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
Q6FRM6 UniProt NPD GO	CWC21_CANGA	Pre-mRNA-splicing factor CWC21	0.79	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				143
Q4WT84 UniProt NPD GO	CLF1_ASPFU	Pre-mRNA-splicing factor clf1	0.79	+	cyt	0	Nucleus (By similarity)				676
Q5B4R9 UniProt NPD GO	SPP2_EMENI	Pre-mRNA-splicing factor spp2	0.79	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				523
Q23868 UniProt NPD GO	TAGC_DICDI	Prestalk-specific protein tagC precursor (EC 3.4.21.-)	0.79	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				1743
Q501J6 UniProt NPD GO	DDX17_MOUSE	Probable ATP-dependent RNA helicase DDX17 (EC 3.6.1.-) (DEAD box protein 17)	0.79	+	nuc	0	Nucleus (By similarity)				650
Q6J5K9 UniProt NPD GO	ARMI_DROME	Probable RNA helicase armi (EC 3.6.1.-) (Armitage protein)	0.79	-	cyt	0	Cytoplasm	cytoplasm [IDA]			1274
Q9SA80 UniProt NPD GO	WRK14_ARATH	Probable WRKY transcription factor 14 (WRKY DNA-binding protein 14) (AR411)	0.79	-	nuc	0	Nucleus (Probable)				430
Q04956 UniProt NPD GO	ATX1_PLAFA	Probable cation-transporting ATPase 1 (EC 3.6.3.-)	0.79	-	nuc	7 *	Membrane; multi-pass membrane protein				1956
P56329 UniProt NPD GO	IF2B_SCHPO	Probable eukaryotic translation initiation factor 2 subunit beta (eIF-2-beta)	0.79	+	nuc	0					321
Q75A47 UniProt NPD GO	NOP14_ASHGO	Probable nucleolar complex protein 14	0.79	-	nuc	0	Nucleus; nucleolus (By similarity)				806
Q5VNU3 UniProt NPD GO	SEC1B_ORYSA	Probable protein transport Sec1b	0.79	-	nuc	0					659
Q9D903 UniProt NPD GO	EBP2_MOUSE	Probable rRNA-processing protein EBP2	0.79	-	nuc	0	Nucleus; nucleolus (By similarity)	nucleolus [TAS]			306
P38070 UniProt NPD GO	KBN8_YEAST	Probable serine/threonine-protein kinase YBR028C (EC 2.7.11.1)	0.79	+	nuc	0		cytoplasm [IDA]			525
P55824 UniProt NPD GO	FAF_DROME	Probable ubiquitin carboxyl-terminal hydrolase FAF (EC 3.1.2.15) (Ubiquitin thioesterase FAF) (Ubiqu ...	0.79	-	end	0		cytoplasm [IDA]			2778
Q9NSV0 UniProt NPD GO	PRR8_HUMAN	Proline-rich protein 8	0.79	-	nuc	0					439
P22969 UniProt NPD GO	RELX_HORSE	Prorelaxin precursor (RXN) [Contains: Relaxin B chain; Relaxin A chain]	0.79	-	exc	0	Secreted protein				182
Q9TRM8 UniProt NPD GO	RELX_CANFA	Prorelaxin precursor [Contains: Relaxin B chain; Relaxin A chain]	0.79	-	exc	0	Secreted protein				177
Q6S5H4 UniProt NPD GO	POT15_HUMAN	Prostate, ovary, testis-expressed protein on chromosome 15	0.79	-	nuc	0			608912		581
P12819 UniProt NPD GO	PRT1A_ONCMY	Protamine 1A (Protamine PRTP43/PPC 2E)	0.79	+	nuc	0	Nucleus				30
P12817 UniProt NPD GO	PRT2A_ONCMY	Protamine 2A	0.79	+	nuc	0	Nucleus				32
P02334 UniProt NPD GO	PRT2C_ONCMY	Protamine 2C	0.79	+	nuc	0	Nucleus				32
P02331 UniProt NPD GO	PRTC3_ONCMY	Protamine CIII (Protamine PPC 6B)	0.79	+	nuc	0	Nucleus				30
P08145 UniProt NPD GO	PRT14_ONCMY	Protamine TP14	0.79	+	nuc	0	Nucleus				32
P08146 UniProt NPD GO	PRT16_ONCMY	Protamine TP16	0.79	+	nuc	0	Nucleus				32
