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
O95070 UniProt NPD GO	YIF1A_HUMAN	Protein YIF1A (YIP1-interacting factor homolog A) (54TMp)	0.02	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				293
Q803Z2 UniProt NPD GO	YIPF3_BRARE	Protein YIPF3 (YIP1 family member 3)	0.02	-	end	5	Cell membrane; multi-pass membrane protein. Cytoplasm (By similarity)				344
Q3UDR8 UniProt NPD GO	YIPF3_MOUSE	Protein YIPF3 (YIP1 family member 3) (Killer lineage protein 1)	0.02	-	end	5	Cell membrane; multi-pass membrane protein. Cytoplasm (By similarity)				347
Q6TUD4 UniProt NPD GO	YIPF3_RAT	Protein YIPF3 (YIP1 family member 3) (Liver regeneration-related protein LRRGT00110)	0.02	-	end	5	Cell membrane; multi-pass membrane protein. Cytoplasm (By similarity)				347
Q6BWH8 UniProt NPD GO	YOP1_DEBHA	Protein YOP1	0.02	-	mit	4 *	Membrane; multi-pass membrane protein (Potential)				177
Q6CE07 UniProt NPD GO	YOP1_YARLI	Protein YOP1	0.02	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				189
Q12402 UniProt NPD GO	YOP1_YEAST	Protein YOP1 (YIP1 partner protein 1) (YPT-interacting protein 2)	0.02	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	integral to membrane [IDA]			179
Q922H1 UniProt NPD GO	ANM3_MOUSE	Protein arginine N-methyltransferase 3 (EC 2.1.1.-) (Heterogeneous nuclear ribonucleoprotein methylt ...	0.02	-	cyt	0	Cytoplasm (By similarity)			1WIR	532
Q17967 UniProt NPD GO	PDI1_CAEEL	Protein disulfide-isomerase 1 precursor (EC 5.3.4.1) (PDI 1) (Prolyl 4-hydroxylase beta 1 subunit)	0.02	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				485
P05307 UniProt NPD GO	PDIA1_BOVIN	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI) (Prolyl 4-hydroxylase subunit beta) (Cellul ...	0.02	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Highly abundant. In some cell types, seems to be ...				510
P21195 UniProt NPD GO	PDIA1_RABIT	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI) (Prolyl 4-hydroxylase subunit beta) (Cellul ...	0.02	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Highly abundant. In some cell types, seems to be ...				509
P34103 UniProt NPD GO	PK4_DICDI	Protein kinase 4 (EC 2.7.11.1) (Fragment)	0.02	-	cyt	0					29
O23676 UniProt NPD GO	MGN_ARATH	Protein mago nashi homolog	0.02	-	cyt	0	Nucleus (By similarity)				150
O65806 UniProt NPD GO	MGN_EUPLA	Protein mago nashi homolog	0.02	-	cyt	0	Nucleus (By similarity)				149
P49030 UniProt NPD GO	MGN_ORYSA	Protein mago nashi homolog (Mago nashi-like protein)	0.02	-	cyt	0	Nucleus (By similarity)				160
Q9CQL1 UniProt NPD GO	MGNR_MOUSE	Protein mago nashi homolog 1-related	0.02	-	cyt	0	Nucleus (By similarity)				146
Q96A72 UniProt NPD GO	MGN2_HUMAN	Protein mago nashi homolog 2	0.02	-	cyt	0	Nucleus (By similarity)				148
P40141 UniProt NPD GO	NG4_DROME	Protein new-glue 4 precursor (NG-4)	0.02	-	cyt	0	Secreted protein (Potential)				57
O42826 UniProt NPD GO	PDH1_SCHPO	Protein pdh1 precursor	0.02	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				226
Q09173 UniProt NPD GO	PP2C3_SCHPO	Protein phosphatase 2C homolog 3 (EC 3.1.3.16) (PP2C-3)	0.02	-	cyt	0					414
Q4WYG7 UniProt NPD GO	PNS1_ASPFU	Protein pns1	0.02	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				537
P20350 UniProt NPD GO	RHOM_DROME	Protein rhomboid (EC 3.4.21.105) (Protein veinlet)	0.02	-	end	7	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi apparatus [IDA] integral to membrane [TAS]			355
Q25214 UniProt NPD GO	SCAL_JUNCO	Protein scalloped (Fragment)	0.02	-	cyt	0	Nucleus (By similarity)				136
P21750 UniProt NPD GO	SALA_DROME	Protein spalt-accessory precursor (Protein spalt-adjacent)	0.02	-	mit	0	Secreted protein				142
Q8VHN8 UniProt NPD GO	SDOS_MOUSE	Protein syndesmos (NUDT16-like protein 1)	0.02	-	nuc	0	Cytoplasm (By similarity)				211
O48650 UniProt NPD GO	SUI1_SALBA	Protein translation factor SUI1 homolog	0.02	-	cyt	0					113
