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
P39702 UniProt NPD GO	VPS8_YEAST	Vacuolar protein sorting-associated protein VPS8	0.49	-	cyt	0	Golgi apparatus; Golgi stack. Associated with the late-Golgi membranes	membrane fraction [IDA]			1274
O49048 UniProt NPD GO	VPS45_ARATH	Vacuolar protein-sorting protein 45 homolog (AtVPS45)	0.49	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein. Bin ...				569
Q6CBS3 UniProt NPD GO	SNF7_YARLI	Vacuolar sorting protein SNF7 (Vacuolar protein sorting-associated protein VPS32)	0.49	-	nuc	0	Cytoplasm (By similarity). Endosome; endosomal membrane; peripheral membrane protein (By similarity) ...				215
P26328 UniProt NPD GO	VSI3_TRYBB	Variant surface glycoprotein ILTAT 1.23 precursor (VSG)	0.49	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				532
Q94392 UniProt NPD GO	NSF_CAEEL	Vesicle-fusing ATPase (EC 3.6.4.6) (Vesicular-fusion protein NSF) (N-ethylmaleimide sensitive fusion ...	0.49	-	cyt	0	Cytoplasm				824
O57483 UniProt NPD GO	CAC1S_RANCA	Voltage-dependent L-type calcium channel subunit alpha-1S (Voltage-gated calcium channel subunit alp ...	0.49	+	end	18	Membrane; multi-pass membrane protein				1688
O60359 UniProt NPD GO	CCG3_HUMAN	Voltage-dependent calcium channel gamma-3 subunit (Neuronal voltage-gated calcium channel gamma-3 su ...	0.49	-	end	4 *	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [NAS]	606403		315
Q4R589 UniProt NPD GO	CCG3_MACFA	Voltage-dependent calcium channel gamma-3 subunit (Neuronal voltage-gated calcium channel gamma-3 su ...	0.49	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				315
Q9JJV5 UniProt NPD GO	CCG3_MOUSE	Voltage-dependent calcium channel gamma-3 subunit (Neuronal voltage-gated calcium channel gamma-3 su ...	0.49	-	end	4 *	Membrane; multi-pass membrane protein				315
Q9EPB8 UniProt NPD GO	VN1A9_MOUSE	Vomeronasal type-1 receptor A9 (Vomeronasal receptor 7) (Pheromone receptor VN7)	0.49	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				315
Q8W0F1 UniProt NPD GO	WOX5_ORYSA	WUSCHEL-related homeobox 5 (Quiescent-specific homeobox)	0.49	-	cyt	0	Nucleus (By similarity)				200
Q9VLU5 UniProt NPD GO	WWOX_DROME	WW domain-containing oxidoreductase (EC 1.1.1.-)	0.49	-	cyt	0	Cytoplasm	cytoplasm [IDA]			409
Q5GH59 UniProt NPD GO	XKR4_RAT	XK-related protein 4	0.49	-	end	7	Membrane; multi-pass membrane protein (Potential)				647
P59326 UniProt NPD GO	YTHD1_MOUSE	YTH domain protein 1 (Dermatomyositis associated with cancer putative autoantigen 1 homolog) (DACA-1 ...	0.49	-	nuc	0					559
Q8K2D3 UniProt NPD GO	YJDC_MOUSE	YjeF domain-containing protein 1	0.49	-	nuc	0	Cytoplasm (By similarity). Processing bodies (PB) (By similarity)				508
Q9BR11 UniProt NPD GO	ZSWM1_HUMAN	Zinc finger SWIM domain-containing protein 1	0.49	-	cyt	0					485
P17014 UniProt NPD GO	ZNF12_HUMAN	Zinc finger protein 12 (Zinc finger protein KOX3) (Zinc finger protein 325) (Gonadotropin-inducible ...	0.49	-	nuc	0	Nucleus (Probable)		194536		501
Q39261 UniProt NPD GO	ZFP2_ARATH	Zinc finger protein 2	0.49	-	nuc	0					150
Q96SE7 UniProt NPD GO	ZN347_HUMAN	Zinc finger protein 347 (Zinc finger protein 1111)	0.49	-	nuc	0	Nucleus (Probable)				839
Q96MX3 UniProt NPD GO	ZN553_HUMAN	Zinc finger protein 553	0.49	-	nuc	0	Nucleus (Probable)				618
Q5MCW4 UniProt NPD GO	ZN569_HUMAN	Zinc finger protein 569	0.49	-	nuc	0	Nucleus (By similarity)				686
Q9BSK1 UniProt NPD GO	ZN577_HUMAN	Zinc finger protein 577	0.49	-	nuc	0	Nucleus (Probable)				478
Q6P3V2 UniProt NPD GO	Z585A_HUMAN	Zinc finger protein 585A	0.49	-	nuc	0	Nucleus (Potential)				769
Q96T25 UniProt NPD GO	ZIC5_HUMAN	Zinc finger protein ZIC 5 (Zinc finger protein of the cerebellum 5)	0.49	-	nuc	0	Nucleus (By similarity)				639
