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
Q12704 UniProt NPD GO	DPOG_SCHPO	DNA polymerase gamma (EC 2.7.7.7) (Mitochondrial DNA polymerase catalytic subunit)	0.56	-	mit	0	Mitochondrion				1018
Q9VPH2 UniProt NPD GO	PRI2_DROME	DNA primase large subunit (EC 2.7.7.-)	0.56	-	cyt	0		alpha DNA polymerase:primase complex [IDA]			533
Q8NK72 UniProt NPD GO	RAD52_MAGGR	DNA repair and recombination protein rhm52 (RAD52 homolog)	0.56	-	nuc	0	Nucleus (By similarity)				565
O43070 UniProt NPD GO	NBS1_SCHPO	DNA repair and telomere maintenance protein nbs1	0.56	-	nuc	0	Nucleus	Mre11 complex [IDA] nucleus [IC]			613
Q2KIZ8 UniProt NPD GO	MCM6_BOVIN	DNA replication licensing factor MCM6	0.56	-	cyt	0	Nucleus (By similarity)				821
Q62724 UniProt NPD GO	MCM6_RAT	DNA replication licensing factor MCM6 (Intestinal DNA replication protein) (Fragment)	0.56	-	mit	0	Nucleus (By similarity)				507
P41389 UniProt NPD GO	MCM5_SCHPO	DNA replication licensing factor mcm5 (Minichromosome maintenance protein 5) (Cell division control ...	0.56	-	cyt	0	Nucleus (Potential)	MCM complex [IDA] nucleus [IDA]			720
O70157 UniProt NPD GO	TOP3A_MOUSE	DNA topoisomerase 3-alpha (EC 5.99.1.2) (DNA topoisomerase III alpha)	0.56	-	nuc	0					1003
P92220 UniProt NPD GO	RPOA_BROIN	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.56	-	cyt	0	Plastid; chloroplast				339
Q5SCX8 UniProt NPD GO	RPOB_HUPLU	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.56	+	cyt	0	Plastid; chloroplast				1080
P16023 UniProt NPD GO	RPOB_MAIZE	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.56	-	nuc	0	Plastid; chloroplast				1075
Q6EW56 UniProt NPD GO	RPOB_NYMAL	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.56	-	nuc	0	Plastid; chloroplast				1071
Q9BBS8 UniProt NPD GO	RPOC1_LOTJA	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.56	-	nuc	0	Plastid; chloroplast				682
P50711 UniProt NPD GO	DEF13_MOUSE	Defensin-related cryptdin 13 precursor	0.56	-	exc	0	Secreted protein				93
Q64016 UniProt NPD GO	DEF17_MOUSE	Defensin-related cryptdin 17 precursor (CRYP17) (Fragment)	0.56	-	nuc	0	Secreted protein				82
P50706 UniProt NPD GO	DEF8_MOUSE	Defensin-related cryptdin 8 precursor (Fragment)	0.56	-	nuc	0	Secreted protein				81
O00933 UniProt NPD GO	GRA7_TOXGO	Dense granule protein 7 precursor (Protein GRA 7) (29 kDa excretory dense granule protein) (p29)	0.56	-	exc	2 *	Secreted protein. Located in dense granules of tachyzoites. Upon infection, secreted into the parasi ...				236
P55849 UniProt NPD GO	DSC1_MOUSE	Desmocollin-1 precursor	0.56	-	end	1	Membrane; single-pass type I membrane protein	desmosome [IDA]			886
O22456 UniProt NPD GO	SEP3_ARATH	Developmental protein SEPALLATA3 (Agamous-like MADS-box protein AGL9)	0.56	-	nuc	0	Nucleus (By similarity)				251
P98078 UniProt NPD GO	DAB2_MOUSE	Disabled homolog 2 (DOC-2) (Mitogen-responsive phosphoprotein)	0.56	-	nuc	0				1P3R	766
P98082 UniProt NPD GO	DAB2_HUMAN	Disabled homolog 2 (Differentially expressed protein 2) (DOC-2)	0.56	-	nuc	0			601236		770
P70175 UniProt NPD GO	DLG3_MOUSE	Discs large homolog 3 (Synapse-associated protein 102) (SAP102)	0.56	-	nuc	0		cytoplasm [IDA]			849
Q8TA83 UniProt NPD GO	DNJ10_CAEEL	DnaJ homolog dnj-10 (DnaJ domain protein 10)	0.56	-	mit	0					456
P25685 UniProt NPD GO	DNJB1_HUMAN	DnaJ homolog subfamily B member 1 (Heat shock 40 kDa protein 1) (Heat shock protein 40) (HSP40) (Dna ...	0.56	-	cyt	0	Cytoplasm. Translocates rapidly from the cytoplasm to the nuclei, and especially to the nucleoli, up ...		604572	1HDJ	339
O82155 UniProt NPD GO	DOF17_ARATH	Dof zinc finger protein DOF1.7 (AtDOF1.7)	0.56	-	nuc	0	Nucleus (Probable)				194
Q8CGW9 UniProt NPD GO	DMRTD_MOUSE	Doublesex- and mab-3-related transcription factor C2 (Doublesex- and mab-3-related transcription fac ...	0.56	-	nuc	0	Nucleus (Potential)				370
Q63932 UniProt NPD GO	MP2K2_MOUSE	Dual specificity mitogen-activated protein kinase kinase 2 (EC 2.7.12.2) (MAP kinase kinase 2) (MAPK ...	0.56	-	mit	0					401
