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
O43543 UniProt NPD GO	XRCC2_HUMAN	DNA-repair protein XRCC2 (X-ray repair cross-complementing protein 2)	0.36	-	nuc	0	Nucleus		600375		280
P27088 UniProt NPD GO	XPA_XENLA	DNA-repair protein complementing XP-A cells homolog (Xeroderma pigmentosum group A-complementing pro ...	0.36	-	nuc	0	Nucleus				267
Q9D9T0 UniProt NPD GO	DYDC1_MOUSE	DPY30 domain-containing protein 1	0.36	-	nuc	0					175
P92172 UniProt NPD GO	DAF7_CAEEL	Dauer larva development regulatory growth factor daf-7 precursor (Abnormal dauer formation protein 7 ...	0.36	+	exc	0	Secreted protein (By similarity)			1ZJX	350
Q9M0L0 UniProt NPD GO	DRE1A_ARATH	Dehydration-responsive element-binding protein 1A (DREB1A protein) (C-repeat-binding factor 3) (C-re ...	0.36	-	cyt	0	Nucleus (Probable)				216
Q804A9 UniProt NPD GO	DAZL_CHICK	Deleted in azoospermia-like (DAZ-like protein)	0.36	-	nuc	0	Cytoplasm (By similarity)				289
O35459 UniProt NPD GO	ECH1_MOUSE	Delta3,5-delta2,4-dienoyl-CoA isomerase, mitochondrial precursor (EC 5.3.3.-)	0.36	-	pox	0	Mitochondrion (By similarity). Peroxisome (By similarity)	mitochondrion [IDA]			327
Q27003 UniProt NPD GO	GRA6_TOXGO	Dense granule protein 6 (Protein GRA 6) (Antigen p32) (Protein p33)	0.36	-	mit	2 *	Secreted protein. Located in dense granules of tachyzoites. Upon infection, secreted into the parasi ...				230
P47089 UniProt NPD GO	DENR_YEAST	Density-regulated protein homolog	0.36	-	cyt	0		cytoplasm [IDA]			198
P05422 UniProt NPD GO	DEM1_PHYSA	Dermorphin-1 precursor [Contains: Deltorphin (Dermenkephalin); Dermorphin]	0.36	+	exc	0	Secreted protein	extracellular region [IDA]			197
P22239 UniProt NPD GO	DHB_CRAPL	Desiccation-related protein clone PCC6-19 (CDET6-19)	0.36	-	nuc	0					155
Q5XFN2 UniProt NPD GO	DESM_CANFA	Desmin	0.36	-	nuc	0	Cytoplasm				468
Q7YRU7 UniProt NPD GO	DSG3_CANFA	Desmoglein-3 precursor	0.36	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				993
Q8CCG4 UniProt NPD GO	DPPA4_MOUSE	Developmental pluripotency-associated protein 4	0.36	-	nuc	0	Nucleus				296
O35626 UniProt NPD GO	RASD1_MOUSE	Dexamethasone-induced Ras-related protein 1	0.36	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				280
Q9JKF8 UniProt NPD GO	RASD1_RAT	Dexamethasone-induced Ras-related protein 1	0.36	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	cytoplasm [NAS] soluble fraction [IDA]			280
Q9NR28 UniProt NPD GO	DBLOH_HUMAN	Diablo homolog, mitochondrial precursor (Second mitochondria-derived activator of caspase) (Smac pro ...	0.36	-	mit	0	Mitochondrion. But released into the cytosol when cells undergo apoptosis	mitochondrion [TAS]	605219	1TW6	239
Q8SUZ5 UniProt NPD GO	DPH1_ENCCU	Diphthamide biosynthesis protein 1	0.36	-	mit	0	Cytoplasm (By similarity)				414
Q5K7J4 UniProt NPD GO	DPH2_CRYNE	Diphthamide biosynthesis protein 2	0.36	-	cyt	0	Cytoplasm (By similarity)				515
P47138 UniProt NPD GO	DPH4_YEAST	Diphthamide biosynthesis protein 4 (J protein type 3)	0.36	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			172
Q9CQ94 UniProt NPD GO	DNJ5B_MOUSE	DnaJ homolog subfamily C member 5B (Beta cysteine string protein) (Beta-CSP)	0.36	-	nuc	1	Membrane; lipid-anchor (By similarity)				199
O57460 UniProt NPD GO	TLL1_BRARE	Dorsal-ventral patterning tolloid-like protein 1 precursor (EC 3.4.24.-) (Mini fin protein)	0.36	-	cyt	0		extracellular region [NAS]			1022
P81481 UniProt NPD GO	IPSG_MUSLU	Double-headed protease inhibitor, submandibular gland	0.36	-	nuc	0	Secreted protein				122
P56555 UniProt NPD GO	DSCR4_HUMAN	Down syndrome critical region protein 4 (Down syndrome critical region protein B)	0.36	-	nuc	0			604829		118
P84616 UniProt NPD GO	DCAL2_DRONO	Dromaiocalcin-2 (DCA-2)	0.36	-	nuc	0	Eggshell matrix				142
Q05116 UniProt NPD GO	MP2K1_XENLA	Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) (MAP kinase kinase 1) (MAPK ...	0.36	-	nuc	0					394
