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
P14187 UniProt NPD GO	CCHL_NEUCR	Cytochrome c heme lyase (EC 4.4.1.17) (CCHL) (Holocytochrome-c synthase)	0.18	-	nuc	0	Mitochondrion; mitochondrial inner membrane				346
Q6P8I6 UniProt NPD GO	COX11_MOUSE	Cytochrome c oxidase assembly protein COX11, mitochondrial precursor	0.18	-	cyt	1	Mitochondrion (By similarity)				275
Q9QXU8 UniProt NPD GO	DC1L1_RAT	Cytoplasmic dynein 1 light intermediate chain 1 (Dynein light intermediate chain 1, cytosolic) (Dyne ...	0.18	-	cyt	0					523
P83049 UniProt NPD GO	XYL2_PIG	D-xylulose reductase (EC 1.1.1.9) (Xylitol dehydrogenase) (XDH) (Fragments)	0.18	-	cyt	0					134
P18153 UniProt NPD GO	D7_AEDAE	D7 protein precursor (Allergen Aed a 2)	0.18	-	exc	0	Secreted protein				321
Q12248 UniProt NPD GO	DAD1_YEAST	DASH complex subunit DAD1 (Outer kinetochore protein DAD1) (DUO1 and DAM1-interacting protein 1)	0.18	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore	DASH complex [IDA] spindle [IPI]			94
P69852 UniProt NPD GO	HSK3_YEAST	DASH complex subunit HSK3 (Outer kinetochore protein HSK3) (Helper of ASK1 protein 3)	0.18	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore	DASH complex [IDA] kinetochore [IPI] spindle [IDA]			69
Q50HP4 UniProt NPD GO	DAD4_SCHPO	DASH complex subunit dad4 (Outer kinetochore protein dad4)	0.18	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore. Kinetochore associ ...	DASH complex [IDA]			72
Q758W7 UniProt NPD GO	RAD17_ASHGO	DNA damage checkpoint control protein RAD17 (EC 3.1.11.2) (DNA repair exonuclease RAD17)	0.18	-	cyt	0	Nucleus (Potential)				389
P27695 UniProt NPD GO	APEX1_HUMAN	DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) (AP endonuclease 1) (APEX nuclease) (APEN) ...	0.18	-	nuc	0	Nucleus	endoplasmic reticulum [TAS] nucleus [IDA] perinuclear region [IDA] ribosome [TAS]	107748	1HD7	317
P41139 UniProt NPD GO	ID4_MOUSE	DNA-binding protein inhibitor ID-4 (Inhibitor of DNA binding 4)	0.18	-	nuc	0	Nucleus				161
Q9H9Y6 UniProt NPD GO	RPA2_HUMAN	DNA-directed RNA polymerase I 135 kDa polypeptide (EC 2.7.7.6) (RNA polymerase I subunit 2) (RPA135) ...	0.18	-	cyt	0	Nucleus		602000		1135
O54888 UniProt NPD GO	RPA2_RAT	DNA-directed RNA polymerase I 135 kDa polypeptide (EC 2.7.7.6) (RNA polymerase I subunit 2) (RPA135) ...	0.18	-	cyt	0	Nucleus				1135
P51293 UniProt NPD GO	RPOA_PORPU	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.18	-	cyt	0	Plastid; chloroplast				311
Q8IYX4 UniProt NPD GO	DND1_HUMAN	Dead end protein homolog 1 (RNA-binding motif, single-stranded-interacting protein 4)	0.18	-	cyt	0			609385		353
Q9QX67 UniProt NPD GO	DAP1_RAT	Death-associated protein 1 (DAP-1) (Rap7a)	0.18	-	nuc	0					101
Q5ADL9 UniProt NPD GO	DCN1_CANAL	Defective in cullin neddylation protein 1	0.18	-	mit	0					304
Q9XFY6 UniProt NPD GO	DEE76_CHLPR	Degreening-related gene dee76 protein	0.18	-	mit	0					321
Q6AYS8 UniProt NPD GO	DHRS8_RAT	Dehydrogenase/reductase SDR family member 8 precursor (EC 1.1.1.-) (17-beta-hydroxysteroid dehydroge ...	0.18	-	mit	1 *	Secreted protein (Potential)				298
P01478 UniProt NPD GO	TXDT1_ATRRO	Delta-atracotoxin-Ar1a (Delta-AcTx-Ar1a) (Delta-AcTx-Ar1) (Robustoxin) (RBX)	0.18	-	nuc	0	Secreted protein			1QDP	42
Q09163 UniProt NPD GO	DLK_MOUSE	Delta-like protein precursor (DLK) (Preadipocyte factor 1) (Pref-1) (Adipocyte differentiation inhib ...	0.18	-	end	1	Membrane; single-pass type I membrane protein				385
Q6C141 UniProt NPD GO	DUT_YARLI	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) (dUTPase) (dUTP pyrophosphatase)	0.18	-	cyt	0					157
O43323 UniProt NPD GO	DHH_HUMAN	Desert hedgehog protein precursor (DHH) (HHG-3) [Contains: Desert hedgehog protein N-product; Desert ...	0.18	-	mit	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...		607080		396
Q61488 UniProt NPD GO	DHH_MOUSE	Desert hedgehog protein precursor (DHH) (HHG-3) [Contains: Desert hedgehog protein N-product; Desert ...	0.18	-	mit	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				396
