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
Q6ENX1 UniProt NPD GO	RPOC2_SACOF	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.93	+	nuc	0	Plastid; chloroplast				1534
O35613 UniProt NPD GO	DAXX_MOUSE	Death domain-associated protein 6 (Daxx)	0.93	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Translocates from the nucleus to the cytoplasm u ...	cytoplasm [ISS] nucleus [ISS] PML body [IDA]			739
Q08495 UniProt NPD GO	DEMA_HUMAN	Dematin (Erythrocyte membrane protein band 4.9)	0.93	-	nuc	0		actin cytoskeleton [TAS]	125305	1ZV6	405
Q5R4B6 UniProt NPD GO	DEMA_PONPY	Dematin (Erythrocyte membrane protein band 4.9)	0.93	-	nuc	0					405
Q80TS7 UniProt NPD GO	DEND_MOUSE	Dendrin	0.93	+	nuc	0					656
O60216 UniProt NPD GO	RAD21_HUMAN	Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 ho ...	0.93	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...		606462		631
Q03063 UniProt NPD GO	DIG1_YEAST	Down-regulator of invasive growth 1 (Regulator of sterile twelve 1) (Regulator of STE12 protein 1)	0.93	-	nuc	0	Nucleus	nucleus [TAS]			452
Q9QXS6 UniProt NPD GO	DREB_MOUSE	Drebrin (Developmentally-regulated brain protein)	0.93	-	nuc	0	Cytoplasm (By similarity)	actin cytoskeleton [IDA]			705
P49759 UniProt NPD GO	CLK1_HUMAN	Dual specificity protein kinase CLK1 (EC 2.7.12.1) (CDC-like kinase 1)	0.93	+	nuc	0	Nucleus		601951	1Z57	484
P22518 UniProt NPD GO	CLK1_MOUSE	Dual specificity protein kinase CLK1 (EC 2.7.12.1) (CDC-like kinase 1) (Protein kinase STY)	0.93	+	nuc	0	Nucleus	nucleus [IDA]			483
Q9HAZ1 UniProt NPD GO	CLK4_HUMAN	Dual specificity protein kinase CLK4 (EC 2.7.12.1) (CDC-like kinase 4)	0.93	+	nuc	0	Nucleus (By similarity)		607969		481
O35493 UniProt NPD GO	CLK4_MOUSE	Dual specificity protein kinase CLK4 (EC 2.7.12.1) (CDC-like kinase 4)	0.93	+	nuc	0	Nucleus (By similarity)	nucleus [IDA]			481
Q9TW65 UniProt NPD GO	DMD_CAEEL	Dystrophin-1	0.93	+	nuc	0		dystrophin-associated glycoprotein complex [IDA]			3674
Q8STF6 UniProt NPD GO	DYC1_CAEEL	Dystrophin-like protein 1 (Dyb-1-binding and CAPON-related protein)	0.93	-	nuc	0		dystrophin-associated glycoprotein complex [IGI]			887
O94451 UniProt NPD GO	PLI1_SCHPO	E3 SUMO--protein ligase pli1 (EC 6.-.-.-)	0.93	-	nuc	0	Nucleus				727
Q7S747 UniProt NPD GO	EPL1_NEUCR	Enhancer of polycomb-like protein 1	0.93	-	mit	0	Nucleus (By similarity)				589
O94842 UniProt NPD GO	CN092_HUMAN	Epidermal Langerhans cell protein LCP1	0.93	+	nuc	0	Nucleus (Probable)				621
Q08509 UniProt NPD GO	EPS8_MOUSE	Epidermal growth factor receptor kinase substrate 8	0.93	+	nuc	0				1I0C	821
Q04637 UniProt NPD GO	IF4G1_HUMAN	Eukaryotic translation initiation factor 4 gamma 1 (eIF-4-gamma 1) (eIF-4G1) (eIF-4G 1) (p220)	0.93	-	nuc	0		cytoplasm [NAS] eukaryotic translation initiation factor 4F... [TAS]	600495	1UG3	1600
Q9NRA8 UniProt NPD GO	4ET_HUMAN	Eukaryotic translation initiation factor 4E transporter (eIF4E transporter) (4E-T) (Eukaryotic trans ...	0.93	-	nuc	0	Cytoplasm. Predominantly. Nucleus. Shuttles between the nucleus and the cytoplasm in a CRM1-dependen ...	cytoplasm [TAS] nucleus [TAS]	607445		985
Q9EST3 UniProt NPD GO	4ET_MOUSE	Eukaryotic translation initiation factor 4E transporter (eIF4E transporter) (4E-T) (Eukaryotic trans ...	0.93	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Shuttles between the nucleus and cytoplasm in a ...				983
Q5BFX0 UniProt NPD GO	EXO84_EMENI	Exocyst complex component exo84	0.93	-	nuc	0	Secretory vesicle (By similarity). Cell periphery. The polarization of EXO84 requires actin cables ( ...				666
Q8CFG0 UniProt NPD GO	SULF2_MOUSE	Extracellular sulfatase Sulf-2 precursor (EC 3.1.6.-) (MSulf-2)	0.93	+	nuc	1 *	Endoplasmic reticulum (By similarity). Golgi apparatus; Golgi stack (By similarity). Cell surface (B ...	cell surface [ISS] extracellular space [ISS]			875
Q9NVF7 UniProt NPD GO	FBX28_HUMAN	F-box only protein 28	0.93	+	nuc	0			609100		368
Q9CPU7 UniProt NPD GO	FBX32_MOUSE	F-box only protein 32 (Muscle atrophy F-box protein) (MAFbx) (Atrogin-1)	0.93	+	cyt	0					355
