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
Q9D7M1 UniProt NPD GO	CT011_MOUSE	Protein C20orf11 homolog (Two-hybrid associated protein 1 with RanBPM) (Twa1)	0.33	-	cyt	0	Nucleus (By similarity)				228
Q9Y316 UniProt NPD GO	CB004_HUMAN	Protein C2orf4 (C21orf19-like protein)	0.33	-	nuc	0					297
O74388 UniProt NPD GO	YNVD_SCHPO	Protein C3H7.13 in chromosome II	0.33	-	nuc	1	Nucleus				301
Q9USJ7 UniProt NPD GO	YJ27_SCHPO	Protein C4B3.07 in chromosome III	0.33	-	mit	0	Cytoplasm. Nucleus	nuclear pore [TAS] nucleus [IDA]			393
Q96JD4 UniProt NPD GO	CF114_HUMAN	Protein C6orf114 (Protein ADG-90)	0.33	-	mit	0					136
Q96G30 UniProt NPD GO	CF117_HUMAN	Protein C6orf117	0.33	-	mit	1 *					205
Q9P0P8 UniProt NPD GO	CF203_HUMAN	Protein C6orf203	0.33	+	mit	0					240
P37267 UniProt NPD GO	CBP4_YEAST	Protein CBP4, mitochondrial precursor	0.33	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane. Associated with the inner membrane	mitochondrial envelope [TAS]			170
P38363 UniProt NPD GO	COS2_YEAST	Protein COS2/COS3	0.33	-	vac	4 *	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			379
Q9P144 UniProt NPD GO	CY014_HUMAN	Protein CYorf14	0.33	-	nuc	1 *					113
Q6MG64 UniProt NPD GO	G7C_RAT	Protein G7c precursor	0.33	-	mit	0					892
P53389 UniProt NPD GO	HOL1_YEAST	Protein HOL1	0.33	-	end	10	Membrane; multi-pass membrane protein (Probable)	mitochondrion [IDA] plasma membrane [IMP]			586
Q80U56 UniProt NPD GO	K0241_MOUSE	Protein KIAA0241	0.33	-	cyt	0	Membrane; single-pass membrane protein (Potential)				649
P53583 UniProt NPD GO	MPA43_YEAST	Protein MPA43	0.33	-	cyt	0		mitochondrion [IDA]			542
Q8VBU2 UniProt NPD GO	NDRG2_RAT	Protein NDRG2 (NDRG1-related protein) (Antidepressant-related protein ADRG123)	0.33	-	nuc	0	Cytoplasm (By similarity). In neurons, seems to concentrate at axonal growth cone				371
Q9QYG0 UniProt NPD GO	NDRG2_MOUSE	Protein NDRG2 (Protein Ndr2)	0.33	-	nuc	0	Cytoplasm				371
Q6NYE2 UniProt NPD GO	RCC2_BRARE	Protein RCC2 homolog	0.33	+	cyt	0	Nucleus; nucleolus (By similarity)				495
P10108 UniProt NPD GO	WNT1_XENLA	Protein Wnt-1 precursor (XWnt-1) (XInt-1)	0.33	-	exc	0	Secreted protein; extracellular space; extracellular matrix				371
Q92048 UniProt NPD GO	WNT2_BRARE	Protein Wnt-2 precursor	0.33	-	mit	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [NAS]			350
Q9Y6F9 UniProt NPD GO	WNT6_HUMAN	Protein Wnt-6 precursor	0.33	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix	extracellular region [NAS]	604663		365
Q64527 UniProt NPD GO	WNT8A_MOUSE	Protein Wnt-8a precursor (Wnt-8d) (Stimulated by retinoic acid protein 11) (Wnt-8)	0.33	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				354
O14904 UniProt NPD GO	WNT9A_HUMAN	Protein Wnt-9a precursor (Wnt-14)	0.33	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix	extracellular region [NAS]	602863		365
O75695 UniProt NPD GO	XRP2_HUMAN	Protein XRP2	0.33	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side		312600	2BX6	349
Q6NZB1 UniProt NPD GO	ANM6_MOUSE	Protein arginine N-methyltransferase 6 (EC 2.1.1.-) (Heterogeneous nuclear ribonucleoprotein methylt ...	0.33	-	cyt	0	Nucleus (By similarity)				378
Q9Z1K5 UniProt NPD GO	ARI1_MOUSE	Protein ariadne-1 homolog (ARI-1) (Ubiquitin-conjugating enzyme E2-binding protein 1) (UbcH7-binding ...	0.33	-	cyt	0	Cytoplasm (By similarity)				555
Q9Y4X5 UniProt NPD GO	ARI1_HUMAN	Protein ariadne-1 homolog (ARI-1) (Ubiquitin-conjugating enzyme E2-binding protein 1) (UbcH7-binding ...	0.33	-	cyt	0	Cytoplasm. Mainly	ubiquitin ligase complex [TAS]	605624	1WD2	557
