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
Q9BBT7 UniProt NPD GO	NUKC_LOTJA	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.48	-	nuc	0	Plastid; chloroplast				230
P00365 UniProt NPD GO	DHE2_NEUCR	NAD-specific glutamate dehydrogenase (EC 1.4.1.2) (NAD-GDH)	0.48	-	cyt	0					1050
P42114 UniProt NPD GO	NDUA6_NEUCR	NADH-ubiquinone oxidoreductase 14.8 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-14.8KD) (CI-14 ...	0.48	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side. The import of this subunit is dependent on ...				123
Q9CZ44 UniProt NPD GO	NSF1C_MOUSE	NSFL1 cofactor p47 (p97 cofactor p47)	0.48	-	cyt	0	Nucleus (By similarity). Predominantly nuclear in interphase cells. Bound to the axial elements of s ...				370
O35987 UniProt NPD GO	NSF1C_RAT	NSFL1 cofactor p47 (p97 cofactor p47) (XY body-associated protein XY40)	0.48	-	cyt	0	Nucleus. Predominantly nuclear in interphase cells. Bound to the axial elements of sex chromosomes i ...			1VAZ	370
P28038 UniProt NPD GO	FL3H_HORVU	Naringenin,2-oxoglutarate 3-dioxygenase (EC 1.14.11.9) (Flavonone-3-hydroxylase) (F3H) (FHT)	0.48	+	cyt	0					377
P08049 UniProt NPD GO	NEP_RABIT	Neprilysin (EC 3.4.24.11) (Neutral endopeptidase) (NEP) (Enkephalinase) (Neutral endopeptidase 24.11 ...	0.48	-	mit	1 *	Membrane; single-pass type II membrane protein				749
P08473 UniProt NPD GO	NEP_HUMAN	Neprilysin (EC 3.4.24.11) (Neutral endopeptidase) (NEP) (Enkephalinase) (Neutral endopeptidase 24.11 ...	0.48	-	cyt	1 *	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	108970	1Y8J	749
Q8JGT4 UniProt NPD GO	UNC5B_XENLA	Netrin receptor UNC5B precursor (UNC-5 homolog) (Protein XUNC-5)	0.48	-	exc	2 *	Membrane; single-pass type I membrane protein (By similarity)				943
O95185 UniProt NPD GO	UNC5C_HUMAN	Netrin receptor UNC5C precursor (Unc-5 homolog C) (Unc-5 homolog 3)	0.48	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)		603610		931
P21661 UniProt NPD GO	NEC2_MOUSE	Neuroendocrine convertase 2 precursor (EC 3.4.21.94) (NEC 2) (PC2) (Prohormone convertase 2) (Propro ...	0.48	-	cyt	0	Secretory vesicle. Localized in the secretion granules				637
P28841 UniProt NPD GO	NEC2_RAT	Neuroendocrine convertase 2 precursor (EC 3.4.21.94) (NEC 2) (PC2) (Prohormone convertase 2) (Propro ...	0.48	-	cyt	0	Secretory vesicle. Localized in the secretion granules				637
P07197 UniProt NPD GO	NFM_HUMAN	Neurofilament triplet M protein (160 kDa neurofilament protein) (Neurofilament medium polypeptide) ( ...	0.48	-	nuc	0		axon [TAS] neurofilament [TAS]	162250		915
Q62765 UniProt NPD GO	NLGN1_RAT	Neuroligin-1 precursor (Neuroligin I)	0.48	-	cyt	1 *	Cell membrane; single-pass type I membrane protein. Enriched in synaptic plasma membranes and cluste ...	integral to plasma membrane [ISS] synapse [IDA]			843
P42675 UniProt NPD GO	NEUL_RABIT	Neurolysin, mitochondrial precursor (EC 3.4.24.16) (Neurotensin endopeptidase) (Mitochondrial oligop ...	0.48	-	mit	0	Mitochondrion (By similarity). Cytoplasm (By similarity)				704
Q5IS67 UniProt NPD GO	NEUM_PANTR	Neuromodulin (Axonal membrane protein GAP-43) (Growth-associated protein 43)	0.48	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity). Cytoplasmic surface of ...				238
P06836 UniProt NPD GO	NEUM_BOVIN	Neuromodulin (Axonal membrane protein GAP-43) (Growth-associated protein 43) (Calmodulin-binding pro ...	0.48	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic surface of growth cone and ...				242
P17677 UniProt NPD GO	NEUM_HUMAN	Neuromodulin (Axonal membrane protein GAP-43) (Growth-associated protein 43) (PP46) (Neural phosphop ...	0.48	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic surface of growth cone and ...		162060		238
Q9ESI7 UniProt NPD GO	DCX_RAT	Neuronal migration protein doublecortin	0.48	-	nuc	0	Cytoplasm (Potential)				365
O88809 UniProt NPD GO	DCX_MOUSE	Neuronal migration protein doublecortin (Lissencephalin-X) (Lis-X) (Doublin)	0.48	-	nuc	0	Cytoplasm (Potential)				366
Q13253 UniProt NPD GO	NOGG_HUMAN	Noggin precursor	0.48	-	nuc	0	Secreted protein	extracellular space [TAS]	184460	1M4U	232
P97466 UniProt NPD GO	NOGG_MOUSE	Noggin precursor	0.48	-	nuc	0	Secreted protein	extracellular space [IDA]			232
Q9W740 UniProt NPD GO	NOGG2_BRARE	Noggin-2 precursor	0.48	-	exc	0	Secreted protein				212