P30258 UniProt NPD GO	PRTZ3_SCYCA	Protamine Z3 (Scylliorhinine Z3)	0.79	+	nuc	0	Nucleus				37
P02325 UniProt NPD GO	PRT1_ESOLU	Protamine-1 (Protamine-I)	0.79	+	nuc	0	Nucleus				32
P02330 UniProt NPD GO	PRT2_ONCMY	Protamine-2 (Protamine II) (Iridine II)	0.79	+	nuc	0	Nucleus				32
P35297 UniProt NPD GO	PRM2_MACMU	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.79	+	nuc	0	Nucleus				102
P43583 UniProt NPD GO	BLM10_YEAST	Proteasome activator BLM10 (Bleomycin resistance protein BLM10)	0.79	-	end	0	Nucleus. Cytoplasm	nucleus [IDA]			2143
O13988 UniProt NPD GO	POT1_SCHPO	Protection of telomeres protein 1	0.79	-	nuc	0	Nucleus (Potential)			1QZH	555
Q9FT92 UniProt NPD GO	Y5843_ARATH	Protein At5g08430	0.79	-	cyt	0				1WH2	553
Q4I327 UniProt NPD GO	BFR2_GIBZE	Protein BFR2	0.79	-	nuc	0	Nucleus; nucleolus (By similarity)				538
Q6CK68 UniProt NPD GO	BUR2_KLULA	Protein BUR2	0.79	-	nuc	0	Nucleus (By similarity)				394
Q8IYJ2 UniProt NPD GO	CJ067_HUMAN	Protein C10orf67	0.79	-	mit	0					184
Q9UU99 UniProt NPD GO	YJX4_SCHPO	Protein C23B6.04c in chromosome III	0.79	-	nuc	0	Cell membrane; peripheral membrane protein. Cell periphery				1008
O60184 UniProt NPD GO	YG49_SCHPO	Protein C23E6.09 in chromosome II	0.79	-	nuc	0	Cytoplasm. Nucleus				1102
Q3U269 UniProt NPD GO	CI097_MOUSE	Protein C9orf97 homolog	0.79	-	nuc	0					495
Q74ZX0 UniProt NPD GO	CSF1_ASHGO	Protein CSF1	0.79	-	vac	0	Membrane; single-pass type II membrane protein (Potential)				2887
Q9H098 UniProt NPD GO	F107B_HUMAN	Protein FAM107B	0.79	-	nuc	0					131
Q8CID3 UniProt NPD GO	FA20A_MOUSE	Protein FAM20A precursor	0.79	-	exc	1 *	Secreted protein (Potential)				541
Q925T8 UniProt NPD GO	FAM5A_RAT	Protein FAM5A precursor (Deleted in bladder cancer 1 protein homolog) (BMP/retinoic acid-inducible n ...	0.79	-	nuc	0	Secreted protein (Potential)				760
Q5ZJ65 UniProt NPD GO	FA76A_CHICK	Protein FAM76A	0.79	-	nuc	0					307
Q69Z89 UniProt NPD GO	K1849_MOUSE	Protein KIAA1849	0.79	-	nuc	0					1099
Q80TH2 UniProt NPD GO	LAP2_MOUSE	Protein LAP2 (Erbb2-interacting protein) (Erbin) (Densin-180-like protein)	0.79	-	nuc	0	Cell membrane; cell-cell junction; hemidesmosome (By similarity). Found in hemidesmosomes, which are ...	basolateral plasma membrane [IDA]			1402
P53050 UniProt NPD GO	MGA1_YEAST	Protein MGA1	0.79	-	nuc	0	Nucleus (Potential)				456
P32047 UniProt NPD GO	MLF3_YEAST	Protein MLF3 (Multicopy suppressor of leflunomide sensitivity 3)	0.79	-	nuc	0	Cytoplasm	cytoplasm [IDA]			452
Q95RW8 UniProt NPD GO	OPTIX_DROME	Protein Optix (Homeobox protein SIX3) (D-Six3)	0.79	-	nuc	0	Nucleus (By similarity)				487
P39081 UniProt NPD GO	PCF11_YEAST	Protein PCF11 (protein 1 of CF I)	0.79	-	nuc	0	Nucleus (Potential)	mRNA cleavage factor complex [IPI]		2BF0	626
Q6Q4H1 UniProt NPD GO	PTDSR_HYDAT	Protein PSR (Phosphatidylserine receptor)	0.79	-	nuc	0	Nucleus	nucleus [IDA]			385
O46341 UniProt NPD GO	A6_DROME	Protein a6	0.79	+	nuc	0					409

You are viewing entries 9501 to 9550 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.