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
Q9TU53 UniProt NPD GO	CUBN_CANFA	Cubilin precursor	0.44	-	exc	0	Endosome; endosomal membrane; peripheral membrane protein (By similarity). Lysosome; lysosomal membr ...				3620
P22226 UniProt NPD GO	BCTN1_BOVIN	Cyclic dodecapeptide precursor (Bactenecin-1) (Bac1) (Cathelicidin-1)	0.44	-	nuc	0	Secreted protein				155
Q03611 UniProt NPD GO	CNG_CAEEL	Cyclic nucleotide-gated cation channel (Abnormal chemotaxis protein 4)	0.44	-	end	3	Membrane; multi-pass membrane protein (Probable)	integral to membrane [NAS]			733
P14905 UniProt NPD GO	CBS2_YEAST	Cytochrome B translational activator protein CBS2	0.44	-	nuc	0	Mitochondrion	mitochondrial inner membrane [TAS]			389
P20817 UniProt NPD GO	CP4AE_RAT	Cytochrome P450 4A14 precursor (EC 1.14.15.3) (CYPIVA14) (Lauric acid omega-hydroxylase) (P450-LA-om ...	0.44	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				507
Q9V558 UniProt NPD GO	CP4P1_DROME	Cytochrome P450 4p1 (EC 1.14.-.-) (CYPIVP1)	0.44	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				513
O81974 UniProt NPD GO	C71D8_SOYBN	Cytochrome P450 71D8 (EC 1.14.-.-) (P450 CP7)	0.44	-	end	2 *					504
Q63688 UniProt NPD GO	CP7B1_RAT	Cytochrome P450 7B1 (EC 1.14.13.100) (25-hydroxycholesterol 7-alpha-hydroxylase) (Oxysterol 7-alpha- ...	0.44	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				414
Q75D23 UniProt NPD GO	COX20_ASHGO	Cytochrome c oxidase protein 20, mitochondrial precursor	0.44	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				194
Q9C551 UniProt NPD GO	RH5_ARATH	DEAD-box ATP-dependent RNA helicase 5 (EC 3.6.1.-)	0.44	+	cyt	0	Nucleus; nucleolus (By similarity)				537
O35347 UniProt NPD GO	DGCR6_MOUSE	DGCR6 protein (DiGeorge syndrome critical region 6 homolog)	0.44	-	nuc	0					198
Q9ARI6 UniProt NPD GO	CMT2_MAIZE	DNA (cytosine-5)-methyltransferase 2 (EC 2.1.1.37) (Chromomethylase 2) (Zea methyltransferase5) (Zme ...	0.44	+	nuc	0	Nucleus (By similarity)				915
Q7YS61 UniProt NPD GO	DNMT2_BOVIN	DNA (cytosine-5)-methyltransferase-like protein 2 (Dnmt2)	0.44	-	mit	0	Nucleus (Probable)				391
P40087 UniProt NPD GO	DDI1_YEAST	DNA damage-inducible protein DDI1 (v-SNARE-master 1)	0.44	-	nuc	0		plasma membrane [IDA]			428
Q92089 UniProt NPD GO	TDT_ONCMY	DNA nucleotidylexotransferase (EC 2.7.7.31) (Terminal addition enzyme) (Terminal deoxynucleotidyltra ...	0.44	-	nuc	0	Nucleus (By similarity)				501
Q14181 UniProt NPD GO	DPOA2_HUMAN	DNA polymerase subunit alpha B (DNA polymerase alpha 70 kDa subunit)	0.44	-	cyt	0	Nucleus	nucleus [NAS]			598
Q3T0X9 UniProt NPD GO	DPOD4_BOVIN	DNA polymerase subunit delta 4 (DNA polymerase subunit delta p12)	0.44	-	mit	0	Nucleus (By similarity)	nucleus [IC]			107
Q61881 UniProt NPD GO	MCM7_MOUSE	DNA replication licensing factor MCM7 (CDC47 homolog)	0.44	-	cyt	0	Nucleus (By similarity)	nucleus [IDA]			719
Q91WD1 UniProt NPD GO	RPO3D_MOUSE	DNA-directed RNA polymerase III subunit D (EC 2.7.7.6) (DNA-directed RNA polymerase III 47 kDa polyp ...	0.44	-	nuc	0	Nucleus (By similarity)				398
Q6NXY9 UniProt NPD GO	RPO3G_MOUSE	DNA-directed RNA polymerase III subunit G (EC 2.7.7.6) (DNA-directed RNA polymerase III 32 kDa polyp ...	0.44	-	nuc	0	Nucleus (Potential)				223
P09562 UniProt NPD GO	RPOA_MAIZE	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.44	-	cyt	0	Plastid; chloroplast				339
P50546 UniProt NPD GO	RPOB_ARATH	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.44	-	nuc	0	Plastid; chloroplast				1072
Q2MIA8 UniProt NPD GO	RPOB_LYCES	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.44	-	cyt	0	Plastid; chloroplast				1070
Q2MIJ5 UniProt NPD GO	RPOB_SOLBU	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.44	-	cyt	0	Plastid; chloroplast				1070
Q2VEI4 UniProt NPD GO	RPOB_SOLTU	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.44	-	cyt	0	Plastid; chloroplast				1070
