	nuc	0					419
Q5XHY8 UniProt NPD GO	CF146_RAT	Protein C6orf146 homolog	0.90	-	nuc	0					419
Q6AXZ4 UniProt NPD GO	CF182_RAT	Protein C6orf182 homolog	0.90	-	nuc	0					430
Q02554 UniProt NPD GO	CUS1_YEAST	Protein CUS1	0.90	-	nuc	0	Nucleus (Potential)	snRNP U2 [IDA]			436
Q08496 UniProt NPD GO	DIA2_YEAST	Protein DIA2 (Digs into agar protein 2)	0.90	-	nuc	0	Nucleus (Probable)	SCF ubiquitin ligase complex [IDA]			746
Q8NA70 UniProt NPD GO	FA47B_HUMAN	Protein FAM47B	0.90	-	nuc	0					645
Q8VED8 UniProt NPD GO	FA54A_MOUSE	Protein FAM54A (DUF729 domain-containing protein 1)	0.90	-	nuc	0					361
Q499E0 UniProt NPD GO	FAM5C_MOUSE	Protein FAM5C precursor	0.90	-	exc	1 *	Secreted protein (Potential)				766
Q8K1M7 UniProt NPD GO	FAM5C_RAT	Protein FAM5C precursor (BMP/retinoic acid-inducible neural-specific protein 3)	0.90	-	exc	1 *	Secreted protein (Potential)	cytoplasm [IMP]			766
Q76B58 UniProt NPD GO	FAM5C_HUMAN	Protein FAM5C precursor (DBCCR1-like protein 1)	0.90	-	exc	0	Secreted protein (Potential)				766
Q75CZ6 UniProt NPD GO	FYV7_ASHGO	Protein FYV7	0.90	-	nuc	0	Nucleus; nucleolus				140
Q6BQV7 UniProt NPD GO	GRC3_DEBHA	Protein GRC3	0.90	+	nuc	0	Nucleus (By similarity)				680
P17629 UniProt NPD GO	HPR1_YEAST	Protein HPR1	0.90	+	nuc	0		Cdc73/Paf1 complex [IPI] THO complex [IMP]			752

You are viewing entries 4301 to 4350 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.