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
Q9P2E7 UniProt NPD GO	PCD10_HUMAN	Protocadherin-10 precursor	0.54	-	end	1	Membrane; single-pass type I membrane protein (By similarity)		608286		1040
Q6WYY1 UniProt NPD GO	PC11X_PANPA	Protocadherin-11 X-linked precursor (Protocadherin-11) (Protocadherin on the X chromosome)	0.54	+	nuc	0	Membrane; single-pass type I membrane protein (Potential)				1347
P53751 UniProt NPD GO	YN94_YEAST	Putative 125.2 kDa membrane glycoprotein in BIO3-HXT17 intergenic region	0.54	-	end	1					1116
Q10944 UniProt NPD GO	PPAY_CAEEL	Putative acid phosphatase B0361.7 precursor (EC 3.1.3.2)	0.54	-	end	1					422
Q95TN4 UniProt NPD GO	COG4_DROME	Putative conserved oligomeric Golgi complex component 4	0.54	-	cyt	0	Golgi apparatus (By similarity)				776
O44502 UniProt NPD GO	COG8_CAEEL	Putative conserved oligomeric Golgi complex component 8	0.54	-	nuc	0	Golgi apparatus (By similarity)				743
Q9FLB4 UniProt NPD GO	DRL31_ARATH	Putative disease resistance protein At5g05400	0.54	-	cyt	0					874
O14232 UniProt NPD GO	YDVG_SCHPO	Putative helicase C6F12.16c (EC 3.6.1.-)	0.54	-	cyt	0	Nucleus (By similarity)				1117
P23249 UniProt NPD GO	MOV10_MOUSE	Putative helicase MOV-10 (EC 3.6.1.-) (Moloney leukemia virus 10 protein)	0.54	-	nuc	0					1004
Q4X180 UniProt NPD GO	ATG15_ASPFU	Putative lipase atg15 (EC 3.1.1.3) (Autophagy-related protein 15)	0.54	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				650
P83097 UniProt NPD GO	WSCK_DROME	Putative tyrosine-protein kinase Wsck precursor (EC 2.7.10.1)	0.54	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				791
Q68EF0 UniProt NPD GO	RAB3I_MOUSE	RAB3A-interacting protein (Rabin-3) (SSX2-interacting protein)	0.54	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Predominantly cytoplasmic but a small proportion ...	cytosol [ISS] nucleus [ISS]			428
Q8IZP6 UniProt NPD GO	R113B_HUMAN	RING finger protein 113B (Zinc finger protein 183-like 1)	0.54	-	nuc	0				2CSY	322
Q5XIK5 UniProt NPD GO	RN146_RAT	RING finger protein 146	0.54	+	nuc	0					352
P53924 UniProt NPD GO	YNL6_YEAST	RING finger protein YNL116W	0.54	-	mit	0		cytoplasm [IDA]			522
Q12159 UniProt NPD GO	YRA1_YEAST	RNA annealing protein YRA1	0.54	-	nuc	0	Nucleus	transcription export complex [IPI]			226
Q08278 UniProt NPD GO	MED7_YEAST	RNA polymerase II mediator complex subunit 7 (RNA polymerase II transcriptional regulation mediator ...	0.54	-	nuc	0	Nucleus	mediator complex [IDA]		1YKH	222
Q5RD94 UniProt NPD GO	MED6_PONPY	RNA polymerase transcriptional regulation mediator, subunit 6 homolog	0.54	-	nuc	0	Nucleus (By similarity)				246
O75586 UniProt NPD GO	MED6_HUMAN	RNA polymerase transcriptional regulation mediator, subunit 6 homolog (Activator-recruited cofactor ...	0.54	-	nuc	0	Nucleus	mediator complex [IDA] nucleus [TAS]	602984		246
Q9Y580 UniProt NPD GO	RBM7_HUMAN	RNA-binding protein 7 (RNA-binding motif protein 7)	0.54	-	nuc	0					266
Q9H6Z4 UniProt NPD GO	RANB3_HUMAN	Ran-binding protein 3 (RanBP3)	0.54	+	nuc	0	Cytoplasm. Nucleus	nucleus [TAS]	603327	2CRF	567
Q8CB96 UniProt NPD GO	RASF4_MOUSE	Ras association domain-containing protein 4	0.54	-	nuc	0					322
O14522 UniProt NPD GO	PTPRT_HUMAN	Receptor-type tyrosine-protein phosphatase T precursor (EC 3.1.3.48) (R-PTP-T) (RPTP-rho)	0.54	+	end	0	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	608712		1463
Q16849 UniProt NPD GO	PTPRN_HUMAN	Receptor-type tyrosine-protein phosphatase-like N precursor (R-PTP-N) (PTP IA-2) (Islet cell antigen ...	0.54	-	end	1	Membrane; single-pass type I membrane protein. Neuroendocrine secretory granules	integral to plasma membrane [TAS]	601773		979
P39743 UniProt NPD GO	RV167_YEAST	Reduced viability upon starvation protein 167	0.54	-	mit	0		actin cortical patch [TAS]			482
Q6RG78 UniProt NPD GO	RGS1_HORSE	Regulator of G-protein signaling 1 (RGS1)	0.54	+	nuc	0					196
