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
P83377 UniProt NPD GO	VA5_POLGA	Venom allergen 5 (Antigen 5) (Ag5) (Allergen Pol g 5)	0.06	-	nuc	0	Secreted protein. Venom reservoirs				206
P35782 UniProt NPD GO	VA52_VESCR	Venom allergen 5.02 (Antigen 5-2) (Ag5-2) (Allergen Vesp c 5.02) (Vesp c V.02)	0.06	-	nuc	0	Secreted protein. Venom reservoirs				202
P19859 UniProt NPD GO	IVBCI_NAJNA	Venom chymotrypsin inhibitor	0.06	-	nuc	0	Secreted protein				57
Q10413 UniProt NPD GO	YD88_SCHPO	Very hypothetical protein C1F3.08c in chromosome I	0.06	-	cyt	1					108
P38184 UniProt NPD GO	YBH3_YEAST	Very hypothetical protein YBL073W	0.06	-	cyt	0					103
Q9CSV6 UniProt NPD GO	SFT2C_MOUSE	Vesicle transport protein SFT2C (SFT2 domain-containing protein 3)	0.06	-	end	4	Membrane; multi-pass membrane protein (Potential)				209
Q7M3T2 UniProt NPD GO	VESP_VESXA	Vespakinin-X	0.06	-		0	Secreted protein. Venom reservoirs				12
P18964 UniProt NPD GO	VSPA_DABRU	Vipera russelli proteinase RVV-V alpha (EC 3.4.21.95) (Factor V-activating proteinase alpha) (Snake ...	0.06	-	cyt	0	Secreted protein				236
Q28412 UniProt NPD GO	PROC_FELCA	Vitamin K-dependent protein C (EC 3.4.21.69) (Autoprothrombin IIA) (Anticoagulant protein C) (Blood ...	0.06	-	cyt	0					157
Q9UF02 UniProt NPD GO	CCG5_HUMAN	Voltage-dependent calcium channel gamma-5 subunit (Neuronal voltage-gated calcium channel gamma-5 su ...	0.06	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)		606405		275
P62955 UniProt NPD GO	CCG7_HUMAN	Voltage-dependent calcium channel gamma-7 subunit (Neuronal voltage-gated calcium channel gamma-7 su ...	0.06	-	mit	4 *	Membrane; multi-pass membrane protein (By similarity)	voltage-gated calcium channel complex [NAS]	606899		275
P62956 UniProt NPD GO	CCG7_MOUSE	Voltage-dependent calcium channel gamma-7 subunit (Neuronal voltage-gated calcium channel gamma-7 su ...	0.06	-	mit	4 *	Membrane; multi-pass membrane protein (By similarity)	voltage-gated calcium channel complex [ISS]			275
P62957 UniProt NPD GO	CCG7_RAT	Voltage-dependent calcium channel gamma-7 subunit (Neuronal voltage-gated calcium channel gamma-7 su ...	0.06	-	mit	4 *	Membrane; multi-pass membrane protein (By similarity)	voltage-gated calcium channel complex [ISS]			275
Q8NFZ6 UniProt NPD GO	VN1R2_HUMAN	Vomeronasal type-1 receptor 2 (V1r-like receptor 2) (hGPCR25)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				395
Q9JHY4 UniProt NPD GO	WFD15_MOUSE	WAP four-disulfide core domain protein 15 precursor (Single WAP motif protein 1) (Elafin-like protei ...	0.06	-	nuc	0	Secreted protein (Potential)				80
Q9BQY6 UniProt NPD GO	WFDC6_HUMAN	WAP four-disulfide core domain protein 6 precursor (Putative protease inhibitor WAP6)	0.06	-	nuc	0	Secreted protein (Potential)				131
Q5U2Y0 UniProt NPD GO	WIPI4_RAT	WD repeat domain phosphoinositide-interacting protein 4 (WIPI-4) (WD repeat protein 45)	0.06	-	cyt	0					309
Q6P5M2 UniProt NPD GO	WDR61_BRARE	WD repeat protein 61	0.06	-	nuc	0					305
Q9P2S5 UniProt NPD GO	WDR8_HUMAN	WD repeat protein 8	0.06	-	cyt	0	Cytoplasm (Potential)		606040		460
Q9JM98 UniProt NPD GO	WDR8_MOUSE	WD repeat protein 8	0.06	-	cyt	0	Cytoplasm (Potential)				462
P35919 UniProt NPD GO	WWA1_ACHFU	WWamide-1	0.06	-		0					7
Q84TH5 UniProt NPD GO	WBC26_ARATH	White-brown complex homolog protein 26	0.06	-	end	7	Membrane; multi-pass membrane protein (By similarity)				662
Q9H6D3 UniProt NPD GO	XKR8_HUMAN	XK-related protein 8	0.06	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				395
Q49LS7 UniProt NPD GO	XKR8_TETNG	XK-related protein 8	0.06	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				404
Q6YDN9 UniProt NPD GO	XTH_BRAOB	Xyloglucan endotransglucosylase/hydrolase precursor (EC 2.4.1.207) (BobXET16A)	0.06	-	exc	1 *	Secreted protein; extracellular space; apoplast (Probable)				295
Q3MIF4 UniProt NPD GO	XYLB_RAT	Xylulose kinase (EC 2.7.1.17) (Xylulokinase)	0.06	-	cyt	0					536
O23810 UniProt NPD GO	YY1_ORYSA	YY1 protein precursor	0.06	-	mit	0					95
Q29NC4 UniProt NPD GO	CBPA1_DROPS	Zinc carboxypeptidase A 1 precursor (EC 3.4.17.-)	0.06	-	exc	0	Secreted protein (By similarity)	extracellular space [ISS]			425
