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
P08433 UniProt NPD GO	PRTZ1_SCYCA	Protamine-Z1 (Scylliorhinine-Z1)	0.80	+	nuc	0	Nucleus				50
P02322 UniProt NPD GO	PRTZ_THUTH	Protamine-Z1/Z2 (Thynnin-Z1/Z2)	0.80	+	nuc	0	Nucleus				34
Q9V677 UniProt NPD GO	ECM29_DROME	Proteasome-associated protein ECM29 homolog	0.80	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS] nucleus [ISS] proteasome complex (sensu Eukaryota) [ISS]			1890
Q61858 UniProt NPD GO	BAT4_MOUSE	Protein BAT4 (HLA-B-associated transcript 4) (G5 protein)	0.80	+	nuc	0					372
Q6FSD4 UniProt NPD GO	BFR2_CANGA	Protein BFR2	0.80	-	nuc	0	Nucleus; nucleolus (By similarity)				522
Q8ND61 UniProt NPD GO	CC020_HUMAN	Protein C3orf20	0.80	-	nuc	0	Membrane; single-pass membrane protein (Potential)				904
O15234 UniProt NPD GO	CASC3_HUMAN	Protein CASC3 (Cancer susceptibility candidate gene 3 protein) (Metastatic lymph node protein 51) (M ...	0.80	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Predominantly. Nucleus (By similarity). Shuttles betw ...		606504		703
O70374 UniProt NPD GO	MTG8R_MOUSE	Protein CBFA2T2 (MTG8-like protein) (MTG8-related protein 1)	0.80	-	nuc	0	Nucleus (By similarity)				574
Q920P3 UniProt NPD GO	FAM5A_MOUSE	Protein FAM5A precursor (Deleted in bladder cancer 1 protein homolog) (BMP/retinoic acid-inducible n ...	0.80	-	mit	0	Secreted protein (Potential)				760
O60477 UniProt NPD GO	FAM5A_HUMAN	Protein FAM5A precursor (Deleted in bladder cancer 1 protein)	0.80	-	nuc	0	Secreted protein (Potential)		602865		761
Q9C0B6 UniProt NPD GO	FAM5B_HUMAN	Protein FAM5B precursor (BMP/retinoic acid-inducible neural-specific protein 2) (DBCCR1-like protein ...	0.80	-	mit	1 *	Secreted protein (Potential)				783
Q80XP8 UniProt NPD GO	FA76B_MOUSE	Protein FAM76B	0.80	-	nuc	0					339
P40209 UniProt NPD GO	GAT2_YEAST	Protein GAT2	0.80	-	nuc	0					560
P41913 UniProt NPD GO	GDS1_YEAST	Protein GDS1	0.80	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA]			522
Q8R0A7 UniProt NPD GO	K0513_MOUSE	Protein KIAA0513	0.80	-	nuc	0					407
Q5XPJ6 UniProt NPD GO	SCAR4_ARATH	Protein SCAR4 (AtSCAR4) (Protein WAVE3)	0.80	-	nuc	0					1170
P36024 UniProt NPD GO	SIS2_YEAST	Protein SIS2 (Halotolerance protein HAL3)	0.80	-	nuc	0	Or: Nucleus (By similarity). Or: Cytoplasm (By similarity)	cytoplasm [IPI] nucleus [IDA]			562
Q9FUA4 UniProt NPD GO	SPT_ARATH	Protein SPATULA	0.80	-	nuc	0					373
Q28BT7 UniProt NPD GO	ZN750_XENTR	Protein ZNF750	0.80	-	nuc	0					671
O17583 UniProt NPD GO	LIN10_CAEEL	Protein lin-10 (Abnormal cell lineage protein 10)	0.80	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein. Golgi apparatus; tr ...	cell soma [IDA] cytoplasm [IDA] Golgi trans cisterna [IDA] neuron projection [IDA] plasma membrane [IDA] trans-Golgi network transport vesicle [IDA]			982
Q21446 UniProt NPD GO	LIN14_CAEEL	Protein lin-10 (Abnormal cell lineage protein 10)	0.80	-	nuc	0	Nucleus				539
Q9GRX4 UniProt NPD GO	NONA_DROLR	Protein no-on-transient A	0.80	+	nuc	0					698
Q9VJ07 UniProt NPD GO	PHLPP_DROME	Protein phosphatase PHLPP-like protein (EC 3.1.3.16) (dPHLPP)	0.80	-	nuc	0					954
P19103 UniProt NPD GO	IPP1_RAT	Protein phosphatase inhibitor 1 (IPP-1) (I-1)	0.80	-	nuc	0					171
P50411 UniProt NPD GO	IPP2_RAT	Protein phosphatase inhibitor 2 (IPP-2)	0.80	-	nuc	0		cytosol [TAS]			204
P43125 UniProt NPD GO	RDGB_DROME	Protein retinal degeneration B (Probable calcium transporter rdgB)	0.80	-	nuc	0		integral to membrane [TAS] subrhabdomeral cisterna [TAS]			1259
Q9W3W5 UniProt NPD GO	WIF1_DROME	Protein shifted precursor (WIF-1-like protein)	0.80	-	exc	0	Secreted protein; extracellular space; extracellular matrix. Colocalizes with HSPG	extracellular matrix (sensu Metazoa) [IDA] extracellular region [IDA]			456
