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
P16164 UniProt NPD GO	URIC_PIG	Uricase (EC 1.7.3.3) (Urate oxidase)	0.08	-	cyt	0	Peroxisome				303
P09556 UniProt NPD GO	PYR5_DICDI	Uridine 5'-monophosphate synthase (UMP synthase) [Includes: Orotate phosphoribosyltransferase (EC 2. ...	0.08	-	pox	0					478
O04905 UniProt NPD GO	UMPK_ARATH	Uridylate kinase (EC 2.7.4.-) (UK) (Uridine monophosphate kinase) (UMP kinase) (UMP/CMP kinase)	0.08	-	cyt	0					202
Q9PTS2 UniProt NPD GO	DCUP_BRARE	Uroporphyrinogen decarboxylase (EC 4.1.1.37) (URO-D) (UPD)	0.08	-	nuc	0	Cytoplasm				369
Q29100 UniProt NPD GO	UPTI_PIG	Uterine plasmin/trypsin inhibitor precursor (UPTI)	0.08	-	exc	0					122
Q8VD96 UniProt NPD GO	UTER_MESAU	Uteroglobin precursor (Secretoglobin family 1A member 1) (Clara cell 10 kDa protein) (CC10)	0.08	-	exc	0	Secreted protein				96
P13548 UniProt NPD GO	VATA_PHAAU	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.08	-	cyt	0					622
P31410 UniProt NPD GO	VATB_HELVI	Vacuolar ATP synthase subunit B (EC 3.6.3.14) (V-ATPase B subunit) (Vacuolar proton pump B subunit)	0.08	-	cyt	0					494
P31401 UniProt NPD GO	VATB_MANSE	Vacuolar ATP synthase subunit B (EC 3.6.3.14) (V-ATPase B subunit) (Vacuolar proton pump B subunit)	0.08	-	cyt	0					494
Q15904 UniProt NPD GO	VAS1_HUMAN	Vacuolar ATP synthase subunit S1 precursor (EC 3.6.3.14) (V-ATPase S1 subunit) (V-ATPase S1 accessor ...	0.08	-	mit	2 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)	proton-transporting two-sector ATPase complex [TAS]	300197		470
Q5U3V9 UniProt NPD GO	SNF8_BRARE	Vacuolar sorting protein SNF8	0.08	-	cyt	0	Cytoplasm (By similarity)				258
P49045 UniProt NPD GO	VPE_SOYBN	Vacuolar-processing enzyme precursor (EC 3.4.22.-) (VPE)	0.08	-	vac	1 *					495
P35781 UniProt NPD GO	VA51_VESCR	Venom allergen 5.01 (Antigen 5-1) (Ag5-1) (Allergen Vesp c 5.01) (Vesp c V.01)	0.08	-	nuc	0	Secreted protein. Venom reservoirs				202
P84001 UniProt NPD GO	29C0_ANCSP	Venom protein ANC29C0 (Fragment)	0.08	-	nuc	0	Secreted protein				50
Q9DF66 UniProt NPD GO	VSP3_TRIJE	Venom serine proteinase 3 precursor (EC 3.4.21.-) (SP3)	0.08	-	exc	0	Secreted protein				258
Q9PTU8 UniProt NPD GO	VSP3_BOTJA	Venom serine proteinase A precursor (EC 3.4.21.-)	0.08	-	exc	0	Secreted protein				258
Q9Y816 UniProt NPD GO	YOND_SCHPO	Very hypothetical protein C1105.13c in chromosome II precursor	0.08	-	mit	1 *					142
P38350 UniProt NPD GO	YB9U_YEAST	Very hypothetical protein YBR277C	0.08	-	exc	0					133
P53310 UniProt NPD GO	YG55_YEAST	Very hypothetical protein YGR242W	0.08	-	nuc	1 *					102
P53928 UniProt NPD GO	YNK9_YEAST	Very hypothetical protein YNL109W	0.08	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				181
Q8HXY7 UniProt NPD GO	ACADV_MACFA	Very-long-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.-) (VLCAD)	0.08	-	mit	0	Mitochondrion; mitochondrial inner membrane				655
P40075 UniProt NPD GO	SCS2_YEAST	Vesicle-associated membrane protein-associated protein SCS2 (VAMP-associated protein SCS2) (VAP homo ...	0.08	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein. Nucleus ...	endoplasmic reticulum [IDA] integral to membrane [IDA]			243
P62763 UniProt NPD GO	VISL1_BOVIN	Visinin-like protein 1 (Neurocalcin alpha)	0.08	-	cyt	0					190
P62760 UniProt NPD GO	VISL1_HUMAN	Visinin-like protein 1 (VILIP) (Hippocalcin-like protein 3) (HLP3)	0.08	-	cyt	0			600817		190
P62761 UniProt NPD GO	VISL1_MOUSE	Visinin-like protein 1 (VILIP) (Neural visinin-like protein 1) (NVL-1) (NVP-1)	0.08	-	cyt	0					190
P62762 UniProt NPD GO	VISL1_RAT	Visinin-like protein 1 (VILIP) (Neural visinin-like protein 1) (NVL-1) (NVP-1) (21 kDa CABP)	0.08	-	cyt	0					190
