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
Q15878 UniProt NPD GO	CAC1E_HUMAN	Voltage-dependent R-type calcium channel subunit alpha-1E (Voltage-gated calcium channel subunit alp ...	0.90	+	end	19	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]	601013		2312
Q96JK2 UniProt NPD GO	WDR22_HUMAN	WD repeat protein 22 (Breakpoint cluster region protein 2) (BCRP2)	0.90	-	nuc	0			603812		942
Q99247 UniProt NPD GO	YO087_YEAST	WD repeat protein YOL087C	0.90	-	nuc	0	Cytoplasm	cytoplasm [IDA]			1116
Q9ZUU0 UniProt NPD GO	WRK44_ARATH	WRKY transcription factor 44 (WRKY DNA-binding protein 44) (TRANSPARENT TESTA GLABRA 2)	0.90	-	nuc	0	Nucleus (Probable)				429
Q8R554 UniProt NPD GO	CEZ2_MOUSE	Zinc finger A20 domain-containing protein ? (EC 3.-.-.-) (Zinc finger protein Cezanne 2) (OTU domain ...	0.90	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				926
Q6DD45 UniProt NPD GO	ZCHC8_XENLA	Zinc finger CCHC domain-containing protein 8	0.90	-	nuc	0					743
Q9D9X6 UniProt NPD GO	ZSWM2_MOUSE	Zinc finger SWIM domain-containing protein 2	0.90	-	nuc	0					631
Q9NUA8 UniProt NPD GO	ZBT40_HUMAN	Zinc finger and BTB domain-containing protein 40	0.90	+	nuc	0	Nucleus (Potential)				1239
Q9UDV6 UniProt NPD GO	ZN212_HUMAN	Zinc finger protein 212 (Zinc finger protein C2H2-150)	0.90	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	602386		495
Q96JG9 UniProt NPD GO	ZN469_HUMAN	Zinc finger protein 469 (Fragment)	0.90	+	nuc	0	Nucleus (Potential)				2469
Q9UKS7 UniProt NPD GO	HELI_HUMAN	Zinc finger protein Helios	0.90	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]	606234		526
Q8S9K3 UniProt NPD GO	VAR3_ARATH	Zinc finger protein VAR3, chloroplast precursor (VARIEGATED 3 protein)	0.90	-	mit	0	Plastid; chloroplast				758
Q01954 UniProt NPD GO	BNC1_HUMAN	Zinc finger protein basonuclin-1	0.90	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Relocates to the midpiece of the flagellum durin ...	nucleus [TAS]	601930		994
Q8C0C0 UniProt NPD GO	ZHX2_MOUSE	Zinc fingers and homeoboxes protein 2 (Zinc finger and homeodomain protein 2) (Alpha-fetoprotein reg ...	0.90	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			836
P54103 UniProt NPD GO	ZRF1_MOUSE	Zuotin-related factor 1	0.90	-	nuc	0	Nucleus				514
Q23529 UniProt NPD GO	ZYG12_CAEEL	Zygote defective protein 12	0.90	-	nuc	1	Nucleus; nuclear membrane. Centrosome. Cytoplasmic, localized to the nuclear envelope and centrosome ...				774
Q14432 UniProt NPD GO	PDE3A_HUMAN	cGMP-inhibited 3',5'-cyclic phosphodiesterase A (EC 3.1.4.17) (Cyclic GMP-inhibited phosphodiesteras ...	0.90	-	end	5	Membrane; peripheral membrane protein (Potential)		123805	1LRC	1141
Q4WXX4 UniProt NPD GO	RNA14_ASPFU	mRNA 3'-end processing protein rna14	0.90	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleus and/or cytoplasm (By similarity)				1029
Q2UKV8 UniProt NPD GO	RNA14_ASPOR	mRNA 3'-end processing protein rna14	0.90	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleus and/or cytoplasm (By similarity)				1078
Q5B3I8 UniProt NPD GO	RNA14_EMENI	mRNA 3'-end processing protein rna14	0.90	-	nuc	1	Nucleus (By similarity). Cytoplasm (By similarity). Nucleus and/or cytoplasm (By similarity)				1141
P25298 UniProt NPD GO	RNA14_YEAST	mRNA 3'-end-processing protein RNA14	0.90	-	nuc	0	Nucleus. Cytoplasm. Nucleus and/or cytoplasm	mitochondrion [IDA] mRNA cleavage factor complex [IPI] nucleus [IDA]			677
Q6C2H4 UniProt NPD GO	CET1_YARLI	mRNA capping enzyme subunit beta (EC 3.1.3.33) (Polynucleotide 5'-triphosphatase) (mRNA 5'-triphosph ...	0.90	-	nuc	0	Nucleus (By similarity)				386
Q7RVQ8 UniProt NPD GO	PACC_NEUCR	pH-response transcription factor pacC/RIM101	0.90	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				621
Q9P413 UniProt NPD GO	PACC_SCLSC	pH-response transcription factor pacC/RIM101	0.90	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				625
