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
Q9Y6G9 UniProt NPD GO	DC1L1_HUMAN	Cytoplasmic dynein 1 light intermediate chain 1 (Dynein light intermediate chain 1, cytosolic) (Dyne ...	0.16	-	cyt	0					523
O93852 UniProt NPD GO	ALO_CANAL	D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) (ALO) (L-galactono-gamma-lactone oxidase)	0.16	-	cyt	0	Mitochondrion; mitochondrial membrane (By similarity). Membrane-embedded (By similarity)				557
Q759Q6 UniProt NPD GO	DAD2_ASHGO	DASH complex subunit DAD2 (Outer kinetochore protein DAD2)	0.16	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				111
Q9M2F9 UniProt NPD GO	RH52_ARATH	DEAD-box ATP-dependent RNA helicase 52 (EC 3.6.1.-)	0.16	-	cyt	0					646
Q9M0V3 UniProt NPD GO	DDB1A_ARATH	DNA damage-binding protein 1a (UV-damaged DNA-binding protein 1a) (DDB1a)	0.16	-	vac	0	Nucleus				1088
O48520 UniProt NPD GO	DPOD2_ARATH	DNA polymerase delta small subunit (EC 2.7.7.7)	0.16	-	cyt	0	Nucleus (By similarity)				456
Q9SK02 UniProt NPD GO	RA51B_ARATH	DNA repair protein RAD51 homolog 2 (AtRAD51B)	0.16	-	cyt	0	Nucleus (By similarity)				370
Q91917 UniProt NPD GO	RA51B_XENLA	DNA repair protein RAD51 homolog B (xRAD51.2)	0.16	-	cyt	0	Nucleus (Probable)				336
Q7ZT46 UniProt NPD GO	PSF2_XENLA	DNA replication complex GINS protein PSF2	0.16	-	cyt	0	Nucleus	nucleus [IDA]			185
P42570 UniProt NPD GO	PLU_DROME	DNA replication inhibitor plutonium	0.16	-	cyt	0					174
Q39147 UniProt NPD GO	3MG_ARATH	DNA-3-methyladenine glycosylase (EC 3.2.2.21) (3-methyladenine DNA glycosidase)	0.16	-	mit	0	Nucleus (Potential)				254
Q712G9 UniProt NPD GO	ID3_CANFA	DNA-binding protein inhibitor ID-3 (Inhibitor of DNA binding 3)	0.16	-	nuc	0	Nucleus (By similarity)				119
Q02535 UniProt NPD GO	ID3_HUMAN	DNA-binding protein inhibitor ID-3 (Inhibitor of DNA binding 3) (ID-like protein inhibitor HLH 1R21) ...	0.16	-	nuc	0	Nucleus	nucleus [IC]	600277		119
Q2T9S3 UniProt NPD GO	RPO3F_BOVIN	DNA-directed RNA polymerase III subunit F (EC 2.7.7.6)	0.16	-	nuc	0	Nucleus (Potential)				316
P49465 UniProt NPD GO	RPOA_ODOSI	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.16	-	nuc	0	Plastid; chloroplast				312
Q92399 UniProt NPD GO	RPB8_SCHPO	DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide (EC 2.7.7.6)	0.16	-	cyt	0	Nucleus	DNA-directed RNA polymerase I complex [IDA] DNA-directed RNA polymerase II, holoenzyme [IDA] DNA-directed RNA polymerase III complex [IDA]			125
P81930 UniProt NPD GO	PSD2_PEA	Defense-related peptide 2 (Defensin-2) (Antifungal protein Psd2)	0.16	-	nuc	0					47
P01541 UniProt NPD GO	THN_DENCL	Denclatoxin B	0.16	-	mit	0	Secreted protein				46
P11936 UniProt NPD GO	DNAS1_PIG	Deoxyribonuclease-1 precursor (EC 3.1.21.1) (Deoxyribonuclease I) (DNase I)	0.16	-	exc	1 *	Secretory protein, stored in zymogen granules and found in the nuclear envelope				284
Q07507 UniProt NPD GO	DERM_HUMAN	Dermatopontin precursor (Tyrosine-rich acidic matrix protein) (TRAMP)	0.16	-	mit	0	Secreted protein; extracellular space; extracellular matrix		125597		201
P51556 UniProt NPD GO	DGKA_RAT	Diacylglycerol kinase alpha (EC 2.7.1.107) (Diglyceride kinase alpha) (DGK-alpha) (DAG kinase alpha) ...	0.16	-	cyt	0					727
Q9R1C6 UniProt NPD GO	DGKE_MOUSE	Diacylglycerol kinase epsilon (EC 2.7.1.107) (Diglyceride kinase epsilon) (DGK-epsilon) (DAG kinase ...	0.16	-	nuc	1 *	Membrane; multi-pass membrane protein (Potential)				564
P22906 UniProt NPD GO	DYR_CANAL	Dihydrofolate reductase (EC 1.5.1.3)	0.16	-	mit	0				1M7A	192
O35435 UniProt NPD GO	PYRD_MOUSE	Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdeha ...	0.16	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane				395
Q63707 UniProt NPD GO	PYRD_RAT	Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdeha ...	0.16	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane			1UUO	395
Q8VHG0 UniProt NPD GO	FMO4_MOUSE	Dimethylaniline monooxygenase [N-oxide-forming] 4 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.16	-	end	0	Microsome (By similarity)				559
Q8C255 UniProt NPD GO	DPEP2_MOUSE	Dipeptidase 2 precursor (EC 3.4.13.19) (Membrane-bound dipeptidase 2) (MBD-2)	0.16	-	exc	1 *	Membrane; lipid-anchor; GPI-anchor				478
