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
Q6IFS7 UniProt NPD GO	HSN2_RAT	Protein HSN2 precursor	0.65	-	nuc	0	Secreted protein (Potential)				434
O75698 UniProt NPD GO	HUG1_HUMAN	Protein HUG-1 (HOX11 upstream gene 1 protein)	0.65	-	nuc	0					362
O94927 UniProt NPD GO	K0841_HUMAN	Protein KIAA0841	0.65	-	nuc	0					633
Q8N8K9 UniProt NPD GO	K1958_HUMAN	Protein KIAA1958	0.65	-	nuc	0					716
O13670 UniProt NPD GO	MTO1_SCHPO	Protein MTO1 homolog, mitochondrial precursor	0.65	-	mit	0	Mitochondrion (By similarity)				666
Q9XGW1 UniProt NPD GO	PINH_ARATH	Protein PINHEAD (Protein ZWILLE)	0.65	-	nuc	0					988
P53539 UniProt NPD GO	FOSB_HUMAN	Protein fosB (G0/G1 switch regulatory protein 3)	0.65	+	nuc	0	Nucleus		164772		338
P97609 UniProt NPD GO	HAIR_RAT	Protein hairless	0.65	-	nuc	0	Nucleus				1181
Q86BY9 UniProt NPD GO	RIG_DROME	Protein rigor mortis	0.65	-	nuc	0	Nucleus. Cytoplasm. During second and third instar larval development, it is localized primarily to ...	cytoplasm [IDA] nucleus [IDA]			1235
Q10669 UniProt NPD GO	SUR2_CAEEL	Protein sur-2	0.65	-	nuc	0					1587
P11939 UniProt NPD GO	FOS_CHICK	Proto-oncogene protein c-fos (Cellular oncogene fos)	0.65	+	nuc	0	Nucleus				367
O88479 UniProt NPD GO	FOS_MESAU	Proto-oncogene protein c-fos (Cellular oncogene fos)	0.65	+	nuc	0	Nucleus				381
P01101 UniProt NPD GO	FOS_MOUSE	Proto-oncogene protein c-fos (Cellular oncogene fos)	0.65	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			380
Q14671 UniProt NPD GO	PUM1_HUMAN	Pumilio homolog 1 (Pumilio-1) (HsPUM)	0.65	-	nuc	0	Cytoplasm (Probable)		607204	1M8Z	1186
Q7L2E3 UniProt NPD GO	DHX30_HUMAN	Putative ATP-dependent RNA helicase DHX30 (EC 3.6.1.-) (DEAH box protein 30)	0.65	-	mit	0					1194
P34466 UniProt NPD GO	IF3X_CAEEL	Putative eukaryotic translation initiation factor 3 subunit (eIF-3)	0.65	-	cyt	0					1247
Q09785 UniProt NPD GO	GCSP_SCHPO	Putative glycine dehydrogenase [decarboxylating], mitochondrial precursor (EC 1.4.4.2) (Glycine deca ...	0.65	-	mit	0	Mitochondrion (By similarity)				1017
Q23223 UniProt NPD GO	YH2O_CAEEL	Putative helicase W08D2.7 (EC 3.6.1.-)	0.65	-	cyt	0	Nucleus (Potential)				1026
P53732 UniProt NPD GO	YN8K_YEAST	Putative mitochondrial 40S ribosomal protein YNR036C	0.65	+	mit	0	Mitochondrion (Potential)				153
Q18846 UniProt NPD GO	KS6A2_CAEEL	Putative ribosomal protein S6 kinase alpha-2 (EC 2.7.11.1) (Ribosomal protein S6 kinase alpha-5 homo ...	0.65	-	cyt	0					772
Q11090 UniProt NPD GO	YWY3_CAEEL	Putative serine/threonine-protein kinase C01C4.3 (EC 2.7.11.1)	0.65	-	nuc	0					407
P34536 UniProt NPD GO	YNC3_CAEEL	Putative zinc finger protein R05D3.3	0.65	-	nuc	0	Nucleus (Potential)				421
Q9H0A6 UniProt NPD GO	RNF32_HUMAN	RING finger protein 32	0.65	-	nuc	0	Cytoplasm	aggresome [IDA]			362
P38336 UniProt NPD GO	POP4_YEAST	RNases MRP/P 32.9 kDa subunit (RNA-processing protein POP4)	0.65	-	nuc	0	Nucleus (Potential)	nucleolar ribonuclease P complex [IDA] ribonuclease MRP complex [IDA]			279
Q5R5R4 UniProt NPD GO	RUFY2_PONPY	RUN and FYVE domain-containing protein 2	0.65	-	nuc	0	Nucleus (By similarity)				606
Q86YS3 UniProt NPD GO	RFIP4_HUMAN	Rab11 family-interacting protein 4 (Rab11-FIP4)	0.65	-	nuc	0	Endosome; recycling endosome; recycling endosomal membrane; peripheral membrane protein. Colocalizes ...				637
