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
Q9DCA7 UniProt NPD GO	D1IP_MOUSE	D1 dopamine receptor-interacting protein calcyon	0.28	-	nuc	1	Membrane; single-pass type III membrane protein (Potential)				226
Q6CSY9 UniProt NPD GO	DAD4_KLULA	DASH complex subunit DAD4 (Outer kinetochore protein DAD4)	0.28	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				72
Q694B9 UniProt NPD GO	ABC3G_SAGLB	DNA dC->dU-editing enzyme APOBEC-3G (EC 3.5.4.-)	0.28	-	nuc	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				381
P40999 UniProt NPD GO	PMT1M_SCHPO	DNA methyltransferase homolog pmt1 (SpIM.SpoI) (M.SpomI)	0.28	-	cyt	0	Nucleus (Probable)				330
Q9NR33 UniProt NPD GO	DPOE4_HUMAN	DNA polymerase epsilon subunit 4 (EC 2.7.7.7) (DNA polymerase II subunit 4) (DNA polymerase epsilon ...	0.28	-	cyt	0	Nucleus (Potential)	nucleus [TAS]	607269		117
Q6FXD0 UniProt NPD GO	DPB4_CANGA	DNA polymerase epsilon subunit D (EC 2.7.7.7) (DNA polymerase II subunit D)	0.28	-	nuc	0	Nucleus (By similarity)				191
P49004 UniProt NPD GO	DPOD2_BOVIN	DNA polymerase subunit delta 2 (EC 2.7.7.7) (DNA polymerase subunit delta p50)	0.28	-	mit	0	Nucleus	nucleus [IC]			469
Q9UHN1 UniProt NPD GO	DPOG2_HUMAN	DNA polymerase subunit gamma 2, mitochondrial precursor (EC 2.7.7.7) (Mitochondrial DNA polymerase a ...	0.28	-	mit	0	Mitochondrion	mitochondrial chromosome [TAS] mitochondrion [NAS]	604983	2G4C	485
P26306 UniProt NPD GO	RAD9_SCHPO	DNA repair protein rad9	0.28	-	cyt	0		checkpoint clamp complex [IDA]			426
P34647 UniProt NPD GO	MCM6_CAEEL	DNA replication licensing factor mcm-6	0.28	-	cyt	0	Nucleus (Potential)				810
O95985 UniProt NPD GO	TOP3B_HUMAN	DNA topoisomerase 3-beta-1 (EC 5.99.1.2) (DNA topoisomerase III beta-1)	0.28	-	nuc	0		nucleus [TAS]	603582		862
Q8L6J4 UniProt NPD GO	RPO1A_TOBAC	DNA-directed RNA polymerase 1A (EC 2.7.7.6) (T7 bacteriophage-type single subunit RNA polymerase 1A) ...	0.28	-	cyt	0					155
P50106 UniProt NPD GO	RPA8_YEAST	DNA-directed RNA polymerase I 14 kDa polypeptide (EC 2.7.7.6) (A14)	0.28	-	mit	0	Nucleus	DNA-directed RNA polymerase I complex [IDA]			137
P11414 UniProt NPD GO	RPB1_CRIGR	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) (RPB1) (Fragment)	0.28	-	nuc	0	Nucleus				467
Q8SL88 UniProt NPD GO	RPOA_EUGST	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.28	-	cyt	0	Plastid; chloroplast				213
Q86YH6 UniProt NPD GO	DLP1_HUMAN	Decaprenyl-diphosphate synthase subunit 2 (EC 2.5.1.-) (Decaprenyl pyrophosphate synthetase subunit ...	0.28	-	mit	0					399
P28312 UniProt NPD GO	DEF5_MOUSE	Defensin-related cryptdin 5 precursor	0.28	-	exc	0	Secreted protein				93
Q95192 UniProt NPD GO	DAZL_MACFA	Deleted in azoospermia-like (DAZ-like autosomal) (Deleted in azoospermia-like 1)	0.28	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Nuclear in spermatogonia until ne ...				295
Q92904 UniProt NPD GO	DAZL_HUMAN	Deleted in azoospermia-like (DAZ-like autosomal) (Deleted in azoospermia-like 1) (DAZ homolog) (SPGY ...	0.28	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Nuclear in spermatogonia until ne ...	cytoplasm [TAS]	601486		295
Q7SIE0 UniProt NPD GO	ARLY1_MELGA	Delta-1 crystallin (Delta crystallin I)	0.28	-	nuc	0				1I0A	466
P30124 UniProt NPD GO	HEM2_PEA	Delta-aminolevulinic acid dehydratase, chloroplast precursor (EC 4.2.1.24) (Porphobilinogen synthase ...	0.28	-	mit	0	Plastid; chloroplast				398
Q15834 UniProt NPD GO	DIPA_HUMAN	Delta-interacting protein A (Hepatitis delta antigen-interacting protein A) (Coiled-coil domain-cont ...	0.28	-	nuc	0			605360		202
Q2QDE7 UniProt NPD GO	DNSL1_RAT	Deoxyribonuclease I-like 1 precursor (EC 3.1.21.-) (DNase I-like 1) (DNase X)	0.28	-	mit	1 *	Endoplasmic reticulum (By similarity)				312
Q7TSF1 UniProt NPD GO	DSG1B_MOUSE	Desmoglein-1 beta precursor (Dsg1-beta) (Desmoglein-5)	0.28	-	end	0	Membrane; single-pass type I membrane protein (By similarity)	desmosome [IDA]			1060
Q02413 UniProt NPD GO	DSG1_HUMAN	Desmoglein-1 precursor (Desmosomal glycoprotein 1) (DG1) (DGI) (Pemphigus foliaceus antigen)	0.28	-	end	0	Membrane; single-pass type I membrane protein (By similarity)	desmosome [NAS]	148700		1049
