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
Q6TCG2 UniProt NPD GO	PAQR9_MOUSE	Progestin and adipoQ receptor family member 9 (Progestin and adipoQ receptor family member IX)	0.13	-	end	6	Membrane; multi-pass membrane protein (Potential)				375
P07490 UniProt NPD GO	GON1_RAT	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.13	-	end	0	Secreted protein				92
O95831 UniProt NPD GO	PDCD8_HUMAN	Programmed cell death protein 8, mitochondrial precursor (EC 1.-.-.-) (Apoptosis-inducing factor)	0.13	-	mit	0	Mitochondrion; mitochondrial intermembrane space. Nucleus. Translocated to the nucleus upon inductio ...	mitochondrion [TAS] nucleus [TAS]	300169	1M6I	613
Q9JHZ2 UniProt NPD GO	ANKH_MOUSE	Progressive ankylosis protein (Fn54 protein)	0.13	-	end	8 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [IDA] outer membrane [IEP]			492
Q9NZ81 UniProt NPD GO	PRR13_HUMAN	Proline-rich protein 13	0.13	-	nuc	0					148
P43119 UniProt NPD GO	PI2R_HUMAN	Prostacyclin receptor (Prostanoid IP receptor) (PGI receptor) (Prostaglandin I2 receptor)	0.13	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600022		386
Q9H7Z7 UniProt NPD GO	PGES2_HUMAN	Prostaglandin E synthase 2 (EC 5.3.99.3) (Microsomal prostaglandin E synthase 2) (mPGES-2) [Contains ...	0.13	-	mit	0	Golgi apparatus; Golgi membrane; single-pass membrane protein. Processed form: Cytoplasm; perinuclea ...		608152		377
O97921 UniProt NPD GO	PTGDS_HORSE	Prostaglandin-H2 D-isomerase precursor (EC 5.3.99.2) (Lipocalin-type prostaglandin-D synthase) (Glut ...	0.13	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Detected on rough endoplasmic re ...	extracellular region [IDA] Golgi apparatus [ISS] nuclear envelope [ISS] rough endoplasmic reticulum [ISS]			194
P22057 UniProt NPD GO	PTGDS_RAT	Prostaglandin-H2 D-isomerase precursor (EC 5.3.99.2) (Lipocalin-type prostaglandin-D synthase) (Glut ...	0.13	-	end	0	Endoplasmic reticulum; rough endoplasmic reticulum. Detected on rough endoplasmic reticulum of arach ...	extracellular region [IDA] Golgi apparatus [IDA] nuclear envelope [NAS] rough endoplasmic reticulum [ISS]			189
P23639 UniProt NPD GO	PSA2_YEAST	Proteasome component Y7 (EC 3.4.25.1) (Macropain subunit Y7) (Proteinase YSCE subunit 7) (Multicatal ...	0.13	-	cyt	0	Cytoplasm. Nucleus	proteasome core complex, alpha-subunit comp... [IPI]		2FNY	250
O42265 UniProt NPD GO	PSA1_CHICK	Proteasome subunit alpha type 1 (EC 3.4.25.1) (Proteasome component C2) (Macropain subunit C2) (Mult ...	0.13	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				260
Q24178 UniProt NPD GO	PSA72_DROME	Proteasome subunit alpha type 7-1A (EC 3.4.25.1) (Testis-specific proteasome 28 kDa subunit 1A) (Tes ...	0.13	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				249
Q29576 UniProt NPD GO	PSB8_PIG	Proteasome subunit beta type 8 (EC 3.4.25.1) (Proteasome component C13) (Macropain subunit C13) (Mul ...	0.13	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				104
P28064 UniProt NPD GO	PSB8_RAT	Proteasome subunit beta type 8 precursor (EC 3.4.25.1) (Proteasome component C13) (Macropain subunit ...	0.13	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	proteasome core complex (sensu Eukaryota) [TAS]			276
Q91WC1 UniProt NPD GO	POTE1_MOUSE	Protection of telomeres 1 (mPot1) (POT1-like telomere end-binding protein)	0.13	-	nuc	0	Nucleus (By similarity). Colocalizes with telomeric DNA (By similarity)				640
Q9CAQ2 UniProt NPD GO	Y1754_ARATH	Protein At1g77540	0.13	-	nuc	0				2GDB	114
Q9CYH2 UniProt NPD GO	CJ058_MOUSE	Protein C10orf58 homolog precursor	0.13	-	cyt	1 *	Secreted protein (Potential)				218
Q8WW14 UniProt NPD GO	CJ082_HUMAN	Protein C10orf82	0.13	-	nuc	0					154
Q8BJ63 UniProt NPD GO	CN108_MOUSE	Protein C14orf108 homolog	0.13	-	mit	0					490