Q42948 UniProt NPD GO	DAPA_TOBAC	Dihydrodipicolinate synthase, chloroplast precursor (EC 4.2.1.52) (DHDPS)	0.18	-	cyt	0	Plastid; chloroplast				359
Q9DBT9 UniProt NPD GO	M2GD_MOUSE	Dimethylglycine dehydrogenase, mitochondrial precursor (EC 1.5.99.2) (ME2GLYDH)	0.18	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]			869
Q63342 UniProt NPD GO	M2GD_RAT	Dimethylglycine dehydrogenase, mitochondrial precursor (EC 1.5.99.2) (ME2GLYDH)	0.18	-	mit	0	Mitochondrion	mitochondrion [TAS]			857
Q9N2I7 UniProt NPD GO	DPP4_FELCA	Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen C ...	0.18	-	exc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				765
Q5AD49 UniProt NPD GO	DPH4_CANAL	Diphthamide biosynthesis protein 4 (J protein type 3)	0.18	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				149
P56619 UniProt NPD GO	DIUH2_TENMO	Diuretic hormone 2 (Diuretic hormone II) (DH II) (Diuretic peptide II) (DP II) (DH(47)) (DH47)	0.18	-	nuc	0	Secreted protein				47
O35824 UniProt NPD GO	DNJA2_RAT	DnaJ homolog subfamily A member 2 (RDJ2)	0.18	-	cyt	0	Membrane; lipid-anchor (Potential)				412
Q80Y75 UniProt NPD GO	DNJBD_MOUSE	DnaJ homolog subfamily B member 13 (Testis spermatocyte apoptosis-related gene 6 protein) (Testis an ...	0.18	-	cyt	0					316
Q9H3Z4 UniProt NPD GO	DNJC5_HUMAN	DnaJ homolog subfamily C member 5 (Cysteine string protein) (CSP)	0.18	-	nuc	1	Membrane; lipid-anchor (By similarity)				198
P70236 UniProt NPD GO	MP2K6_MOUSE	Dual specificity mitogen-activated protein kinase kinase 6 (EC 2.7.12.2) (MAP kinase kinase 6) (MAPK ...	0.18	-	cyt	0					334
Q6GQJ8 UniProt NPD GO	DUS22_XENLA	Dual specificity protein phosphatase 22 (EC 3.1.3.48) (EC 3.1.3.16)	0.18	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				209
Q5RD73 UniProt NPD GO	DUS3_PONPY	Dual specificity protein phosphatase 3 (EC 3.1.3.48) (EC 3.1.3.16)	0.18	-	nuc	0					185
P51452 UniProt NPD GO	DUS3_HUMAN	Dual specificity protein phosphatase 3 (EC 3.1.3.48) (EC 3.1.3.16) (Dual specificity protein phospha ...	0.18	-	nuc	0			600183	1VHR	185
P93746 UniProt NPD GO	EC1_ARATH	EC protein homolog 1	0.18	-	nuc	0					84
P20799 UniProt NPD GO	NO12A_PEA	Early nodulin 12A precursor (N-12A)	0.18	-	exc	1 *	Cell wall (Potential)				110
Q13508 UniProt NPD GO	NAR3_HUMAN	Ecto-ADP-ribosyltransferase 3 precursor (EC 2.4.2.31) (NAD(P)(+)--arginine ADP-ribosyltransferase 3) ...	0.18	-	end	1	Cell membrane; lipid-anchor; GPI-anchor	integral to plasma membrane [TAS]	603086		389
Q91YE3 UniProt NPD GO	EGLN1_MOUSE	Egl nine homolog 1 (EC 1.14.11.-) (Hypoxia-inducible factor prolyl hydroxylase 2) (HIF-prolyl hydrox ...	0.18	-	nuc	0					400
Q875S0 UniProt NPD GO	EF2_SACKL	Elongation factor 2 (EF-2)	0.18	-	cyt	0	Cytoplasm (By similarity)				842
Q96X45 UniProt NPD GO	EF2_NEUCR	Elongation factor 2 (EF-2) (Colonial temperature-sensitive 3)	0.18	-	cyt	0	Cytoplasm (By similarity)				844
Q9CZR8 UniProt NPD GO	EFTS_MOUSE	Elongation factor Ts, mitochondrial precursor (EF-Ts) (EF-TsMt)	0.18	-	mit	0	Mitochondrion (By similarity)				324
P84172 UniProt NPD GO	EFTU_CHICK	Elongation factor Tu, mitochondrial precursor (EF-Tu) (Fragment)	0.18	-	mit	0	Mitochondrion (By similarity)				352
P25358 UniProt NPD GO	ELO2_YEAST	Elongation of fatty acids protein 2 (GNS1 protein) (v-SNARE bypass mutant gene 2 protein)	0.18	-	end	7	Membrane; multi-pass membrane protein	endoplasmic reticulum [IDA] endoplasmic reticulum membrane [TAS]			347
P42664 UniProt NPD GO	UVS2_XENLA	Embryonic protein UVS.2 precursor (EC 3.4.24.-)	0.18	-	cyt	0					514
P36907 UniProt NPD GO	CHIX_PEA	Endochitinase precursor (EC 3.2.1.14)	0.18	-	exc	0					320
O23051 UniProt NPD GO	KAO1_ARATH	Ent-kaurenoic acid oxidase 1 (EC 1.14.13.79) (AtKAO1) (Cytochrome P450 88A3)	0.18	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				490
O13148 UniProt NPD GO	EPA4A_BRARE	Ephrin type-A receptor 4a (EC 2.7.10.1) (Tyrosine-protein kinase receptor ZEK2) (EPH-like kinase 2) ...	0.18	-	cyt	0	Membrane; single-pass type I membrane protein				292

You are viewing entries 52951 to 53000 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.