P27487 UniProt NPD GO	DPP4_HUMAN	Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen C ...	0.16	-	cyt	1 *	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein. Also exists i ...		102720	2BUB	766
P22411 UniProt NPD GO	DPP4_PIG	Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen C ...	0.16	-	cyt	1 *	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein. Also exists i ...			2BUC	766
Q6BPU5 UniProt NPD GO	DPH1_DEBHA	Diphthamide biosynthesis protein 1	0.16	-	cyt	0	Cytoplasm (By similarity)				420
Q4WN99 UniProt NPD GO	DPH2_ASPFU	Diphthamide biosynthesis protein 2	0.16	-	cyt	0	Cytoplasm (By similarity)				565
Q5B2Q1 UniProt NPD GO	DPH2_EMENI	Diphthamide biosynthesis protein 2	0.16	-	cyt	0	Cytoplasm (By similarity)				582
Q4I7G0 UniProt NPD GO	DPH4_GIBZE	Diphthamide biosynthesis protein 4	0.16	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				188
P83253 UniProt NPD GO	DISA_VIPLE	Disintegrin lebein-alpha (Platelet aggregation activation inhibitor)	0.16	-	nuc	0	Secreted protein				64
P60904 UniProt NPD GO	DNJC5_MOUSE	DnaJ homolog subfamily C member 5 (Cysteine string protein) (CSP)	0.16	-	nuc	0	Membrane; lipid-anchor (By similarity)			2CTW	198
P60905 UniProt NPD GO	DNJC5_RAT	DnaJ homolog subfamily C member 5 (Cysteine string protein) (CSP)	0.16	-	nuc	0	Membrane; lipid-anchor				198
P48439 UniProt NPD GO	OST3_YEAST	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST3 precursor (EC 2.4.1.119) ...	0.16	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)	integral to membrane [IMP] oligosaccharyl transferase complex [IPI]			350
P09172 UniProt NPD GO	DOPO_HUMAN	Dopamine beta-hydroxylase precursor (EC 1.14.17.1) (Dopamine beta-monooxygenase)	0.16	-	end	1 *	Exists both in a soluble form (in chromaffin granules) and as membrane bound (the membrane bound for ...	chromaffin granule [NAS] cytoplasm [TAS] extracellular region [NAS] membrane fraction [TAS] soluble fraction [TAS]	609312		603
Q9DFI0 UniProt NPD GO	DMT3B_BRARE	Doublesex- and mab-3-related transcription factor 3b (Dmrt7b/Dmrt10) (Fragment)	0.16	-	nuc	0	Nucleus (Potential)				31
Q08902 UniProt NPD GO	YO378_YEAST	Drug resistance protein YOR378W	0.16	-	end	12	Cell membrane; multi-pass membrane protein				515
Q62862 UniProt NPD GO	MP2K5_RAT	Dual specificity mitogen-activated protein kinase kinase 5 (EC 2.7.12.2) (MAP kinase kinase 5) (MAPK ...	0.16	-	cyt	0	Isoform Beta: Cytoplasm. Isoform Alpha-1, isoform Alpha-2: Membrane. The alternatively spliced exon ...				448
Q9D7X3 UniProt NPD GO	DUS3_MOUSE	Dual specificity protein phosphatase 3 (EC 3.1.3.48) (EC 3.1.3.16) (T-DSP11)	0.16	-	nuc	0					185
Q6UY11 UniProt NPD GO	EGFL9_HUMAN	EGF-like domain-containing protein 9 precursor (Multiple EGF-like domain protein 9)	0.16	-	end	1	Membrane; single-pass type I membrane protein (Potential)				383
Q14246 UniProt NPD GO	EMR1_HUMAN	EGF-like module-containing mucin-like hormone receptor-like 1 precursor (Cell surface glycoprotein E ...	0.16	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600493		886
Q9DCM0 UniProt NPD GO	ETHE1_MOUSE	ETHE1 protein, mitochondrial precursor (EC 3.-.-.-) (Ethylmalonic encephalopathy protein 1 homolog) ...	0.16	-	mit	0	Cytoplasm (By similarity). Or: Nucleus (By similarity). Or: Mitochondrion; mitochondrial matrix (By ...	mitochondrion [IDA]			254
Q02921 UniProt NPD GO	NO93_SOYBN	Early nodulin 93 (N-93)	0.16	-	nuc	2 *					105
Q01381 UniProt NPD GO	ELYS_HALFU	Egg-lysin precursor (Sperm-lysin)	0.16	-	vac	1 *				3LYN	154
Q9H6Z9 UniProt NPD GO	EGLN3_HUMAN	Egl nine homolog 3 (EC 1.14.11.-) (Hypoxia-inducible factor prolyl hydroxylase 3) (HIF-prolyl hydrox ...	0.16	-	mit	0	Cytoplasm. Nucleus		606426		239
Q2TBV3 UniProt NPD GO	ETFB_BOVIN	Electron transfer flavoprotein subunit beta (Beta-ETF)	0.16	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				254
P38117 UniProt NPD GO	ETFB_HUMAN	Electron transfer flavoprotein subunit beta (Beta-ETF)	0.16	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [TAS]	130410	2A1U	254

You are viewing entries 55551 to 55600 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.