P16914 UniProt NPD GO	ELAV_DROME	Protein elav (Embryonic lethal abnormal visual protein)	0.33	-	cyt	0		Cajal body [IDA] nucleus [IDA]			483
Q10459 UniProt NPD GO	MOM2_CAEEL	Protein mom-2 precursor	0.33	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix				362
Q7RYM7 UniProt NPD GO	PBN1_NEUCR	Protein pbn-1	0.33	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				501
Q8BVQ5 UniProt NPD GO	PPME1_MOUSE	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.33	-	mit	0					385
Q7SGG8 UniProt NPD GO	PPME1_NEUCR	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.33	-	nuc	0					454
Q09912 UniProt NPD GO	PSI1_SCHPO	Protein psi1 (Protein psi)	0.33	-	cyt	0					379
P87216 UniProt NPD GO	VIP1_SCHPO	Protein vip1	0.33	-	nuc	0					257
O43548 UniProt NPD GO	TGM5_HUMAN	Protein-glutamine gamma-glutamyltransferase 5 (EC 2.3.2.13) (Transglutaminase-5) (TGase 5) (Transglu ...	0.33	-	cyt	0	Cytoplasm. Associated with intermediate filaments		609796		719
Q9Y5I2 UniProt NPD GO	PCDAA_HUMAN	Protocadherin alpha 10 precursor (PCDH-alpha10)	0.33	+	end	1 *	Cell membrane; single-pass type I membrane protein (By similarity). Isoform 2: Secreted protein (Pot ...	integral to plasma membrane [TAS]	606316		948
Q5DRF4 UniProt NPD GO	PCDAA_PANTR	Protocadherin alpha 10 precursor (PCDH-alpha10)	0.33	+	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				948
Q5DRF1 UniProt NPD GO	PCDAD_PANTR	Protocadherin alpha 13 precursor (PCDH-alpha13)	0.33	+	nuc	0	Membrane; single-pass type I membrane protein (By similarity)				950
Q5DRE0 UniProt NPD GO	PCDB1_PANTR	Protocadherin beta 1 precursor (PCDH-beta1)	0.33	-	mit	2 *	Membrane; single-pass type I membrane protein (By similarity)				818
Q5DRD6 UniProt NPD GO	PCDBD_PANTR	Protocadherin beta 13 precursor (PCDH-beta13)	0.33	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				798
Q96JQ0 UniProt NPD GO	PCD16_HUMAN	Protocadherin-16 precursor (Dachsous 1) (Cadherin-19) (Fibroblast cadherin 1)	0.33	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)	membrane [NAS]	603057		3298
P0C150 UniProt NPD GO	COX10_MAGGR	Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) (Heme O synthase)	0.33	-	end	8	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				552
Q7XNS7 UniProt NPD GO	ARD3_ORYSA	Putative 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 3 (EC 1.13.-.-) (Aci-reductone dioxyge ...	0.33	-	cyt	0					206
O01513 UniProt NPD GO	YS4L_CAEEL	Putative 40S ribosomal protein S4-like	0.33	-	cyt	0	Mitochondrion (Potential)				183
Q9VR93 UniProt NPD GO	RL33_DROME	Putative 60S ribosomal protein L33	0.33	-	nuc	1 *					63
Q5R889 UniProt NPD GO	SAHH3_PONPY	Putative adenosylhomocysteinase 3 (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase 3) (AdoHcyase 3) ...	0.33	-	cyt	0					508
Q9C502 UniProt NPD GO	CAP11_ARATH	Putative clathrin assembly protein At1g33340	0.33	-	mit	0					374
Q9LQZ2 UniProt NPD GO	DRE2D_ARATH	Putative dehydration-responsive element-binding protein 2D (DREB2D protein)	0.33	-	nuc	0	Nucleus (Probable)				206
Q9BXT6 UniProt NPD GO	M10L1_HUMAN	Putative helicase Mov10l1 (EC 3.6.1.-) (Moloney leukemia virus 10-like protein 1) (MOV10-like 1)	0.33	-	cyt	0		intracellular [IC]	605794		1211
Q9SHZ1 UniProt NPD GO	DEGP3_ARATH	Putative protease Do-like 3, mitochondrial precursor (EC 3.4.21.-)	0.33	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				559
P34322 UniProt NPD GO	NCX7_CAEEL	Putative sodium/calcium exchanger 7 precursor (Na(+)/Ca(2+)-exchange protein 7)	0.33	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				672

You are viewing entries 37901 to 37950 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.