Q9JHX0 UniProt NPD GO	RGS2_RAT	Regulator of G-protein signaling 2 (RGS2)	0.54	-	nuc	0					211
O46469 UniProt NPD GO	RGS9_BOVIN	Regulator of G-protein signaling 9 (RGS9)	0.54	-	nuc	0				1FQK	484
Q5R551 UniProt NPD GO	TIG2_PONPY	Retinoic acid receptor responder protein 2 precursor	0.54	+	exc	0	Secreted protein (Potential)				163
Q967S7 UniProt NPD GO	GAGHB_DROME	Retrovirus-related Gag polyprotein from transposon HMS-Beagle	0.54	-	nuc	0					467
Q8CIN9 UniProt NPD GO	RFFL_RAT	Rififylin (RING finger and FYVE-like domain-containing protein 1) (FYVE-RING finger protein Sakura)	0.54	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	ubiquitin ligase complex [IDA]			362
Q6ZQM0 UniProt NPD GO	RFFL_MOUSE	Rififylin (RING finger and FYVE-like domain-containing protein 1) (Fring)	0.54	-	nuc	0	Cytoplasm; perinuclear region. Membrane; peripheral membrane protein. Associated with perinuclear ve ...	cytoplasmic membrane-bound vesicle [IDA]			377
Q63046 UniProt NPD GO	RUNX1_RAT	Runt-related transcription factor 1 (Core-binding factor, alpha 2 subunit) (CBF-alpha 2) (Acute myel ...	0.54	-	nuc	0	Nucleus	nucleus [IDA]			450
Q03347 UniProt NPD GO	RUNX1_MOUSE	Runt-related transcription factor 1 (Core-binding factor, alpha 2 subunit) (CBF-alpha 2) (Acute myel ...	0.54	-	nuc	0	Nucleus			1IO4	451
O94692 UniProt NPD GO	RUVB2_SCHPO	RuvB-like helicase 2 (EC 3.6.1.-)	0.54	-	cyt	0	Nucleus (By similarity)				465
Q62420 UniProt NPD GO	SH3G2_MOUSE	SH3-containing GRB2-like protein 2 (EC 2.3.1.-) (SH3 domain protein 2A) (Endophilin 1) (SH3p4)	0.54	+	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Concentrated in pr ...			1ZWW	352
P49771 UniProt NPD GO	FLT3L_HUMAN	SL cytokine precursor (Fms-related tyrosine kinase 3 ligand) (Flt3 ligand) (Flt3L)	0.54	-	exc	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein	soluble fraction [TAS]	600007	1ETE	235
Q16512 UniProt NPD GO	PKN1_HUMAN	Serine/threonine-protein kinase N1 (EC 2.7.11.13) (Protein kinase C-like 1) (Protein-kinase C-relate ...	0.54	-	nuc	0	Cytoplasm (By similarity)		601032	1URF	942
Q60670 UniProt NPD GO	SN1L1_MOUSE	Serine/threonine-protein kinase SNF1-like kinase 1 (EC 2.7.11.1) (Serine/threonine-protein kinase SN ...	0.54	-	nuc	0	Cytoplasm. Nucleus (Potential). May translocate to the nucleus on activation	cytoplasm [IDA]			779
Q8K3G5 UniProt NPD GO	VRK3_MOUSE	Serine/threonine-protein kinase VRK3 (EC 2.7.11.1) (Vaccinia-related kinase 3)	0.54	-	nuc	0		nucleus [IDA]			453
O61661 UniProt NPD GO	CHK1_DROME	Serine/threonine-protein kinase grp (EC 2.7.11.1) (Protein grapes) (Chk1 homolog)	0.54	+	cyt	0	Nucleus	nucleus [IDA]			512
Q4INW6 UniProt NPD GO	PTPA2_GIBZE	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.54	-	cyt	0	Cytoplasm (By similarity)				432
Q75E32 UniProt NPD GO	PP4R3_ASHGO	Serine/threonine-protein phosphatase 4 regulatory subunit 3 (PP4R3)	0.54	-	cyt	0	Nucleus (By similarity)				687
Q19550 UniProt NPD GO	SRA28_CAEEL	Serpentine receptor class alpha-28 (Protein sra-28)	0.54	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				341
Q10934 UniProt NPD GO	SRA32_CAEEL	Serpentine receptor class alpha-32 (Protein sra-32)	0.54	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				338
Q92783 UniProt NPD GO	STAM1_HUMAN	Signal transducing adapter molecule 1 (STAM-1)	0.54	-	nuc	0	Cytoplasm (Probable)		601899		539
P70297 UniProt NPD GO	STAM1_MOUSE	Signal transducing adapter molecule 1 (STAM-1)	0.54	-	nuc	0	Cytoplasm (Probable)				547
Q61079 UniProt NPD GO	SIM2_MOUSE	Single-minded homolog 2 (SIM transcription factor) (mSIM)	0.54	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			657
Q9NJP2 UniProt NPD GO	NACH_DROVI	Sodium channel protein Nach (Fragment)	0.54	-	cyt	1	Membrane; multi-pass membrane protein	integral to membrane [ISS]			384
Q6FT03 UniProt NPD GO	SNX3_CANGA	Sorting nexin-3	0.54	-	nuc	0	Cytoplasm (By similarity)				164

You are viewing entries 22751 to 22800 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.