P62764 UniProt NPD GO	VISL1_CHICK	Visinin-like protein 1 (VILIP) (OZ1)	0.08	-	cyt	0					190
P33532 UniProt NPD GO	BSU1_SCHPO	Vitamin B6 transporter bsu1 (Vitamin B6 uptake protein 1) (Changed amiloride resistance protein 1) ( ...	0.08	-	end	11	Membrane; multi-pass membrane protein. During mitosis, localizes also to the septum	integral to plasma membrane [NAS] plasma membrane [TAS]			526
Q9Y4P8 UniProt NPD GO	WIPI2_HUMAN	WD repeat domain phosphoinositide-interacting protein 2 (WIPI-2) (WIPI49-like protein 2)	0.08	-	cyt	0			609225		454
Q5F201 UniProt NPD GO	WDR16_MOUSE	WD repeat protein 16	0.08	-	cyt	0	Cytoplasm (By similarity)				620
P09762 UniProt NPD GO	WIN2_SOLTU	Wound-induced protein WIN2 precursor	0.08	-	exc	0					211
Q49LS6 UniProt NPD GO	XKR9_TETNG	XK-related protein 9	0.08	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				380
P38952 UniProt NPD GO	XEN3_XENLA	Xenoxin-3	0.08	-	nuc	0	Secreted protein				66
O75191 UniProt NPD GO	XYLB_HUMAN	Xylulose kinase (EC 2.7.1.17) (Xylulokinase)	0.08	-	cyt	0			604049		527
P93236 UniProt NPD GO	ABA2_LYCES	Zeaxanthin epoxidase, chloroplast precursor (EC 1.14.13.90)	0.08	-	mit	0	Plastid; chloroplast (By similarity)				669
O43598 UniProt NPD GO	RCL_HUMAN	c-Myc-responsive protein Rcl	0.08	-	cyt	0	Nucleus (By similarity)	nucleus [TAS]			174
P12370 UniProt NPD GO	KAPC_DROME	cAMP-dependent protein kinase catalytic subunit (EC 2.7.11.11) (PKA C)	0.08	-	cyt	0		plasma membrane [IDA]			352
Q7YQJ3 UniProt NPD GO	IPKG_BOVIN	cAMP-dependent protein kinase inhibitor gamma (PKI-gamma)	0.08	-	nuc	0					76
Q9DAT5 UniProt NPD GO	TRMU_MOUSE	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (EC 2.1.1.61)	0.08	-	mit	0	Mitochondrion	mitochondrion [IDA]			417
O95620 UniProt NPD GO	DUS4L_HUMAN	tRNA-dihydrouridine synthase 4-like (EC 1.-.-.-) (PP35)	0.08	-	cyt	0					317
Q338A9 UniProt NPD GO	ARD1_ORYSA	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 1 (EC 1.13.-.-) (Aci-reductone dioxygenase 1) ( ...	0.07	-	nuc	0					199
P40545 UniProt NPD GO	HIS4_YEAST	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase ( ...	0.07	-	cyt	0	Cytoplasm (By similarity)	intracellular [TAS]		2AGK	261
Q8NCC3 UniProt NPD GO	LYPA3_HUMAN	1-O-acylceramide synthase precursor (EC 2.3.1.-) (ACS) (Lysosomal phospholipase A2) (Lysophospholipa ...	0.07	-	mit	0	Lysosome (By similarity). Secreted protein	lysosome [NAS]	609362		412
Q8LG50 UniProt NPD GO	LPAT2_ARATH	1-acyl-sn-glycerol-3-phosphate acyltransferase 2 (EC 2.3.1.51) (Lysophosphatidyl acyltransferase 2)	0.07	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				389
Q9D1E8 UniProt NPD GO	PLCE_MOUSE	1-acyl-sn-glycerol-3-phosphate acyltransferase epsilon (EC 2.3.1.51) (1-AGP acyltransferase 5) (1-AG ...	0.07	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				365
Q9XFS9 UniProt NPD GO	DXR_ARATH	1-deoxy-D-xylulose 5-phosphate reductoisomerase, chloroplast precursor (EC 1.1.1.267) (DXP reductois ...	0.07	-	cyt	0	Plastid; chloroplast				477
Q9XES0 UniProt NPD GO	DXR_MENPI	1-deoxy-D-xylulose 5-phosphate reductoisomerase, chloroplast precursor (EC 1.1.1.267) (DXP reductois ...	0.07	-	cyt	0	Plastid; chloroplast				470
P84745 UniProt NPD GO	VVP2_BOTJR	1095.6 Da venom vasodilator peptide	0.07	-		0	Secreted protein				11
Q92781 UniProt NPD GO	RDH1_HUMAN	11-cis retinol dehydrogenase (EC 1.1.1.105) (11-cis RDH)	0.07	-	mit	0	Membrane; peripheral membrane protein		601617		318
Q9FUP0 UniProt NPD GO	OPR3_ARATH	12-oxophytodienoate reductase 3 (EC 1.3.1.42) (12-oxophytodienoate-10,11-reductase 3) (OPDA-reductas ...	0.07	-	cyt	0	Peroxisome			2G5W	391

You are viewing entries 69251 to 69300 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.