Q03554 UniProt NPD GO	GOT1_YEAST	Protein transport protein GOT1 (Golgi transport protein 1)	0.02	-	end	3 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi membrane [IDA]			138
P53024 UniProt NPD GO	SEC13_PICPA	Protein transport protein SEC13	0.02	-	cyt	0	Cytoplasm. Endoplasmic reticulum. Golgi apparatus; Golgi stack. Transitional face of the endoplasmic ...				289
P38379 UniProt NPD GO	SC61A_PYRSA	Protein transport protein Sec61 subunit alpha	0.02	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				494
P79088 UniProt NPD GO	SC61A_SCHPO	Protein transport protein sec61 subunit alpha	0.02	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			479
Q09723 UniProt NPD GO	TR112_SCHPO	Protein trm112 (tRNA methyltransferase 112)	0.02	-	cyt	0	Cytoplasm. Nucleus (By similarity)				126
Q9XYQ2 UniProt NPD GO	UN119_DROME	Protein unc-119 homolog (DmUNC-119)	0.02	-	cyt	0					265
O78460 UniProt NPD GO	YCF12_GUITH	Protein ycf12	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				34
Q9T096 UniProt NPD GO	YIPL5_ARATH	Protein yippee-like At4g27740	0.02	-	cyt	0					148
Q871R7 UniProt NPD GO	YOP1_NEUCR	Protein yop-1	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				168
Q43209 UniProt NPD GO	PIMT_WHEAT	Protein-L-isoaspartate O-methyltransferase (EC 2.1.1.77) (Protein-beta-aspartate methyltransferase) ...	0.02	-	cyt	0	Cytoplasm				230
P07479 UniProt NPD GO	IPRB_SAGSA	Proteinase inhibitor B precursor (Double-headed proteinase inhibitor B) (API-B)	0.02	-	vac	0	Secreted protein				181
P01080 UniProt NPD GO	IP2K_SOLTU	Proteinase inhibitor type-2 K precursor (Proteinase inhibitor type II K) (IIK) [Contains: Proteinase ...	0.02	-	nuc	1 *				4SGB	153
Q41488 UniProt NPD GO	IP25_SOLTU	Proteinase inhibitor type-2 P303.51 precursor (Proteinase inhibitor type II P303.51)	0.02	-	exc	1 *					154
Q00782 UniProt NPD GO	IP2X_SOLTU	Proteinase inhibitor type-2 precursor (Proteinase inhibitor type II)	0.02	-	exc	1 *					158
O00254 UniProt NPD GO	PAR3_HUMAN	Proteinase-activated receptor 3 precursor (PAR-3) (Thrombin receptor-like 2) (Coagulation factor II ...	0.02	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	601919		374
P36964 UniProt NPD GO	DMB_SQUAC	Proteolipid protein DM beta	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				278
Q7Z2H8 UniProt NPD GO	S36A1_HUMAN	Proton-coupled amino acid transporter 1 (Proton/amino acid transporter 1) (Solute carrier family 36 ...	0.02	-	end	11	Cell membrane; multi-pass membrane protein (By similarity). Lysosome; lysosomal membrane; multi-pass ...		606561		476
Q8K4D3 UniProt NPD GO	S36A1_MOUSE	Proton-coupled amino acid transporter 1 (Proton/amino acid transporter 1) (Solute carrier family 36 ...	0.02	-	end	11	Cell membrane; multi-pass membrane protein (By similarity). Lysosome; lysosomal membrane; multi-pass ...				475
O24163 UniProt NPD GO	PPOC_TOBAC	Protoporphyrinogen oxidase, chloroplast precursor (EC 1.3.3.4) (PPO I) (Protoporphyrinogen IX oxidas ...	0.02	-	nuc	0	Plastid; chloroplast				548
P29265 UniProt NPD GO	PH3_PRUSE	Prunasin beta-glucosidase IIB (EC 3.2.1.118) (Prunasin hydrolase isozyme IIB) (PH IIB) (Fragment)	0.02	-		0					15
Q9H0N5 UniProt NPD GO	PHS2_HUMAN	Pterin-4-alpha-carbinolamine dehydratase 2 (EC 4.2.1.96) (PHS 2) (4-alpha-hydroxy-tetrahydropterin d ...	0.02	-	cyt	0			609836		103
Q9DG45 UniProt NPD GO	PHS2_CHICK	Pterin-4-alpha-carbinolamine dehydratase 2 (EC 4.2.1.96) (PHS 2) (4-alpha-hydroxy-tetrahydropterin d ...	0.02	-	cyt	0					103
P50403 UniProt NPD GO	SFTPA_CAVPO	Pulmonary surfactant-associated protein A precursor (SP-A) (PSP-A) (PSAP)	0.02	-	exc	0	Secreted protein; extracellular space				247
P15781 UniProt NPD GO	PSPB_BOVIN	Pulmonary surfactant-associated protein B (SP-B) (6 kDa protein) (Pulmonary surfactant-associated pr ...	0.02	-	cyt	0	Secreted protein; extracellular space				79

You are viewing entries 85351 to 85400 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.