Q60HE4 UniProt NPD GO	NDP_MACFA	Norrin precursor (Norrie disease protein homolog)	0.48	-	mit	0	Secreted protein (Potential)				133
Q00604 UniProt NPD GO	NDP_HUMAN	Norrin precursor (Norrie disease protein)	0.48	-	mit	0	Secreted protein (Potential)	extracellular space [TAS]	310600		133
O18087 UniProt NPD GO	NH127_CAEEL	Nuclear hormone receptor family member nhr-127	0.48	-	cyt	0	Nucleus (Potential)				355
O01930 UniProt NPD GO	NH136_CAEEL	Nuclear hormone receptor family member nhr-136	0.48	-	nuc	0	Nucleus (Potential)				435
Q17771 UniProt NPD GO	NHR35_CAEEL	Nuclear hormone receptor family member nhr-35	0.48	-	nuc	0	Nucleus (Potential)				542
Q95X91 UniProt NPD GO	NHR96_CAEEL	Nuclear hormone receptor family member nhr-96	0.48	-	mit	0	Nucleus (Potential)				402
Q9FMV5 UniProt NPD GO	NFYC4_ARATH	Nuclear transcription factor Y subunit C-4 (AtNF-YC-4)	0.48	+	nuc	0	Nucleus (By similarity)				250
Q80W85 UniProt NPD GO	NPM2_MOUSE	Nucleoplasmin-2	0.48	+	nuc	0	Nucleus. Found in the oocyte nucleus before nuclear membrane breakdown, after which it is redistribu ...	cytoplasmic chromatin [ISS] nuclear chromatin [ISS] nucleus [ISS]			207
Q7SZC5 UniProt NPD GO	NDC1_BRARE	Nucleoporin NDC1 (Transmembrane protein 48)	0.48	-	end	6 *	Nucleus; nuclear envelope; nuclear pore complex; central core structure; multi-pass membrane protein ...				671
Q8R4R6 UniProt NPD GO	NUP53_MOUSE	Nucleoporin NUP53 (Nuclear pore complex protein Nup53) (Nucleoporin Nup35) (35 kDa nucleoporin) (Mit ...	0.48	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity). Tightly associated with the nuclear ...			1WWH	325
Q60M68 UniProt NPD GO	NDC1_CAEBR	Nucleoporin ndc-1	0.48	-	end	5	Nucleus; nuclear envelope; nuclear pore complex; central core structure; multi-pass membrane protein ...				587
Q758U2 UniProt NPD GO	SIL1_ASHGO	Nucleotide exchange factor SIL1 precursor	0.48	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				383
P18750 UniProt NPD GO	ZO61_XENLA	Oocyte zinc finger protein XLCOF6.1 (Fragment)	0.48	-	nuc	0	Nucleus (Potential)				224
Q14995 UniProt NPD GO	NR1D2_HUMAN	Orphan nuclear receptor NR1D2 (Rev-erb-beta) (EAR-1R) (Orphan nuclear hormone receptor BD73)	0.48	-	nuc	0	Nucleus (By similarity)	nucleus [TAS]	602304		579
P23498 UniProt NPD GO	OSTP_CHICK	Osteopontin precursor (Bone sialoprotein-1) (Secreted phosphoprotein 1) (SPP-1)	0.48	-	exc	0	Secreted protein				264
P31098 UniProt NPD GO	OSTK_BOVIN	Osteopontin-K precursor	0.48	-	exc	0	Secreted protein				277
Q9H5P4 UniProt NPD GO	PDZD7_HUMAN	PDZ domain-containing protein 7	0.48	-	nuc	0					517
Q9NQV7 UniProt NPD GO	PRDM9_HUMAN	PR domain zinc finger protein 9 (PR domain-containing protein 9)	0.48	-	nuc	0	Nucleus (Potential)		609760		689
Q9NAN2 UniProt NPD GO	PAR6_CAEEL	Partitioning defective protein 6	0.48	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Membrane-associated at the periphery of blastomere ...	cytoplasm [IDA] integral to membrane [IDA]			309
Q8K126 UniProt NPD GO	RF1M_MOUSE	Peptide chain release factor 1, mitochondrial precursor (MRF-1)	0.48	-	mit	0	Mitochondrion				446
Q60HE1 UniProt NPD GO	PEX3_MACFA	Peroxisomal biogenesis factor 3 (Peroxin-3) (Peroxisomal assembly protein PEX3)	0.48	-	nuc	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein (By similarity)				373
Q9UVU5 UniProt NPD GO	PEX6_PICAN	Peroxisomal biogenesis factor 6 (Peroxin-6)	0.48	-	nuc	0					1135
Q9HG09 UniProt NPD GO	PEX14_PICPA	Peroxisomal membrane protein PEX14 (Peroxin-14)	0.48	-	nuc	0	Peroxisome; peroxisomal membrane; peripheral membrane protein; cytoplasmic side	peroxisomal membrane [IDA]			425
Q6BM14 UniProt NPD GO	PEX5_DEBHA	Peroxisomal targeting signal receptor (Peroxin-5) (PTS1 receptor)	0.48	-	nuc	0	Cytoplasm (By similarity). Peroxisome; peroxisomal membrane; peripheral membrane protein (By similar ...				603
Q28177 UniProt NPD GO	BFSP2_BOVIN	Phakinin (Beaded filament structural protein 2) (Lens fiber cell beaded filament protein CP 49) (CP4 ...	0.48	-	mit	0	Membrane. Cytoplasm. Membrane- and cytoskeleton-associated				415
P16331 UniProt NPD GO	PH4H_MOUSE	Phenylalanine-4-hydroxylase (EC 1.14.16.1) (PAH) (Phe-4-monooxygenase)	0.48	-	cyt	0					452
P04176 UniProt NPD GO	PH4H_RAT	Phenylalanine-4-hydroxylase (EC 1.14.16.1) (PAH) (Phe-4-monooxygenase)	0.48	-	cyt	0				2PHM	452

You are viewing entries 26401 to 26450 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.