Q9SZ69 UniProt NPD GO	ZF2N3_ARATH	Zinc finger A20 and AN1 domains-containing protein At4g12040	0.06	-	nuc	0				1WG2	175
P17033 UniProt NPD GO	ZNF27_HUMAN	Zinc finger protein 27 (Zinc finger protein KOX22) (Fragment)	0.06	-	nuc	0	Nucleus (Potential)		194555		56
Q8N8N7 UniProt NPD GO	ZADH1_HUMAN	Zinc-binding alcohol dehydrogenase domain-containing protein 1 (EC 1.-.-.-)	0.06	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [NAS]	608642		351
Q5R806 UniProt NPD GO	ZADH1_PONPY	Zinc-binding alcohol dehydrogenase domain-containing protein 1 (EC 1.-.-.-)	0.06	-	cyt	0	Cytoplasm (By similarity)				351
P48831 UniProt NPD GO	ZP3_CANFA	Zona pellucida sperm-binding protein 3 precursor (Zona pellucida glycoprotein ZP3) (Sperm receptor) ...	0.06	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				426
O35820 UniProt NPD GO	RCL_RAT	c-Myc-responsive protein Rcl	0.06	-	cyt	0	Nucleus				163
P00517 UniProt NPD GO	KAPCA_BOVIN	cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.11.11) (PKA C-alpha)	0.06	-	cyt	0	Inactive holoenzyme, monomeric catalytic subunit: Cytoplasm. Monomeric catalytic subunit: Nucleus. T ...			2GNL	350
Q8MJ44 UniProt NPD GO	KAPCA_CANFA	cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.11.11) (PKA C-alpha)	0.06	-	cyt	0	Inactive holoenzyme, monomeric catalytic subunit: Cytoplasm (By similarity). Monomeric catalytic sub ...				349
P25321 UniProt NPD GO	KAPCA_CRIGR	cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.11.11) (PKA C-alpha)	0.06	-	cyt	0	Inactive holoenzyme, monomeric catalytic subunit: Cytoplasm (By similarity). Monomeric catalytic sub ...				350
P17612 UniProt NPD GO	KAPCA_HUMAN	cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.11.11) (PKA C-alpha)	0.06	-	cyt	0	Inactive holoenzyme, monomeric catalytic subunit: Cytoplasm (By similarity). Monomeric catalytic sub ...	cAMP-dependent protein kinase complex [NAS]	601639		350
P36887 UniProt NPD GO	KAPCA_PIG	cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.11.11) (PKA C-alpha)	0.06	-	cyt	0	Inactive holoenzyme, monomeric catalytic subunit: Cytoplasm (By similarity). Monomeric catalytic sub ...			1CTP	350
P27791 UniProt NPD GO	KAPCA_RAT	cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.11.11) (PKA C-alpha)	0.06	-	cyt	0	Inactive holoenzyme, monomeric catalytic subunit: Cytoplasm (By similarity). Monomeric catalytic sub ...				350
Q9MZD9 UniProt NPD GO	KAPCA_SHEEP	cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.11.11) (PKA C-alpha)	0.06	-	cyt	0	Inactive holoenzyme, monomeric catalytic subunit: Cytoplasm (By similarity). Monomeric catalytic sub ...				350
Q9USZ6 UniProt NPD GO	MRT4_SCHPO	mRNA turnover protein 4 homolog	0.06	-	cyt	0	Nucleus; nucleolus (By similarity)				241
Q8J257 UniProt NPD GO	PACC_PARBR	pH-response transcription factor pacC/RIM101 (Fragment)	0.06	-	mit	0					58
O75648 UniProt NPD GO	TRMU_HUMAN	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (EC 2.1.1.61)	0.06	-	mit	0	Mitochondrion (By similarity)	mitochondrion [ISS]			421
O82784 UniProt NPD GO	MDL4_PRUSE	(R)-mandelonitrile lyase 4 precursor (EC 4.1.2.10) (Hydroxynitrile lyase 4) ((R)-oxynitrilase 4)	0.05	-	cyt	0	Protein body (By similarity). Primarily found within protein bodies of the cotyledonary parenchyma c ...				574
Q96VA4 UniProt NPD GO	GLGB_ASPOR	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Glycogen branching enzyme)	0.05	-	cyt	0					689
Q5KP87 UniProt NPD GO	GLGB_CRYNE	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Glycogen branching enzyme)	0.05	-	cyt	0					682
O17433 UniProt NPD GO	1CPX_DIRIM	1-Cys peroxiredoxin (EC 1.11.1.15) (Thioredoxin peroxidase) (1-CysPxn)	0.05	-	cyt	0	Cytoplasm (By similarity)				235
Q42670 UniProt NPD GO	PLSC_COCNU	1-acyl-sn-glycerol-3-phosphate acyltransferase (EC 2.3.1.51) (1-AGP acyltransferase) (1-AGPAT) (Lyso ...	0.05	-	end	1	Membrane; multi-pass membrane protein (Potential)				308
Q9XFW4 UniProt NPD GO	LPAT2_BRANA	1-acyl-sn-glycerol-3-phosphate acyltransferase 2 (EC 2.3.1.51) (Lysophosphatidyl acyltransferase 2)	0.05	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				390

You are viewing entries 73501 to 73550 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.