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
Q06155 UniProt NPD GO	VAP1_STRPU	Vesicle-associated protein (VAP-1) (Fragment)	0.04	-	cyt	0	Microsome; microsomal membrane; peripheral membrane protein. Initially a peripheral membrane protein ...				433
Q7Z5L0 UniProt NPD GO	VMO1_HUMAN	Vitelline membrane outer layer protein 1 homolog precursor	0.04	-	exc	0	Secreted protein (Probable)				202
O73706 UniProt NPD GO	CAC1B_CHICK	Voltage-dependent N-type calcium channel subunit alpha-1B (Voltage-gated calcium channel subunit alp ...	0.04	-	end	2 *	Membrane; multi-pass membrane protein				159
P68002 UniProt NPD GO	VDAC2_BOVIN	Voltage-dependent anion-selective channel protein 2 (Outer mitochondrial membrane protein porin 2)	0.04	-	cyt	0	Mitochondrion; mitochondrial outer membrane (By similarity)				294
Q80XI7 UniProt NPD GO	VOME_MOUSE	Vomeromodulin precursor	0.04	-	cyt	0					591
Q8N1V2 UniProt NPD GO	WDR16_HUMAN	WD repeat protein 16 (WD40-repeat protein up-regulated in HCC)	0.04	-	cyt	0	Cytoplasm		609804		620
Q6GMD2 UniProt NPD GO	WDR61_XENLA	WD repeat protein 61	0.04	-	nuc	0					305
Q6PBD6 UniProt NPD GO	WDR61_XENTR	WD repeat protein 61	0.04	-	nuc	0					305
P25678 UniProt NPD GO	TXW2A_NAJHA	Weak toxin CM-2a	0.04	-	nuc	0	Secreted protein				61
P05119 UniProt NPD GO	IP21_LYCES	Wound-induced proteinase inhibitor 2 precursor (Wound-induced proteinase inhibitor II)	0.04	-	exc	1 *	Secreted protein			1PJU	148
P27571 UniProt NPD GO	XIST_MOUSE	X inactive-specific transcript protein (Fragment)	0.04	-	end	9 *		chromosome [IDA]			298
Q4VV71 UniProt NPD GO	XKR8_GASAC	XK-related protein 8	0.04	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				404
Q49LS0 UniProt NPD GO	XKR8_PANTR	XK-related protein 8	0.04	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				395
P07198 UniProt NPD GO	XENO_XENLA	Xenopsin precursor [Contains: Xenopsin precursor fragment (XPF); Xenopsin]	0.04	-	exc	0	Secreted protein				81
Q9SV60 UniProt NPD GO	XTH2_ARATH	Xyloglucan endotransglucosylase/hydrolase protein 2 precursor (EC 2.4.1.207) (At-XTH2) (XTH-2)	0.04	-	exc	0	Secreted protein; extracellular space; apoplast (Probable)				292
Q9ZSK5 UniProt NPD GO	ZOG_PHALU	Zeatin O-glucosyltransferase (EC 2.4.1.203) (Trans-zeatin O-beta-D-glucosyltransferase)	0.04	-	cyt	0					459
O81360 UniProt NPD GO	ABA2_PRUAR	Zeaxanthin epoxidase, chloroplast precursor (EC 1.14.13.90) (PA-ZE)	0.04	-	mit	0	Plastid; chloroplast (By similarity)				661
Q29RY4 UniProt NPD GO	RNZ1_BOVIN	Zinc phosphodiesterase ELAC protein 1 (EC 3.1.26.11) (Ribonuclease Z 1) (RNase Z 1) (tRNase Z 1) (tR ...	0.04	-	cyt	0	Nucleus (By similarity)				363
Q9H777 UniProt NPD GO	RNZ1_HUMAN	Zinc phosphodiesterase ELAC protein 1 (EC 3.1.26.11) (Ribonuclease Z 1) (RNase Z 1) (tRNase Z 1) (tR ...	0.04	-	cyt	0	Nucleus (Probable)		608079		363
Q9TTF3 UniProt NPD GO	ZNT4_BOVIN	Zinc transporter 4 (ZnT-4) (Solute carrier family 30 member 4) (Fragment)	0.04	-	nuc	0	Endosome; endosomal membrane; multi-pass membrane protein (Probable)				50
O82643 UniProt NPD GO	ZIP9_ARATH	Zinc transporter 9 (ZRT/IRT-like protein 9)	0.04	-	end	6 *	Cell membrane; multi-pass membrane protein (Potential)				344
P48833 UniProt NPD GO	ZP3_RABIT	Zona pellucida sperm-binding protein 3 precursor (Zona pellucida glycoprotein ZP3) (Sperm receptor) ...	0.04	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				415
Q8GSP8 UniProt NPD GO	ZYS3_CHLRE	Zygote-specific protein 3 precursor	0.04	-	vac	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum lumen [IDA]			371
Q80VJ3 UniProt NPD GO	RCL_MOUSE	c-Myc-responsive protein Rcl	0.04	-	cyt	0	Nucleus (By similarity)				173
O50048 UniProt NPD GO	MDL2_PRUSE	(R)-mandelonitrile lyase 2 precursor (EC 4.1.2.10) (Hydroxynitrile lyase 2) ((R)-oxynitrilase 2)	0.03	-	cyt	0	Protein body (By similarity). Primarily found within protein bodies of the cotyledonary parenchyma c ...				576