Q9CR63 UniProt NPD GO	CN112_MOUSE	Protein C14orf112 homolog precursor	0.13	-	mit	0					106
Q5RCY6 UniProt NPD GO	CN112_PONPY	Protein C14orf112 homolog precursor	0.13	-	nuc	1 *					106
Q9P0S2 UniProt NPD GO	CN112_HUMAN	Protein C14orf112 precursor	0.13	-	nuc	1 *					106
Q9BTJ7 UniProt NPD GO	CU097_HUMAN	Protein C21orf97	0.13	-	nuc	0					228
Q8BZI6 UniProt NPD GO	CV013_MOUSE	Protein C22orf13 homolog	0.13	-	cyt	0					239
Q5ZKP2 UniProt NPD GO	CB025_CHICK	Protein C2orf25 homolog, mitochondrial precursor	0.13	-	mit	0	Mitochondrion (Potential)				296
Q9CWV0 UniProt NPD GO	CG030_MOUSE	Protein C7orf30 homolog	0.13	-	mit	0					228
Q9BV86 UniProt NPD GO	CI032_HUMAN	Protein C9orf32	0.13	-	cyt	0				2EX4	222
Q6P6V6 UniProt NPD GO	GP108_RAT	Protein GPR108 precursor	0.13	-	end	7	Membrane; multi-pass membrane protein				577
Q9CX00 UniProt NPD GO	K0174_MOUSE	Protein KIAA0174	0.13	-	mit	0					362
Q6SEH5 UniProt NPD GO	LDOC1_GORGO	Protein LDOC1	0.13	-	mit	0	Nucleus (By similarity)				145
Q6SEH4 UniProt NPD GO	LDOC1_PANPA	Protein LDOC1	0.13	-	mit	0	Nucleus (By similarity)				146
O95751 UniProt NPD GO	LDOC1_HUMAN	Protein LDOC1 (Leucine zipper protein down-regulated in cancer cells)	0.13	-	mit	0	Nucleus	nucleus [TAS]	300402		146
Q6DIX1 UniProt NPD GO	NDRG4_XENTR	Protein NDRG4	0.13	-	end	0					405
O96690 UniProt NPD GO	PDF_DROME	Protein PDF precursor [Contains: PDF precursor-related peptide (PAP); Neuropeptide PDF (Pigment-disp ...	0.13	-	exc	1 *	Secreted protein (By similarity)	extracellular region [IC]			102
P16148 UniProt NPD GO	PLZ12_LUPPO	Protein PPLZ12	0.13	-	cyt	0					184
Q05676 UniProt NPD GO	SOM1_YEAST	Protein SOM1, mitochondrial precursor	0.13	-	nuc	0	Mitochondrion; mitochondrial inner membrane (Potential)	mitochondrial inner membrane peptidase complex [IPI]			74
Q86Y78 UniProt NPD GO	U3023_HUMAN	Protein UNQ3023/PRO9821 precursor	0.13	-	nuc	0	Secreted protein (Probable)				171
P28113 UniProt NPD GO	WNT1_EUMSK	Protein Wnt-1 (Fragment)	0.13	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				126
P27467 UniProt NPD GO	WNT3A_MOUSE	Protein Wnt-3a precursor	0.13	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	extracellular space [IDA]			352
P31285 UniProt NPD GO	WNT3A_XENLA	Protein Wnt-3a precursor (XWnt-3a)	0.13	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix				352
P28103 UniProt NPD GO	WNT5A_ALOVU	Protein Wnt-5a (Fragment)	0.13	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				116
P28104 UniProt NPD GO	WNT5B_ALOVU	Protein Wnt-5b (Fragment)	0.13	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				116
O00755 UniProt NPD GO	WNT7A_HUMAN	Protein Wnt-7a precursor	0.13	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix		601570		349
P28106 UniProt NPD GO	WNT7B_ALOVU	Protein Wnt-7b (Fragment)	0.13	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
Q9NR22 UniProt NPD GO	ANM8_HUMAN	Protein arginine N-methyltransferase 8 (EC 2.1.1.-) (Heterogeneous nuclear ribonucleoprotein methylt ...	0.13	-	mit	0		plasma membrane [IDA]			394
P13667 UniProt NPD GO	PDIA4_HUMAN	Protein disulfide-isomerase A4 precursor (EC 5.3.4.1) (Protein ERp-72) (ERp72)	0.13	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum lumen [TAS]			645
Q09566 UniProt NPD GO	LON1_CAEEL	Protein lon-1 precursor	0.13	-	nuc	0					312
P40371 UniProt NPD GO	PP2C1_SCHPO	Protein phosphatase 2C homolog 1 (EC 3.1.3.16) (PP2C-1)	0.13	-	cyt	0					347
O62830 UniProt NPD GO	PP2CB_BOVIN	Protein phosphatase 2C isoform beta (EC 3.1.3.16) (PP2C-beta)	0.13	+	cyt	0					484
Q4IQC1 UniProt NPD GO	PPME1_GIBZE	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.13	-	cyt	0					400

You are viewing entries 60251 to 60300 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.