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
Q12882 UniProt NPD GO	DPYD_HUMAN	Dihydropyrimidine dehydrogenase [NADP+] precursor (EC 1.3.1.2) (DPD) (DHPDHase) (Dihydrouracil dehyd ...	0.29	-	cyt	0	Cytoplasm	cytoplasm [NAS]	274270		1025
P17635 UniProt NPD GO	FMO2_RABIT	Dimethylaniline monooxygenase [N-oxide-forming] 2 (EC 1.14.13.8) (Pulmonary flavin-containing monoox ...	0.29	-	end	1	Microsome				534
Q5M872 UniProt NPD GO	DPEP2_RAT	Dipeptidase 2 precursor (EC 3.4.13.19)	0.29	-	end	0	Membrane; lipid-anchor; GPI-anchor (By similarity)				481
Q59MG1 UniProt NPD GO	DPH1_CANAL	Diphthamide biosynthesis protein 1	0.29	+	mit	0	Cytoplasm (By similarity)				426
Q10206 UniProt NPD GO	DPH2_SCHPO	Diphthamide biosynthesis protein 2	0.29	-	cyt	0	Cytoplasm (By similarity)				503
Q8MPX3 UniProt NPD GO	DNJ20_CAEEL	DnaJ homolog dnj-20 precursor (DnaJ domain protein 20)	0.29	-	exc	0					249
Q862Z4 UniProt NPD GO	DNJB3_MACFU	DnaJ homolog subfamily B member 3 (Spermatogenic cell-specific DNAJ homolog)	0.29	-	cyt	0					242
O54946 UniProt NPD GO	DNJB6_MOUSE	DnaJ homolog subfamily B member 6 (Heat shock protein J2) (HSJ-2) (MRJ) (mDj4)	0.29	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			242
Q9WU83 UniProt NPD GO	DPM1_CRIGR	Dolichol-phosphate mannosyltransferase (EC 2.4.1.83) (Dolichol-phosphate mannose synthase) (Dolichyl ...	0.29	-	mit	0	Endoplasmic reticulum (By similarity)				266
O70152 UniProt NPD GO	DPM1_MOUSE	Dolichol-phosphate mannosyltransferase (EC 2.4.1.83) (Dolichol-phosphate mannose synthase) (Dolichyl ...	0.29	-	mit	0	Endoplasmic reticulum	endoplasmic reticulum membrane [ISS] mannosyltransferase complex [ISS]			260
P09040 UniProt NPD GO	DSK_DROME	Drosulfakinins precursor [Contains: Drosulfakinin-0 (DSK-0); Drosulfakinin-1 (Drosulfakinin I) (DSK- ...	0.29	-	exc	1 *					141
Q39491 UniProt NPD GO	PTP3_CHLEU	Dual specificity protein phosphatase (EC 3.1.3.48) (EC 3.1.3.16)	0.29	-	nuc	0					276
O75935 UniProt NPD GO	DCTN3_HUMAN	Dynactin subunit 3 (Dynactin complex subunit 22 kDa subunit) (p22)	0.29	-	cyt	0	Cytoplasm. Centrosome. Kinetochore. Spindle. Localizes to punctate cytoplasmic structures and to the ...	dynactin complex [IPI] perinuclear region [IDA]	607387		186
O55058 UniProt NPD GO	FBLN4_CRIGR	EGF-containing fibulin-like extracellular matrix protein 2 precursor (Fibulin-4) (FIBL-4) (H411 prot ...	0.29	-	exc	0	Secreted protein				443
Q91VF5 UniProt NPD GO	EMID1_MOUSE	EMI domain-containing protein 1 precursor (Protein Emu1) (Emilin and multimerin domain-containing pr ...	0.29	-	mit	0	Secreted protein; extracellular space; extracellular matrix	endoplasmic reticulum [IDA] extracellular matrix (sensu Metazoa) [IDA] Golgi apparatus [IDA]			444
Q9TU32 UniProt NPD GO	LMAN1_CERAE	ERGIC-53 protein precursor (ER-Golgi intermediate compartment 53 kDa protein) (Lectin, mannose-bindi ...	0.29	-	cyt	1	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				510
P11728 UniProt NPD GO	NO75_MEDSA	Early nodulin 75 (N-75) (NGM-75) (Fragment)	0.29	-	nuc	0					97
Q90495 UniProt NPD GO	ECAR_ECHCA	Ecarin precursor (EC 3.4.24.-)	0.29	-	nuc	0					616
Q95NE0 UniProt NPD GO	NAR4_PANTR	Ecto-ADP-ribosyltransferase 4 precursor (EC 2.4.2.31) (NAD(P)(+)--arginine ADP-ribosyltransferase 4) ...	0.29	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	membrane [ISS]			314
P29691 UniProt NPD GO	EF2_CAEEL	Elongation factor 2 (EF-2)	0.29	-	nuc	0	Cytoplasm				851
P27539 UniProt NPD GO	GDF1_HUMAN	Embryonic growth/differentiation factor 1 precursor (GDF-1)	0.29	-	exc	0	Secreted protein		602880		372
Q5XFR0 UniProt NPD GO	EPAB2_MOUSE	Embryonic polyadenylate-binding protein 2 (Embryonic poly(A)-binding protein 2) (Embryonic poly(A)-b ...	0.29	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]			273
P54837 UniProt NPD GO	ERV25_YEAST	Endoplasmic reticulum vesicle protein 25 precursor	0.29	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein. Golgi ap ...	ER to Golgi transport vesicle [IDA]			211
P08113 UniProt NPD GO	ENPL_MOUSE	Endoplasmin precursor (Heat shock protein 90 kDa beta member 1) (94 kDa glucose-regulated protein) ( ...	0.29	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [IDA]			802