P00519 UniProt NPD GO	ABL1_HUMAN	Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) (p150) (c-ABL) (Abelson murine leukemia vi ...	0.80	-	nuc	0	Cytoplasm	nucleus [NAS]	189980	2G2H	1130
P34640 UniProt NPD GO	YOQ2_CAEEL	Putative ATP-dependent RNA helicase ZK512.2 (EC 3.6.1.-)	0.80	+	cyt	0					578
O75153 UniProt NPD GO	IF3X_HUMAN	Putative eukaryotic translation initiation factor 3 subunit (eIF-3)	0.80	-	cyt	0					1309
Q8IA43 UniProt NPD GO	GLT10_DROME	Putative polypeptide N-acetylgalactosaminyltransferase 10 (EC 2.4.1.41) (Protein-UDP acetylgalactosa ...	0.80	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi stack [ISS]			630
P50636 UniProt NPD GO	RNF19_MOUSE	RING finger protein 19 (XY body protein) (XYbp) (Gametogenesis expressed protein GEG-154) (UBCM4-int ...	0.80	-	nuc	2	Expressed primarily in the XY body of pachytene spermatocytes and in the centrosome of somatic and g ...				840
Q5AL29 UniProt NPD GO	REXO3_CANAL	RNA exonuclease 3 (EC 3.1.-.-)	0.80	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				404
Q5M9F1 UniProt NPD GO	RBM34_RAT	RNA-binding protein 34 (RNA-binding motif protein 34)	0.80	+	nuc	0	Nucleus; nucleolus (By similarity)				428
Q6PAL8 UniProt NPD GO	RA6I1_MOUSE	Rab6-interacting protein 1 (Rab6IP1)	0.80	-	cyt	0					1287
O54916 UniProt NPD GO	REPS1_MOUSE	RalBP1-associated Eps domain-containing protein 1 (RalBP1-interacting protein 1)	0.80	-	nuc	0				1FI6	743
Q8C0Q9 UniProt NPD GO	RPGF5_MOUSE	Rap guanine nucleotide exchange factor 5 (Guanine nucleotide exchange factor for Rap1) (M-Ras-regula ...	0.80	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			814
Q4QR82 UniProt NPD GO	RASF6_RAT	Ras association domain-containing protein 6	0.80	-	nuc	0					341
Q4QQW1 UniProt NPD GO	REEP4_RAT	Receptor expression-enhancing protein 4	0.80	-	exc	2 *	Membrane; multi-pass membrane protein (By similarity)				257
Q6XUX1 UniProt NPD GO	RIPK5_MOUSE	Receptor-interacting serine/threonine-protein kinase 5 (EC 2.7.11.1) (Dusty protein kinase) (Dusty P ...	0.80	-	cyt	0	Cytoplasm (Probable)				927
O43566 UniProt NPD GO	RGS14_HUMAN	Regulator of G-protein signaling 14 (RGS14)	0.80	+	nuc	0			602513		594
P49803 UniProt NPD GO	RGS7_RAT	Regulator of G-protein signaling 7 (RGS7)	0.80	-	nuc	0					477
Q8IWN7 UniProt NPD GO	RP1L1_HUMAN	Retinitis pigmentosa 1-like 1 protein	0.80	-	nuc	0			608581		2480
Q9H9Y2 UniProt NPD GO	RPF1_HUMAN	Ribosome production factor 1 (Ribosome biogenesis protein RPF1) (Brix domain-containing protein 5)	0.80	-	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			349
Q7TND5 UniProt NPD GO	RPF1_MOUSE	Ribosome production factor 1 (Ribosome biogenesis protein RPF1) (Brix domain-containing protein 5)	0.80	-	nuc	0	Nucleus; nucleolus (By similarity)	nucleolus [ISS]			349
Q5R631 UniProt NPD GO	RPF1_PONPY	Ribosome production factor 1 (Ribosome biogenesis protein RPF1) (Brix domain-containing protein 5)	0.80	-	nuc	0	Nucleus; nucleolus (By similarity)	nucleolus [ISS]			349
Q28298 UniProt NPD GO	RRBP1_CANFA	Ribosome-binding protein 1 (180 kDa ribosome receptor) (RRp)	0.80	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein	integral to endoplasmic reticulum membrane [IDA]			1534
Q7TPD3 UniProt NPD GO	ROBO2_MOUSE	Roundabout homolog 2 precursor	0.80	-	exc	1	Membrane; single-pass type I membrane protein (Potential)	axolemma [IDA] cell surface [ISS]			1470
P58467 UniProt NPD GO	SETD4_MOUSE	SET domain-containing protein 4	0.80	+	mit	0					439
P55194 UniProt NPD GO	3BP1_MOUSE	SH3 domain-binding protein 1 (3BP-1)	0.80	-	nuc	0				1ABO	601

You are viewing entries 9051 to 9100 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.