O43091 UniProt NPD GO	DPS1_SCHPO	Decaprenyl-diphosphate synthase subunit 1 (EC 2.5.1.-) (Decaprenyl pyrophosphate synthetase subunit ...	0.44	-	mit	0					378
Q4PF67 UniProt NPD GO	DCN1_USTMA	Defective in cullin neddylation protein 1	0.44	-	nuc	0					319
Q8RX73 UniProt NPD GO	DDPS3_ARATH	Dehydrodolichyl diphosphate synthase 3 (EC 2.5.1.-) (Dedol-PP synthase 3)	0.44	-	vac	1 *					302
P02542 UniProt NPD GO	DESM_CHICK	Desmin	0.44	-	mit	0	Cytoplasm				463
P17661 UniProt NPD GO	DESM_HUMAN	Desmin	0.44	-	mit	0	Cytoplasm	intermediate filament [TAS]	604765		469
P02541 UniProt NPD GO	DESM_MESAU	Desmin	0.44	-	mit	0	Cytoplasm				468
Q28060 UniProt NPD GO	DSC3_BOVIN	Desmocollin-3 precursor	0.44	-	end	1	Membrane; single-pass type I membrane protein				896
Q6V1X1 UniProt NPD GO	DPP8_HUMAN	Dipeptidyl peptidase 8 (EC 3.4.14.5) (Dipeptidyl peptidase VIII) (DP8) (Prolyl dipeptidase DPP8) (Di ...	0.44	-	cyt	0	Cytoplasm	cytoplasm [NAS]	606819		898
P82707 UniProt NPD GO	DIUH_ZOONE	Diuretic hormone (DH) (Diuretic peptide) (DP)	0.44	-	nuc	0	Secreted protein				46
P82373 UniProt NPD GO	DIUH_DIPPU	Diuretic hormone class 1 (Diuretic hormone class I) (Diuretic peptide) (DP) (DH(46))	0.44	-	nuc	0	Secreted protein				46
Q9NVH1 UniProt NPD GO	DCJ11_HUMAN	DnaJ homolog subfamily C member 11	0.44	-	cyt	0					559
Q9P104 UniProt NPD GO	DOK5_HUMAN	Docking protein 5 (Downstream of tyrosine kinase 5) (IRS6) (Protein dok-5)	0.44	-	mit	0			608334	1J0W	306
Q8LDR0 UniProt NPD GO	DOF54_ARATH	Dof zinc finger protein DOF5.4 (AtDOF5.4) (OBF-binding protein 4)	0.44	+	nuc	0	Nucleus (Probable)				307
O70146 UniProt NPD GO	TESK1_MOUSE	Dual specificity testis-specific protein kinase 1 (EC 2.7.12.1) (Testicular protein kinase 1)	0.44	-	nuc	0					627
P98110 UniProt NPD GO	LYAM2_PIG	E-selectin precursor (Endothelial leukocyte adhesion molecule 1) (ELAM-1) (Leukocyte-endothelial cel ...	0.44	+	exc	1	Membrane; single-pass type I membrane protein				484
Q9WUF2 UniProt NPD GO	EGR4_MOUSE	Early growth response protein 4 (EGR-4)	0.44	-	nuc	0	Nucleus				478
Q00911 UniProt NPD GO	EGR4_RAT	Early growth response protein 4 (EGR-4) (Early response protein NGFI-C) (Nerve growth factor-induced ...	0.44	-	nuc	0	Nucleus				478
O35709 UniProt NPD GO	ENC1_MOUSE	Ectoderm-neural cortex 1 protein (ENC-1)	0.44	-	mit	0	Cytoplasm. Interacts with the actin cytoskeleton				589
O54693 UniProt NPD GO	EDA_MOUSE	Ectodysplasin-A (EDA protein homolog) (Tabby protein) [Contains: Ectodysplasin-A, membrane form; Ect ...	0.44	-	nuc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	apical part of cell [IDA] endoplasmic reticulum membrane [IDA] integral to plasma membrane [IDA]			391
P97675 UniProt NPD GO	ENPP3_RAT	Ectonucleotide pyrophosphatase/phosphodiesterase 3 (E-NPP 3) (Phosphodiesterase I/nucleotide pyropho ...	0.44	-	nuc	1 *	Membrane; single-pass type II membrane protein	cell surface [TAS]			875
P16521 UniProt NPD GO	EF3A_YEAST	Elongation factor 3A (EF-3A) (EF-3) (Translation elongation factor 3A) (Eukaryotic elongation factor ...	0.44	+	nuc	0	Cytoplasm	ribosome [IDA]			1043
P53978 UniProt NPD GO	EF3B_YEAST	Elongation factor 3B (EF-3B) (Translation elongation factor 3B) (Homolog of EF-3)	0.44	+	cyt	0		cytosolic ribosome (sensu Eukaryota) [IPI]			1043
P35016 UniProt NPD GO	ENPL_CATRO	Endoplasmin homolog precursor (GRP94 homolog)	0.44	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				817
P48299 UniProt NPD GO	EDN3_MOUSE	Endothelin-3 precursor (ET-3) (Preproendothelin-3) (PPET3)	0.44	-	nuc	0	Secreted protein				214
P42893 UniProt NPD GO	ECE1_RAT	Endothelin-converting enzyme 1 (EC 3.4.24.71) (ECE-1)	0.44	-	end	1	Membrane; single-pass type II membrane protein				762

You are viewing entries 28901 to 28950 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.