O48707 UniProt NPD GO	ARD1_ARATH	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 1 (EC 1.13.-.-) (Aci-reductone dioxygenase 1)	0.03	-	cyt	0					199
Q75AP1 UniProt NPD GO	HIS4_ASHGO	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase ( ...	0.03	-	cyt	0	Cytoplasm (By similarity)				263
Q6CQL7 UniProt NPD GO	HIS4_KLULA	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase ( ...	0.03	-	cyt	0	Cytoplasm (By similarity)				267
Q9NRZ5 UniProt NPD GO	PLCD_HUMAN	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (EC 2.3.1.51) (1-AGP acyltransferase 4) (1-AGPA ...	0.03	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				378
Q7M523 UniProt NPD GO	1A1D_WILSA	1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) (ACC deaminase) (ACCD)	0.03	-	cyt	0				1J0E	341
Q9FR99 UniProt NPD GO	ACCO_MUSAC	1-aminocyclopropane-1-carboxylate oxidase (EC 1.14.17.4) (ACC oxidase) (Ethylene-forming enzyme) (EF ...	0.03	-	nuc	0					306
P23279 UniProt NPD GO	1A11_CUCPE	1-aminocyclopropane-1-carboxylate synthase 1 (EC 4.4.1.14) (ACC synthase) (S-adenosyl-L-methionine m ...	0.03	-	cyt	0					493
Q00379 UniProt NPD GO	1A12_CUCPE	1-aminocyclopropane-1-carboxylate synthase 2 (EC 4.4.1.14) (ACC synthase) (S-adenosyl-L-methionine m ...	0.03	-	cyt	0					494
P29535 UniProt NPD GO	1A14_LYCES	1-aminocyclopropane-1-carboxylate synthase 4 (EC 4.4.1.14) (ACC synthase 4) (S-adenosyl-L-methionine ...	0.03	-	cyt	0					476
P28037 UniProt NPD GO	FTHFD_RAT	10-formyltetrahydrofolate dehydrogenase (EC 1.5.1.6) (10-FTHFDH) (Aldehyde dehydrogenase 1 family me ...	0.03	-	cyt	0	Cytoplasm	cytosol [TAS]		1S3I	902
P82431 UniProt NPD GO	CWP23_TOBAC	100 kDa cell wall protein (Fragment)	0.03	-		0	Cell wall				15
O74703 UniProt NPD GO	TDF1_TUBDR	11.9 kDa wall protein precursor	0.03	-	cyt	0					114
P80708 UniProt NPD GO	TBF1_TUBBO	11.9 kDa wall protein precursor (TB 11.9)	0.03	-	cyt	0					120
Q84Q77 UniProt NPD GO	HSP23_ORYSA	17.4 kDa class I heat shock protein 3	0.03	-	mit	0	Nucleus				161
P04793 UniProt NPD GO	HSP13_SOYBN	17.5 kDa class I heat shock protein (HSP 17.5-M)	0.03	-	cyt	0	Cytoplasm				153
P27396 UniProt NPD GO	HSP11_DAUCA	17.8 kDa class I heat shock protein (Clone DCHSP17.7)	0.03	-	cyt	0	Cytoplasm				157
P27879 UniProt NPD GO	HSP11_MEDSA	18.1 kDa class I heat shock protein (Fragment)	0.03	-	cyt	0	Cytoplasm				143
Q01545 UniProt NPD GO	HSP22_IPONI	18.8 kDa class II heat shock protein	0.03	+	cyt	0	Cytoplasm (By similarity)				167
P30792 UniProt NPD GO	PMGI_MAIZE	2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.1) (Phosphoglyceromutase) (BPG ...	0.03	-	cyt	0	Cytoplasm				559
P83662 UniProt NPD GO	ACMSD_PIG	2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (EC 4.1.1.45) (Fragments)	0.03	-	nuc	0					138
Q9AV97 UniProt NPD GO	KDSA_ARATH	2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) (Phospho-2-dehydro-3-deoxyoctonate aldolase) ...	0.03	-	cyt	0	Cytoplasm (By similarity)				290
P80552 UniProt NPD GO	NCP_PIG	20 kDa neutrophil cationic protein (NCP) (Fragment)	0.03	-	nuc	0					25
P80838 UniProt NPD GO	CWP17_ARATH	23 kDa cell wall protein (Fragment)	0.03	-		0	Cell wall				20
Q94JS4 UniProt NPD GO	SMT3B_ARATH	24-methylenesterol C-methyltransferase 3 (EC 2.1.1.143) (24-sterol C-methyltransferase 3) (Sterol-C- ...	0.03	-	end	1 *	Membrane; single-pass membrane protein (Potential)				359
O75832 UniProt NPD GO	PSD10_HUMAN	26S proteasome non-ATPase regulatory subunit 10 (26S proteasome regulatory subunit p28) (Gankyrin)	0.03	-	cyt	0		proteasome regulatory particle (sensu Eukar... [TAS]	603480	1UOH	226

You are viewing entries 78801 to 78850 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.