P45985 UniProt NPD GO	MP2K4_HUMAN	Dual specificity mitogen-activated protein kinase kinase 4 (EC 2.7.12.2) (MAP kinase kinase 4) (JNK- ...	0.36	-	nuc	0			601335		399
Q13561 UniProt NPD GO	DCTN2_HUMAN	Dynactin subunit 2 (Dynactin complex 50 kDa subunit) (50 kDa dynein-associated polypeptide) (p50 dyn ...	0.36	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	centrosome [TAS] dynactin complex [TAS] kinetochore [TAS]	607376		400
Q9NZN3 UniProt NPD GO	EHD3_HUMAN	EH-domain-containing protein 3	0.36	-	nuc	0		nucleus [TAS]	605891		546
Q96HE7 UniProt NPD GO	ERO1A_HUMAN	ERO1-like protein alpha precursor (EC 1.8.4.-) (ERO1-Lalpha) (Oxidoreductin-1-Lalpha) (Endoplasmic o ...	0.36	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side. Th ...	endoplasmic reticulum [IDA]			468
P39677 UniProt NPD GO	EFG2_YEAST	Elongation factor G 2, mitochondrial precursor (mEF-G-2)	0.36	-	nuc	0	Mitochondrion	mitochondrion [IDA]			819
Q08000 UniProt NPD GO	EM3_WHEAT	Em protein H2	0.36	-	nuc	0					93
P06215 UniProt NPD GO	CHIT_PHAVU	Endochitinase precursor (EC 3.2.1.14)	0.36	-	exc	1 *	Vacuole (By similarity). Vacuolar and protoplast (By similarity)				328
P05315 UniProt NPD GO	CHIT_SOLTU	Endochitinase precursor (EC 3.2.1.14)	0.36	-	exc	1 *	Vacuole (By similarity). Vacuolar and protoplast (By similarity)			1P3Z	328
P54424 UniProt NPD GO	GUN1_USTMA	Endoglucanase 1 precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase 1) (Cellulase 1) (EG 1)	0.36	-	exc	0	Secreted protein				393
Q765Z4 UniProt NPD GO	EDN3_CANFA	Endothelin-3 precursor (ET-3) (Preproendothelin-3) (PPET3)	0.36	-	nuc	0	Secreted protein				198
P97739 UniProt NPD GO	ECE1_CAVPO	Endothelin-converting enzyme 1 (EC 3.4.24.71) (ECE-1)	0.36	-	mit	1	Membrane; single-pass type II membrane protein				754
Q9UVY5 UniProt NPD GO	CPSKS_GIBFU	Ent-kaurene synthase (EC 4.2.3.19) (EC 5.5.1.13) (Ent-copalyl diphosphate synthase) (CPS/KS) (GfCPS/ ...	0.36	-	nuc	0					952
O09127 UniProt NPD GO	EPHA8_MOUSE	Ephrin type-A receptor 8 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EEK) (EPH- and EL ...	0.36	-	end	1	Membrane; single-pass type I membrane protein				1004
P52800 UniProt NPD GO	EFNB2_MOUSE	Ephrin-B2 precursor (EPH-related receptor tyrosine kinase ligand 5) (LERK-5) (HTK ligand) (HTK-L) (E ...	0.36	-	nuc	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA]		1KGY	336
Q6JVL5 UniProt NPD GO	LCN12_MOUSE	Epididymal-specific lipocalin-12 precursor	0.36	-	end	0	Secreted protein (By similarity)				193
Q3ZC12 UniProt NPD GO	IF34_BOVIN	Eukaryotic translation initiation factor 3 subunit 4 (eIF-3 delta)	0.36	-	nuc	0					320
P34167 UniProt NPD GO	IF4B_YEAST	Eukaryotic translation initiation factor 4B (eIF-4B)	0.36	-	nuc	0		ribosome [TAS]			436
P55010 UniProt NPD GO	IF5_HUMAN	Eukaryotic translation initiation factor 5 (eIF-5)	0.36	-	nuc	0		cytoplasm [TAS] cytosol [NAS]	601710	2IU1	431
Q5SPJ8 UniProt NPD GO	XPOT_BRARE	Exportin-T (tRNA exportin) (Exportin(tRNA))	0.36	-	pox	0	Cytoplasm (By similarity). Nucleus (By similarity)				961
P08294 UniProt NPD GO	SODE_HUMAN	Extracellular superoxide dismutase [Cu-Zn] precursor (EC 1.15.1.1) (EC-SOD)	0.36	-	exc	0	Secreted protein; extracellular space. 99% of EC-SOD is anchored to heparan sulfate proteoglycans in ...	soluble fraction [TAS]	185490		240
Q08420 UniProt NPD GO	SODE_RAT	Extracellular superoxide dismutase [Cu-Zn] precursor (EC 1.15.1.1) (EC-SOD) (Superoxide dismutase B) ...	0.36	-	exc	0	Secreted protein; extracellular space	extracellular space [TAS]			244
O74511 UniProt NPD GO	EKC1_SCHPO	Extragenic suppressor of kinetochore protein 1	0.36	-	nuc	0	Nucleus. Associated with chromatin	centric heterochromatin [IDA]			838
O60053 UniProt NPD GO	POF12_SCHPO	F-box protein pof12	0.36	-	cyt	0					440
Q9EPX5 UniProt NPD GO	FXL12_MOUSE	F-box/LRR-repeat protein 12 (F-box and leucine-rich repeat protein 12) (F-box protein FBL12)	0.36	-	cyt	0		cytoplasm [IDA] ubiquitin ligase complex [IPI]			326

You are viewing entries 34901 to 34950 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.