Q3U0S6 UniProt NPD GO	RAIN_MOUSE	Ras-interacting protein 1 (Rain)	0.65	-	nuc	0	Cytoplasm (By similarity). Associated with perinuclear vesicles. Golgi apparatus; Golgi stack (By si ...				961
Q94C77 UniProt NPD GO	RPKL_ARATH	Receptor protein kinase-like protein At4g34220 precursor	0.65	+	exc	2 *	Membrane; single-pass membrane protein (Potential)				757
P97347 UniProt NPD GO	RPTN_MOUSE	Repetin	0.65	-	nuc	0		cornified envelope [IDA]			1130
Q9I9D5 UniProt NPD GO	RX1_ASTFA	Retinal homeobox protein Rx1	0.65	+	nuc	0	Nucleus (By similarity)				334
P51126 UniProt NPD GO	RARA_XENLA	Retinoic acid receptor alpha (RAR-alpha)	0.65	+	nuc	0	Nucleus				458
Q61085 UniProt NPD GO	RHPN1_MOUSE	Rhophilin-1 (GTP-Rho-binding protein 1)	0.65	-	nuc	0					643
Q9SH88 UniProt NPD GO	RRS1_ARATH	Ribosome biogenesis regulatory protein homolog	0.65	+	nuc	0	Nucleus (By similarity)				318
P27010 UniProt NPD GO	SCRY2_OCTDO	S-crystallin 2 (OL2)	0.65	-	nuc	0					215
Q6NRI0 UniProt NPD GO	SAP3A_XENLA	SAPS domain family member 3-A	0.65	-	nuc	0					852
Q9GZW5 UniProt NPD GO	SCND2_HUMAN	SCAN domain-containing protein 2	0.65	-	nuc	0	Nucleus (Potential)				306
Q9UDX3 UniProt NPD GO	S14L4_HUMAN	SEC14-like protein 4 (Tocopherol-associated protein 3)	0.65	-	nuc	0					406
P78314 UniProt NPD GO	3BP2_HUMAN	SH3 domain-binding protein 2 (3BP-2)	0.65	-	nuc	0			118400	2CR4	561
P53036 UniProt NPD GO	SAP4_YEAST	SIT4-associating protein SAP4	0.65	-	cyt	0		mitochondrion [IDA]			818
Q9NR83 UniProt NPD GO	S2A4R_HUMAN	SLC2A4 regulator (GLUT4 enhancer factor) (GEF) (Huntington disease gene regulatory region-binding pr ...	0.65	-	nuc	0	Cytoplasm. Nucleus. Shuttles between the cytoplasm and the nucleus	nucleus [NAS]	609493		387
Q8IW52 UniProt NPD GO	SLIK4_HUMAN	SLIT and NTRK-like protein 4 precursor	0.65	-	end	1	Membrane; single-pass membrane protein (Potential)		300562		837
Q810B8 UniProt NPD GO	SLIK4_MOUSE	SLIT and NTRK-like protein 4 precursor	0.65	-	end	1	Membrane; single-pass membrane protein (Potential)				837
Q5A8H7 UniProt NPD GO	SWC5_CANAL	SWR1-complex protein 5	0.65	-	nuc	0	Nucleus (By similarity)				338
Q8NFY4 UniProt NPD GO	SEM6D_HUMAN	Semaphorin-6D precursor	0.65	-	end	1	Isoform 1, isoform 2, isoform 3, isoform 4, isoform 5: Cell membrane; single-pass type I membrane pr ...		609295		1073
O55131 UniProt NPD GO	SEPT7_MOUSE	Septin-7 (CDC10 protein homolog)	0.65	-	nuc	0		synaptosome [IDA]			436
Q07965 UniProt NPD GO	SRYA_DROSU	Serendipity locus protein alpha	0.65	+	nuc	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein; cytoplasmic side (By similari ...				543
O55099 UniProt NPD GO	AURKB_RAT	Serine/threonine-protein kinase 12 (EC 2.7.11.1) (Aurora- and Ipl1-like midbody-associated protein 1 ...	0.65	-	nuc	0	Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metaphase and then ...	midbody [IDA] spindle [IDA]			343
Q15208 UniProt NPD GO	STK38_HUMAN	Serine/threonine-protein kinase 38 (EC 2.7.11.1) (NDR1 protein kinase) (Nuclear Dbf2-related kinase ...	0.65	-	cyt	0	Nucleus. Cytoplasm. Low levels present in the cytoplasm	nucleus [IDA]	606964	1PSB	465
Q4P0K0 UniProt NPD GO	ATG1_USTMA	Serine/threonine-protein kinase ATG1 (EC 2.7.11.1) (Autophagy-related protein 1)	0.65	-	nuc	0	Cytoplasm (By similarity)				990
Q754N7 UniProt NPD GO	CBK1_ASHGO	Serine/threonine-protein kinase CBK1 (EC 2.7.11.1)	0.65	-	nuc	0					719

You are viewing entries 16551 to 16600 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.