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
Q80TL4 UniProt NPD GO	K1045_MOUSE	Protein KIAA1045	0.50	-	nuc	0					400
Q525S7 UniProt NPD GO	SEY1_MAGGR	Protein SEY1	0.50	-	cyt	2	Membrane; multi-pass membrane protein (Potential)				848
O00744 UniProt NPD GO	WN10B_HUMAN	Protein Wnt-10b precursor (Wnt-12)	0.50	-	nuc	0	Secreted protein; extracellular space; extracellular matrix		601906		389
O96570 UniProt NPD GO	A37C_DROLE	Protein anon-37Cs	0.50	-	mit	0	Cytoplasm (By similarity)	cytoplasm [ISS]			544
Q09276 UniProt NPD GO	DYF8_CAEEL	Protein dyf-8 (Abnormal dye filling protein 8)	0.50	-	nuc	1					446
P45442 UniProt NPD GO	LAG2_CAEEL	Protein lag-2 precursor (Lethal protein 461)	0.50	-	exc	1	Membrane; single-pass type I membrane protein				402
Q8UVV7 UniProt NPD GO	LIX1_CHICK	Protein limb expression 1	0.50	-	mit	0					281
P27792 UniProt NPD GO	LYL1_MOUSE	Protein lyl-1 (Lymphoblastic leukemia-derived sequence 1)	0.50	-	nuc	0	Nucleus (Potential)				278
P42003 UniProt NPD GO	MAD_DROME	Protein mothers against dpp	0.50	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			455
Q8N2R0 UniProt NPD GO	OSR2_HUMAN	Protein odd-skipped-related 2	0.50	-	nuc	0	Nucleus (Potential)				312
Q5HZV9 UniProt NPD GO	PP1R7_RAT	Protein phosphatase 1 regulatory subunit 7 (Protein phosphatase 1 regulatory subunit 22)	0.50	-	nuc	0	Nucleus				360
P49598 UniProt NPD GO	PP2C4_ARATH	Protein phosphatase 2C (EC 3.1.3.16) (PP2C)	0.50	-	nuc	0					399
Q8SXT3 UniProt NPD GO	HFW2_DROME	Protein singed wings 2 precursor	0.50	-	cyt	0					499
Q24212 UniProt NPD GO	STNB_DROME	Protein stoned-B (StonedB) (Stn-B)	0.50	-	nuc	0	Cytoplasm. Colocalizes with synaptic vesicle pools. Colocalizes with the endocytic network within sy ...	coated vesicle [TAS] endocytic vesicle [IDA] synaptic vesicle [TAS]			1262
P31569 UniProt NPD GO	YCF2_OENVI	Protein ycf2 (Fragment)	0.50	-	cyt	0	Plastid; chloroplast; chloroplast stroma (By similarity)				630
Q9Y5I4 UniProt NPD GO	PCDC2_HUMAN	Protocadherin alpha C2 precursor (PCDH-alpha-C2)	0.50	+	nuc	2 *	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606321		1007
Q5DRE1 UniProt NPD GO	PCDC2_PANTR	Protocadherin alpha C2 precursor (PCDH-alpha-C2)	0.50	+	nuc	2 *	Membrane; single-pass type I membrane protein (By similarity)				1007
Q99PJ1 UniProt NPD GO	PCD15_MOUSE	Protocadherin-15 precursor	0.50	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1943
Q7YR46 UniProt NPD GO	PS1C1_PANTR	Psoriasis susceptibility 1 candidate gene 1 protein homolog (SEEK1 protein)	0.50	-	nuc	0					152
P34668 UniProt NPD GO	YO12_CAEEL	Putative ATP-dependent RNA helicase ZK686.2 (EC 3.6.1.-)	0.50	-	mit	0					593
Q9C5J9 UniProt NPD GO	Y5483_ARATH	Putative GTP-binding protein At5g64813	0.50	-	nuc	0					342
Q9STS6 UniProt NPD GO	LBD27_ARATH	Putative LOB domain-containing protein 27	0.50	-	nuc	1 *					328
Q8LF20 UniProt NPD GO	CAP2_ARATH	Putative clathrin assembly protein At2g25430	0.50	-	nuc	0					653
Q21270 UniProt NPD GO	COG6_CAEEL	Putative conserved oligomeric Golgi complex component 6	0.50	-	nuc	0	Golgi apparatus (By similarity)				642
O94587 UniProt NPD GO	OXA13_SCHPO	Putative inner membrane protein oxa1-3, mitochondrial precursor (Sp3)	0.50	-	mit	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				202
Q6BLM0 UniProt NPD GO	ATG15_DEBHA	Putative lipase ATG15 (EC 3.1.1.3) (Autophagy-related protein 15)	0.50	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				615
Q9D9W0 UniProt NPD GO	CU056_MOUSE	Putative protein C21orf56 homolog	0.50	-	nuc	0					342
Q9US49 UniProt NPD GO	SGT1_SCHPO	Putative protein SGT1 homolog C1002.10c	0.50	-	nuc	0		nucleus [IDA]			590