Q6PCT2 UniProt NPD GO	FXL19_HUMAN	F-box/LRR-repeat protein 19 (F-box and leucine-rich repeat protein 19)	0.93	-	nuc	0		cytoplasm [ISS]	609085		674
Q6P9Q4 UniProt NPD GO	FHOD1_MOUSE	FH1/FH2 domain-containing protein (Formin homolog overexpressed in spleen) (FHOS) (Formin homology 2 ...	0.93	-	nuc	0	Cytoplasm (By similarity). Predominantly (By similarity)				1196
O35601 UniProt NPD GO	FYB_MOUSE	FYN-binding protein (FYN-T-binding protein) (FYB-120/130) (p120/p130) (SLP-76-associated phosphoprot ...	0.93	-	nuc	0	Cytoplasm. Nucleus				819
Q99689 UniProt NPD GO	FEZ1_HUMAN	Fasciculation and elongation protein zeta 1 (Zygin-1) (Zygin I)	0.93	+	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocated from the plasma membrane to t ...		604825		392
P11596 UniProt NPD GO	TRSF_DROME	Female-specific protein transformer	0.93	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Speckled subnuclear compartment				197
O96020 UniProt NPD GO	CCNE2_HUMAN	G1/S-specific cyclin-E2	0.93	-	mit	0	Nucleus		603775		404
Q8W4H1 UniProt NPD GO	GAT28_ARATH	GATA transcription factor 28	0.93	-	nuc	0	Nucleus (Probable)				510
O13156 UniProt NPD GO	GFRA1_CHICK	GDNF family receptor alpha-1 precursor (GFR-alpha-1) (GDNF receptor alpha) (GDNFR-alpha) (TGF-beta-r ...	0.93	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				469
Q8VD04 UniProt NPD GO	GRAP1_MOUSE	GRIP1-associated protein 1 (GRASP-1) (HCMV-interacting protein)	0.93	-	nuc	0					806
Q74ZH7 UniProt NPD GO	BEM3_ASHGO	GTPase-activating protein BEM3	0.93	-	nuc	0	Cytoplasm (By similarity)				1013
Q96IK5 UniProt NPD GO	GMCL1_HUMAN	Germ cell-less protein-like 1	0.93	+	mit	0	Nucleus; nucleoplasm; nuclear matrix (By similarity)				515
Q920G9 UniProt NPD GO	GMCL1_MOUSE	Germ cell-less protein-like 1 (mGcl-1) (DP-interacting protein) (DIP)	0.93	+	mit	0	Nucleus; nucleoplasm; nuclear matrix	nuclear matrix [IDA]			524
P55937 UniProt NPD GO	GOGA3_MOUSE	Golgin subfamily A member 3 (Golgin-160) (Male-enhanced antigen 2) (MEA-2)	0.93	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane p ...	ER-Golgi intermediate compartment [IDA] Golgi membrane [IDA]			1487
Q13972 UniProt NPD GO	GNRP_HUMAN	Guanine nucleotide-releasing protein (GNRP) (Ras-specific nucleotide exchange factor CDC25) (Ras-spe ...	0.93	-	nuc	0		plasma membrane [NAS] synaptosome [NAS]	606600		1275
Q06629 UniProt NPD GO	HDA2_YEAST	HDA1 complex subunit 2 (Histone deacetylase complex 1 subunit 2)	0.93	-	nuc	0	Nucleus	histone deacetylase complex [IMP] nucleus [IDA]			674
Q9BW71 UniProt NPD GO	HIRP3_HUMAN	HIRA-interacting protein 3	0.93	-	nuc	0	Nucleus (Potential)	nucleus [TAS]	603365		556
P41153 UniProt NPD GO	HSF8_LYCPE	Heat shock factor protein HSF8 (Heat shock transcription factor 8) (HSTF 8) (Heat stress transcripti ...	0.93	+	nuc	0	Nucleus				527
Q80UW0 UniProt NPD GO	H6ST2_MOUSE	Heparan-sulfate 6-O-sulfotransferase 2 (EC 2.8.2.-) (HS6ST-2) (mHS6ST-2) (Fragment)	0.93	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)				538
P27204 UniProt NPD GO	H1L6_ENSMI	Histone H1-like protein EM6 (Fragments)	0.93	+	mit	0	Nucleus				101
Q5SVQ0 UniProt NPD GO	MYST2_MOUSE	Histone acetyltransferase MYST2 (EC 2.3.1.48) (MYST protein 2) (MOZ, YBF2/SAS3, SAS2 and TIP60 prote ...	0.93	+	nuc	0	Nucleus (By similarity)				613
Q810T5 UniProt NPD GO	MYST2_RAT	Histone acetyltransferase MYST2 (EC 2.3.1.48) (MYST protein 2) (MOZ, YBF2/SAS3, SAS2 and TIP60 prote ...	0.93	+	nuc	0	Nucleus (By similarity)				612
Q2LAE1 UniProt NPD GO	ASHH2_ARATH	Histone-lysine N-methyltransferase, H3 lysine-4 and H3 lysine-36 specific ASHH2 (EC 2.1.1.43) (H3-K4 ...	0.93	-	nuc	0	Nucleus (Probable). Associates with centromeric constitutive heterochromatin (Probable)				1759
Q80W88 UniProt NPD GO	HOMEZ_MOUSE	Homeobox and leucine zipper protein Homez (Homeodomain leucine zipper-containing factor)	0.93	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			518
P46605 UniProt NPD GO	HOX1A_MAIZE	Homeobox protein HOX1A	0.93	+	nuc	0	Nucleus				719
P24061 UniProt NPD GO	HXA7_COTJA	Homeobox protein Hox-A7 (Quox-1)	0.93	+	nuc	0	Nucleus				242

You are viewing entries 2751 to 2800 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.