Q9UI46 UniProt NPD GO	DNAI1_HUMAN	Dynein intermediate chain 1, axonemal (Axonemal dynein intermediate chain 1)	0.56	-	nuc	0		cilium [TAS] cytoskeleton [TAS]	604366		699
Q8R368 UniProt NPD GO	DYXC1_MOUSE	Dyslexia susceptibility 1 candidate gene 1 protein homolog	0.56	-	nuc	0	Nucleus (By similarity)				420
Q13474 UniProt NPD GO	DRP2_HUMAN	Dystrophin-related protein 2	0.56	+	nuc	0			300052		954
Q96CJ1 UniProt NPD GO	EAF2_HUMAN	ELL-associated factor 2 (Testosterone-regulated apoptosis inducer and tumor suppressor protein)	0.56	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Colocalizes with ELL to nuclear speckles		607659		260
Q9BZQ6 UniProt NPD GO	EDEM3_HUMAN	ER degradation-enhancing alpha-mannosidase-like 3	0.56	-	end	0	Endoplasmic reticulum (Potential)				889
Q08109 UniProt NPD GO	HRD1_YEAST	ERAD-associated E3 ubiquitin-protein ligase HDR1 (EC 6.3.2.-) (HMG-CoA reductase degradation protein ...	0.56	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum membrane [IDA]			551
P61554 UniProt NPD GO	EFR1_GORGO	ERV-FRD provirus ancestral Env polyprotein precursor (Envelope polyprotein) (Syncytin-2) [Contains: ...	0.56	-	exc	2					538
P61557 UniProt NPD GO	EFR1_PANTR	ERV-FRD provirus ancestral Env polyprotein precursor (Envelope polyprotein) (Syncytin-2) [Contains: ...	0.56	-	exc	2					538
P22413 UniProt NPD GO	ENPP1_HUMAN	Ectonucleotide pyrophosphatase/phosphodiesterase 1 (E-NPP 1) (Phosphodiesterase I/nucleotide pyropho ...	0.56	-	nuc	1	Membrane; single-pass type II membrane protein	integral to membrane [TAS] membrane [TAS]	602475		925
Q756F2 UniProt NPD GO	PPN1_ASHGO	Endopolyphosphatase (EC 3.6.1.10)	0.56	-	nuc	0	Vacuole; vacuolar membrane; single-pass type II membrane protein				594
P23769 UniProt NPD GO	GATA2_HUMAN	Endothelial transcription factor GATA-2 (GATA-binding protein 2)	0.56	-	nuc	0	Nucleus	nucleus [TAS]	137295		480
P05305 UniProt NPD GO	EDN1_HUMAN	Endothelin-1 precursor (Preproendothelin-1) (PPET1) [Contains: Endothelin-1 (ET-1); Big endothelin-1 ...	0.56	-	nuc	0	Secreted protein	extracellular space [TAS] soluble fraction [TAS]	131240	1V6R	212
Q9Z2B5 UniProt NPD GO	E2AK3_MOUSE	Eukaryotic translation initiation factor 2-alpha kinase 3 precursor (EC 2.7.11.1) (PRKR-like endopla ...	0.56	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	cytoplasm [IDA]			1114
O77503 UniProt NPD GO	I2C2_RABIT	Eukaryotic translation initiation factor 2C 2 (eIF2C 2) (eIF-2C 2) (Argonaute-2) (Fragment)	0.56	-	cyt	0	Cytoplasm; cytoplasmic bodies (By similarity)				840
Q3T102 UniProt NPD GO	IF36_BOVIN	Eukaryotic translation initiation factor 3 subunit 6 (eIF-3 p48) (eIF3e)	0.56	-	cyt	0	Cytoplasm (By similarity)				445
P60229 UniProt NPD GO	IF36_MOUSE	Eukaryotic translation initiation factor 3 subunit 6 (eIF-3 p48) (eIF3e) (Mammary tumor-associated p ...	0.56	-	cyt	0	Cytoplasm				445
P60228 UniProt NPD GO	IF36_HUMAN	Eukaryotic translation initiation factor 3 subunit 6 (eIF-3 p48) (eIF3e) (Viral integration site pro ...	0.56	-	cyt	0	Cytoplasm		602210		445
Q9DC63 UniProt NPD GO	FBX3_MOUSE	F-box only protein 3	0.56	-	cyt	0					480
Q5E9G6 UniProt NPD GO	FBX8_BOVIN	F-box only protein 8	0.56	-	nuc	0					319
Q9NRD0 UniProt NPD GO	FBX8_HUMAN	F-box only protein 8 (F-box/SEC7 protein FBS)	0.56	-	nuc	0		ubiquitin ligase complex [NAS]	605649		319
Q25011 UniProt NPD GO	FANA_HELAS	FMRFamide-activated amiloride-sensitive sodium channel (FANACH)	0.56	-	mit	1	Membrane; multi-pass membrane protein				625
Q9GM96 UniProt NPD GO	RFRP_BOVIN	FMRFamide-related peptides precursor [Contains: Neuropeptide RFRP-1; Neuropeptide RFRP-2; Neuropepti ...	0.56	-	exc	0	Secreted protein				196
P97808 UniProt NPD GO	FXYD5_MOUSE	FXYD domain-containing ion transport regulator 5 precursor (Oncoprotein-induced protein 2) (Ion chan ...	0.56	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				184

You are viewing entries 21301 to 21350 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.