P53394 UniProt NPD GO	SULX_YEAST	Putative sulfate transporter YPR003C	0.50	+	end	10	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			754
Q9STN3 UniProt NPD GO	SPT51_ARATH	Putative transcription elongation factor SPT5 homolog 1	0.50	+	nuc	0	Nucleus (By similarity)				1054
Q6NQG7 UniProt NPD GO	ATL1L_ARATH	RING-H2 finger protein ATL1L	0.50	-	nuc	1					219
Q8C2Q3 UniProt NPD GO	RBM14_MOUSE	RNA-binding protein 14 (RNA-binding motif protein 14)	0.50	-	nuc	0	Nucleus (By similarity)	mediator complex [ISS] ribonucleoprotein complex [ISS] transcription factor complex [ISS]			669
Q5RC41 UniProt NPD GO	RBM14_PONPY	RNA-binding protein 14 (RNA-binding motif protein 14)	0.50	-	nuc	0	Nucleus (By similarity)				669
Q96PK6 UniProt NPD GO	RBM14_HUMAN	RNA-binding protein 14 (RNA-binding motif protein 14) (RRM-containing coactivator activator/modulato ...	0.50	-	nuc	0	Nucleus (Probable)	mediator complex [NAS] ribonucleoprotein complex [TAS] transcription factor complex [IPI]			669
Q8BW10 UniProt NPD GO	NOB1_MOUSE	RNA-binding protein NOB1	0.50	-	nuc	0	Nucleus (By similarity)			2CON	403
Q6VEU1 UniProt NPD GO	NOB1_RAT	RNA-binding protein NOB1	0.50	-	nuc	0	Nucleus (By similarity)				410
Q569B7 UniProt NPD GO	RWDD4_RAT	RWD domain-containing protein 4	0.50	+	nuc	0					188
Q8WZA2 UniProt NPD GO	RPGF4_HUMAN	Rap guanine nucleotide exchange factor 4 (cAMP-regulated guanine nucleotide exchange factor II) (cAM ...	0.50	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein (By similarity)	membrane fraction [TAS]	606058		1011
P50904 UniProt NPD GO	RASA1_RAT	Ras GTPase-activating protein 1 (GTPase-activating protein) (GAP) (Ras p21 protein activator) (p120G ...	0.50	-	cyt	0	Cytoplasm	cytoplasm [ISS]			1038
O95294 UniProt NPD GO	RASL1_HUMAN	RasGAP-activating-like protein 1	0.50	-	nuc	0			604118		804
Q9H6H4 UniProt NPD GO	REEP4_HUMAN	Receptor expression-enhancing protein 4	0.50	-	end	2 *	Membrane; multi-pass membrane protein (By similarity)		609349		257
Q99M80 UniProt NPD GO	PTPRT_MOUSE	Receptor-type tyrosine-protein phosphatase T precursor (EC 3.1.3.48) (R-PTP-T) (RPTP-rho) (mRPTPrho) ...	0.50	-	end	1	Membrane; single-pass type I membrane protein				1454
P35822 UniProt NPD GO	PTPRK_MOUSE	Receptor-type tyrosine-protein phosphatase kappa precursor (EC 3.1.3.48) (Protein-tyrosine phosphata ...	0.50	-	end	2 *	Membrane; single-pass type I membrane protein				1457
Q80ZD1 UniProt NPD GO	RGS9_TAMST	Regulator of G-protein signaling 9 (RGS9)	0.50	-	mit	0					484
P40348 UniProt NPD GO	RFC2_YEAST	Replication factor C subunit 2 (Replication factor C2) (Activator 1 41 kDa subunit)	0.50	-	nuc	0	Nucleus (Probable)	DNA replication factor C complex [IDA]		1SXJ	353
Q9Y2V3 UniProt NPD GO	RX_HUMAN	Retinal homeobox protein Rx (Retina and anterior neural fold homeobox protein)	0.50	+	nuc	0	Nucleus		601881		346
Q05343 UniProt NPD GO	RXRA_RAT	Retinoic acid receptor RXR-alpha (Retinoid X receptor alpha)	0.50	+	nuc	0	Nucleus				467
Q38717 UniProt NPD GO	RNS4_ANTHI	Ribonuclease S-4 precursor (EC 3.1.27.1) (Stylar glycoprotein 4) (S4-RNase)	0.50	-	nuc	1 *	Secreted protein; extracellular space				233
P50648 UniProt NPD GO	RIR1_PLAF4	Ribonucleoside-diphosphate reductase large chain (EC 1.17.4.1) (Ribonucleotide reductase R1 subunit) ...	0.50	-	nuc	0					806
P25270 UniProt NPD GO	PET56_YEAST	Ribose methyltransferase PET56 (EC 2.1.1.-) (Mitochondrial large ribosomal RNA ribose methylase) (21 ...	0.50	-	mit	0	Mitochondrion	mitochondrion [IDA]			412

You are viewing entries 25201 to 25250 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.