Q7Z6J9 UniProt NPD GO	SEN54_HUMAN	tRNA-splicing endonuclease subunit Sen54 (tRNA-intron endonuclease Sen54) (HsSen54)	0.90	-	nuc	0	Nucleus (Probable). Nucleus; nucleolus (Probable). May be transiently localized in the nucleolus (Pr ...		608755		526
Q07722 UniProt NPD GO	PLCB4_BOVIN	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (EC 3.1.4.11) (Phosphoinositide pho ...	0.89	-	nuc	0					1023
Q7ZYS1 UniProt NPD GO	RL19_XENLA	60S ribosomal protein L19	0.89	+	nuc	0					197
P12687 UniProt NPD GO	RM02_YEAST	60S ribosomal protein L2, mitochondrial precursor (YmL2) (YMR6)	0.89	-	nuc	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			371
Q99P21 UniProt NPD GO	MUTYH_MOUSE	A/G-specific adenine DNA glycosylase (EC 3.2.2.-) (MutY homolog) (mMYH)	0.89	-	mit	0	Nucleus (By similarity)				515
O15072 UniProt NPD GO	ATS3_HUMAN	ADAMTS-3 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 3) ...	0.89	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [NAS]	605011		1205
P38065 UniProt NPD GO	AP2A_YEAST	AP-2 complex subunit alpha (Alpha-adaptin) (Clathrin assembly protein large alpha chain) (Clathrin a ...	0.89	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane				1025
P20448 UniProt NPD GO	DBP4_YEAST	ATP-dependent RNA helicase DBP4 (EC 3.6.1.-) (DEAD box protein 4) (Helicase CA4) (Helicase UF1)	0.89	+	nuc	0	Nucleus; nucleolus	nucleolus [TAS]			770
Q6CKZ4 UniProt NPD GO	DBP6_KLULA	ATP-dependent RNA helicase DBP6 (EC 3.6.1.-)	0.89	-	nuc	0	Nucleus; nucleolus (By similarity)				630
Q4IJ56 UniProt NPD GO	DBP9_GIBZE	ATP-dependent RNA helicase DBP9 (EC 3.6.1.-)	0.89	+	nuc	0	Nucleus; nucleolus (By similarity)				615
Q5KIK3 UniProt NPD GO	DRS1_CRYNE	ATP-dependent RNA helicase DRS1 (EC 3.6.1.-)	0.89	+	nuc	0	Nucleus; nucleolus (By similarity)				808
Q2UUN6 UniProt NPD GO	HAS1_ASPOR	ATP-dependent RNA helicase has1 (EC 3.6.1.-)	0.89	+	nuc	0	Nucleus; nucleolus (By similarity)				596
Q2TZH2 UniProt NPD GO	MRH4_ASPOR	ATP-dependent RNA helicase mrh4, mitochondrial precursor (EC 3.6.1.-)	0.89	-	mit	0	Mitochondrion (By similarity)				628
P62284 UniProt NPD GO	ASPM_ATEGE	Abnormal spindle-like microcephaly-associated protein homolog (Fragment)	0.89	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...				1564
P32874 UniProt NPD GO	HFA1_YEAST	Acetyl-CoA carboxylase, mitochondrial precursor (EC 6.4.1.2) (ACC) [Includes: Biotin carboxylase (EC ...	0.89	+	nuc	0	Cytoplasm	mitochondrion [IDA]			2273
O13735 UniProt NPD GO	FAT1_SCHPO	Actin-interacting protein 3 homolog	0.89	-	nuc	0					1385
Q9Z103 UniProt NPD GO	ADNP_MOUSE	Activity-dependent neuroprotector (Activity-dependent neuroprotective protein)	0.89	+	nuc	0	Nucleus (Potential)				828
Q9U9K0 UniProt NPD GO	ADD1_CAEEL	Adducin-related protein 1	0.89	+	nuc	0					732
Q6AY08 UniProt NPD GO	AL2SB_RAT	Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 12 protein homolog	0.89	-	nuc	0					411
Q6ZPS6 UniProt NPD GO	AKIB1_MOUSE	Ankyrin repeat and IBR domain-containing protein 1 (Fragment)	0.89	-	nuc	0					1087
O60039 UniProt NPD GO	APSB_EMENI	Anucleate primary sterigmata protein B	0.89	+	nuc	0	Cytoplasm				1051
Q5R6Z9 UniProt NPD GO	DCR1C_PONPY	Artemis protein (EC 3.1.-.-) (DNA cross-link repair 1C protein)	0.89	-	nuc	0	Nucleus (By similarity)				692
P53762 UniProt NPD GO	ARNT_MOUSE	Aryl hydrocarbon receptor nuclear translocator (ARNT protein) (Dioxin receptor, nuclear translocator ...	0.89	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA] transcription factor complex [TAS]			791
P41739 UniProt NPD GO	ARNT_RAT	Aryl hydrocarbon receptor nuclear translocator (ARNT protein) (Dioxin receptor, nuclear translocator ...	0.89	+	nuc	0	Nucleus				800
Q9HBZ2 UniProt NPD GO	ARNT2_HUMAN	Aryl hydrocarbon receptor nuclear translocator 2 (ARNT protein 2)	0.89	+	nuc	0	Nucleus (Potential)	nucleus [IDA]	606036		706
O35625 UniProt NPD GO	AXN1_MOUSE	Axin-1 (Axis inhibition protein 1) (Fused protein)	0.89	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [IDA] cytoplasmic membrane-bound vesicle [IDA]			863

You are viewing entries 4501 to 4550 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.