Q59P50 UniProt NPD GO	YSH1_CANAL	Endoribonuclease YSH1 (EC 3.1.27.-) (mRNA 3'-end-processing protein YSH1)	0.29	-	cyt	0	Nucleus (By similarity)				870
O13794 UniProt NPD GO	YSH1_SCHPO	Endoribonuclease ysh1 (EC 3.1.27.-) (mRNA 3'-end-processing protein ysh1)	0.29	-	cyt	0	Nucleus (By similarity)				775
Q8VBX1 UniProt NPD GO	LIPE_RAT	Endothelial lipase precursor (EC 3.1.1.3) (Endothelial-derived lipase) (EDL)	0.29	-	mit	0	Secreted protein (By similarity)				493
P13095 UniProt NPD GO	ESM4_DROME	Enhancer of split m4 protein (E(spl)m4)	0.29	-	nuc	0		nucleus [TAS]			152
Q63189 UniProt NPD GO	EMBP_RAT	Eosinophil granule major basic protein precursor (MBP)	0.29	-	vac	0	Matrix of eosinophil's large specific granule (crystalloid core) (By similarity)				227
P29317 UniProt NPD GO	EPHA2_HUMAN	Ephrin type-A receptor 2 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor ECK) (Epithelial ...	0.29	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	176946	1MQB	976
P54758 UniProt NPD GO	EPHA6_RAT	Ephrin type-A receptor 6 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EHK-2) (EPH homol ...	0.29	+	nuc	1	Membrane; single-pass type I membrane protein				1035
P30944 UniProt NPD GO	CADH1_XENLA	Epithelial-cadherin precursor (E-cadherin) (Uvomorulin) (xTCAD-1)	0.29	-	end	1 *	Membrane; single-pass type I membrane protein				872
P02664 UniProt NPD GO	CASE_MOUSE	Epsilon-casein precursor	0.29	-	exc	0	Secreted protein				143
Q3SZ65 UniProt NPD GO	IF4A2_BOVIN	Eukaryotic initiation factor 4A-II (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-2) (eIF4A-II) (eIF ...	0.29	-	cyt	0					407
Q14240 UniProt NPD GO	IF4A2_HUMAN	Eukaryotic initiation factor 4A-II (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-2) (eIF4A-II) (eIF ...	0.29	-	cyt	0		eukaryotic translation initiation factor 4F... [TAS]	601102		407
Q4R4Y9 UniProt NPD GO	IF4A2_MACFA	Eukaryotic initiation factor 4A-II (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-2) (eIF4A-II) (eIF ...	0.29	-	cyt	0					408
P10630 UniProt NPD GO	IF4A2_MOUSE	Eukaryotic initiation factor 4A-II (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-2) (eIF4A-II) (eIF ...	0.29	-	cyt	0					407
Q5R4X1 UniProt NPD GO	IF4A2_PONPY	Eukaryotic initiation factor 4A-II (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-2) (eIF4A-II) (eIF ...	0.29	-	cyt	0					407
Q15056 UniProt NPD GO	IF4H_HUMAN	Eukaryotic translation initiation factor 4H (eIF-4H) (Williams-Beuren syndrome chromosome region 1 p ...	0.29	-	nuc	0	Cytoplasm; perinuclear region (By similarity)	eukaryotic translation initiation factor 4F... [TAS]	603431		247
P15217 UniProt NPD GO	EGIP_ANTCR	Exogastrula-inducing polypeptide precursor (EGIP) [Contains: Exogastrula-inducing peptide C (EGIP-C) ...	0.29	-	exc	0					325
Q08354 UniProt NPD GO	EZY1_CHLRE	Ezy-1 protein precursor	0.29	-	mit	0					453
Q08355 UniProt NPD GO	EZY2_CHLRE	Ezy-1 protein precursor	0.29	-	mit	0					456
Q9UK22 UniProt NPD GO	FBX2_HUMAN	F-box only protein 2	0.29	-	cyt	0			607112		296
Q9QZH7 UniProt NPD GO	FXL20_RAT	F-box/LRR-repeat protein 20 (F-box and leucine-rich repeat protein 20) (F-box/LRR-repeat protein 2-l ...	0.29	-	mit	0	Cytoplasm				276
Q18223 UniProt NPD GO	FBSP1_CAEEL	F-box/SPRY-domain protein 1 (F-box synaptic protein 1)	0.29	-	cyt	0					332
Q9WVA8 UniProt NPD GO	NPFF_MOUSE	FMRFamide-related peptides precursor [Contains: Neuropeptide SF (NPSF); Neuropeptide FF (NPFF); Neur ...	0.29	-	exc	0	Secreted protein				114
Q5H8B9 UniProt NPD GO	FREM3_MOUSE	FRAS1-related extracellular matrix protein 3 precursor (NV domain-containing protein 2)	0.29	-	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				2123
P12276 UniProt NPD GO	FAS_CHICK	Fatty acid synthase (EC 2.3.1.85) [Includes: [Acyl-carrier-protein] S-acetyltransferase (EC 2.3.1.38 ...	0.29	-	cyt	0					2511
P12785 UniProt NPD GO	FAS_RAT	Fatty acid synthase (EC 2.3.1.85) [Includes: [Acyl-carrier-protein] S-acetyltransferase (EC 2.3.1.38 ...	0.29	-	nuc	0				1N8L	2505
Q9ZNZ7 UniProt NPD GO	GLTB1_ARATH	Ferredoxin-dependent glutamate synthase 1, chloroplast precursor (EC 1.4.7.1) (Fd-GOGAT 1)	0.29	-	nuc	0	Plastid; chloroplast; chloroplast stroma (By similarity)				1648

You are viewing entries 41201 to 41250 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.