Q20459 UniProt NPD GO	NAS25_CAEEL	Zinc metalloproteinase nas-25 precursor (EC 3.4.24.21) (Nematode astacin 25)	0.49	-	exc	1 *	Secreted protein (Potential)				399
Q8CGS5 UniProt NPD GO	RNZ2_RAT	Zinc phosphodiesterase ELAC protein 2 (EC 3.1.26.11) (Ribonuclease Z 2) (RNase Z 2) (tRNase Z 2) (tR ...	0.49	-	mit	0	Nucleus (Probable)				827
P47979 UniProt NPD GO	ZFS1_SCHPO	Zinc-finger protein zfs1	0.49	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			404
Q7Z7L7 UniProt NPD GO	ZYGBL_HUMAN	Zyg-11 protein homolog (Zyg-11 homolog B-like)	0.49	-	cyt	0					766
Q90352 UniProt NPD GO	AVT_CATCO	[Arg8]-vasotocin receptor (AVT)	0.49	-	end	7 *	Membrane; multi-pass membrane protein				434
P31321 UniProt NPD GO	KAP1_HUMAN	cAMP-dependent protein kinase type I-beta regulatory subunit	0.49	-	cyt	0		cAMP-dependent protein kinase complex [NAS]	176911		380
P12849 UniProt NPD GO	KAP1_MOUSE	cAMP-dependent protein kinase type I-beta regulatory subunit	0.49	-	cyt	0		cytoplasm [TAS]			380
P12368 UniProt NPD GO	KAP2_RAT	cAMP-dependent protein kinase type II-alpha regulatory subunit	0.49	-	cyt	0					400
P14099 UniProt NPD GO	PDE2A_BOVIN	cGMP-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) (Cyclic GMP-stimulated phosphodiesterase ...	0.49	-	mit	0	Membrane; peripheral membrane protein (Potential)				921
Q06102 UniProt NPD GO	YTH1_YEAST	mRNA 3'-end-processing protein YTH1 (Yeast 30 kDa homolog 1)	0.49	-	nuc	0	Nucleus	mRNA cleavage and polyadenylation specifici... [IPI]			208
Q7SGR2 UniProt NPD GO	YTH1_NEUCR	mRNA 3'-end-processing protein yth-1	0.49	-	mit	0	Nucleus (By similarity)				317
Q2URI6 UniProt NPD GO	YTH1_ASPOR	mRNA 3'-end-processing protein yth1	0.49	-	nuc	0	Nucleus (By similarity)				255
Q5V9L7 UniProt NPD GO	PALH_BOTCI	pH-response regulator protein palH/RIM21	0.49	-	end	4	Cell membrane; multi-pass membrane protein (By similarity)				742
Q9BZE2 UniProt NPD GO	PUS3_HUMAN	tRNA pseudouridine synthase 3 (EC 5.4.99.-) (tRNA-uridine isomerase 3) (tRNA pseudouridylate synthas ...	0.49	-	cyt	0	Nucleus (Potential)				481
Q96G46 UniProt NPD GO	DUS3L_HUMAN	tRNA-dihydrouridine synthase 3-like (EC 1.-.-.-)	0.49	-	cyt	0					650
Q8R3B1 UniProt NPD GO	PLCD1_MOUSE	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta 1 (EC 3.1.4.11) (Phosphoinositide ph ...	0.48	-	cyt	0		cytosol [IDA]			756
P10895 UniProt NPD GO	PLCD1_BOVIN	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta 1 (EC 3.1.4.11) (Phosphoinositide ph ...	0.48	-	cyt	0					695
P00973 UniProt NPD GO	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1 (EC 2.7.7.-) ((2-5')oligo(A) synthetase 1) (2-5A synthetase 1) (p4 ...	0.48	-	cyt	0	Mitochondrion. Nucleus. Microsome. Associated with different subcellular fractions such as mitochond ...	cytoplasm [TAS]	164350		400
Q05823 UniProt NPD GO	RN5A_HUMAN	2-5A-dependent ribonuclease (EC 3.1.26.-) (2-5A-dependent RNase) (Ribonuclease L) (RNase L) (Ribonuc ...	0.48	-	mit	0	Cytoplasm. Mitochondrion		176807	1WDY	741
Q99N91 UniProt NPD GO	RM34_MOUSE	39S ribosomal protein L34, mitochondrial precursor (L34mt) (MRP-L34)	0.48	-	mit	0	Mitochondrion (Potential)	mitochondrial large ribosomal subunit [IDA] mitochondrion [IDA]			92
P52812 UniProt NPD GO	RS11_ANOGA	40S ribosomal protein S11	0.48	-	nuc	0					153
Q01607 UniProt NPD GO	RT12_OENHO	40S ribosomal protein S12, mitochondrial precursor	0.48	-	mit	0	Mitochondrion				188
Q56JV1 UniProt NPD GO	RS26_BOVIN	40S ribosomal protein S26	0.48	-	nuc	0					114
P62854 UniProt NPD GO	RS26_HUMAN	40S ribosomal protein S26	0.48	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	603701		114
P61251 UniProt NPD GO	RS26_MACFA	40S ribosomal protein S26	0.48	-	nuc	0					114
P62855 UniProt NPD GO	RS26_MOUSE	40S ribosomal protein S26	0.48	-	nuc	0					114

You are viewing entries 26001 to 26050 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.