P81425 UniProt NPD GO	DPP4_BOVIN	Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen C ...	0.28	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				765
Q6FTG1 UniProt NPD GO	DPH1_CANGA	Diphthamide biosynthesis protein 1	0.28	-	cyt	0	Cytoplasm (By similarity)				428
P83041 UniProt NPD GO	DISI5_CERCE	Disintegrin CC5 [Contains: Disintegrin CC5B]	0.28	-	nuc	0	Secreted protein				65
O13898 UniProt NPD GO	PMT1_SCHPO	Dolichyl-phosphate-mannose--protein mannosyltransferase 1 (EC 2.4.1.109)	0.28	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Nucleus; nuclear ...	dolichyl-phosphate-mannose-protein mannosyl... [IDA] endomembrane system [IDA]			893
Q63980 UniProt NPD GO	MP2K1_CRIGR	Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) (MAP kinase kinase 1) (MAPK ...	0.28	-	cyt	0					393
P28563 UniProt NPD GO	DUS1_MOUSE	Dual specificity protein phosphatase 1 (EC 3.1.3.48) (EC 3.1.3.16) (MAP kinase phosphatase 1) (MKP-1 ...	0.28	-	cyt	0					367
Q9H1R2 UniProt NPD GO	DUS15_HUMAN	Dual specificity protein phosphatase 15 (EC 3.1.3.48) (EC 3.1.3.16) (Vaccinia virus VH1-related dual ...	0.28	-	nuc	0	Cytoplasm (Probable). Isoform 3: cell membrane; lipid-anchor; cytoplasmic side			1YZ4	295
O54838 UniProt NPD GO	DUS5_RAT	Dual specificity protein phosphatase 5 (EC 3.1.3.48) (EC 3.1.3.16) (MAP-kinase phosphatase CPG21)	0.28	-	nuc	0	Nucleus (By similarity)				384
Q7Z419 UniProt NPD GO	IBRD2_HUMAN	E3 ubiquitin ligase IBRDC2 (EC 6.3.2.-) (IBR domain-containing protein 2) (p53-inducible RING finger ...	0.28	-	nuc	1		integral to membrane [ISS] ubiquitin ligase complex [IC]			303
Q8BGF6 UniProt NPD GO	ELMD2_MOUSE	ELMO domain-containing protein 2	0.28	-	cyt	0					293
P61563 UniProt NPD GO	ENW1_PANTR	ERV-W1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (ERVWE1 envelope protein) ...	0.28	-	end	1	TM: Cell membrane; single-pass type I membrane protein. SU: Cell membrane; peripheral membrane prote ...				538
Q02919 UniProt NPD GO	NO36B_SOYBN	Early nodulin 36B (Fragment)	0.28	-	mit	1 *					93
P08297 UniProt NPD GO	NO75_SOYBN	Early nodulin 75 precursor (N-75) (NGM-75)	0.28	-	nuc	1 *					309
Q06841 UniProt NPD GO	NO75_LUPLU	Early nodulin 75 protein (N-75) (NGM-75) (Fragment)	0.28	-	nuc	0					434
Q93070 UniProt NPD GO	NAR4_HUMAN	Ecto-ADP-ribosyltransferase 4 precursor (EC 2.4.2.31) (NAD(P)(+)--arginine ADP-ribosyltransferase 4) ...	0.28	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	membrane [NAS]	110600		314
Q8R2Q4 UniProt NPD GO	EFG2_MOUSE	Elongation factor G 2, mitochondrial precursor (mEF-G 2) (Elongation factor G2)	0.28	-	mit	0	Mitochondrion (By similarity)				777
Q07187 UniProt NPD GO	EM1_ARATH	Em-like protein GEA1 (EM1)	0.28	-	nuc	0					152
P53753 UniProt NPD GO	ENG1_YEAST	Endo-1,3(4)-beta-glucanase 1 precursor (EC 3.2.1.6) (Endo-1,4-beta-glucanase 1) (Endo-1,3-beta-gluca ...	0.28	-	exc	0	Cell wall. Localizes asymmetrically to the daughter side of the septum	cell septum [IDA] cell wall (sensu Fungi) [IDA]			1117
Q7M4F2 UniProt NPD GO	CUD8_SCHGR	Endocuticle structural glycoprotein SgAbd-8	0.28	-	nuc	0					139
P37176 UniProt NPD GO	EGLN_PIG	Endoglin precursor	0.28	-	end	1	Membrane; single-pass type I membrane protein				653
Q759T8 UniProt NPD GO	ERV25_ASHGO	Endoplasmic reticulum vesicle protein 25 precursor	0.28	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				209
P41148 UniProt NPD GO	ENPL_CANFA	Endoplasmin precursor (Heat shock protein 90 kDa beta member 1) (94 kDa glucose-regulated protein) ( ...	0.28	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Sarcoplasmic reticulum			1YT2	804
Q9WVG5 UniProt NPD GO	LIPE_MOUSE	Endothelial lipase precursor (EC 3.1.1.3) (Endothelial cell-derived lipase) (EDL)	0.28	-	cyt	0	Secreted protein				500
Q93104 UniProt NPD GO	ERH_AEDAE	Enhancer of rudimentary homolog	0.28	-	nuc	0					103
P97545 UniProt NPD GO	CCL11_RAT	Eotaxin precursor (Small inducible cytokine A11) (CCL11) (Eosinophil chemotactic protein)	0.28	-	exc	0	Secreted protein				97

You are viewing entries 42201 to 42250 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.