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
P18890 UniProt NPD GO	K1688_RAT	Protein KIAA1688 homolog (Preoptic regulatory factor 2) (PORF-2) (Fragment)	0.10	-	cyt	0					101
P17260 UniProt NPD GO	KRE1_YEAST	Protein KRE1 precursor	0.10	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA]			313
Q9BQ69 UniProt NPD GO	LRP16_HUMAN	Protein LRP16	0.10	-	mit	0					325
P48059 UniProt NPD GO	PINC_HUMAN	Protein PINCH (Particularly interesting new Cys-His protein) (LIM and senescent cell antigen-like do ...	0.10	-	cyt	0	Cytoplasm (Potential)		602567	2COR	324
P24480 UniProt NPD GO	S10AB_RABIT	Protein S100-A11 (S100 calcium-binding protein A11) (Protein S100C) (Calgizzarin)	0.10	-	cyt	0				1NSH	102
Q01589 UniProt NPD GO	SED1_YEAST	Protein SED1 precursor	0.10	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA] mitochondrion [IDA] ribosome [IDA]			338
P41544 UniProt NPD GO	SYS1_YEAST	Protein SYS1	0.10	-	end	4 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi trans face [IDA] integral to Golgi membrane [IDA]			203
P28137 UniProt NPD GO	WNT6_PLEJO	Protein Wnt-6 (Fragment)	0.10	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				117
P28122 UniProt NPD GO	WNT71_EPTST	Protein Wnt-7(I) (Fragment)	0.10	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P54898 UniProt NPD GO	ARG56_NEUCR	Protein arg-6, mitochondrial precursor [Contains: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1. ...	0.10	-	mit	0	Mitochondrion				871
Q00002 UniProt NPD GO	PDI_ALTAL	Protein disulfide-isomerase (EC 5.3.4.1) (PDI) (Allergen Alt a 4) (Fragment)	0.10	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				436
Q5R6T1 UniProt NPD GO	PDIA6_PONPY	Protein disulfide-isomerase A6 precursor (EC 5.3.4.1)	0.10	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				440
Q15084 UniProt NPD GO	PDIA6_HUMAN	Protein disulfide-isomerase A6 precursor (EC 5.3.4.1) (Protein disulfide isomerase P5) (Thioredoxin ...	0.10	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum [TAS] ER-Golgi intermediate compartment [IDA]		1X5D	440
Q02293 UniProt NPD GO	PFTB_RAT	Protein farnesyltransferase subunit beta (EC 2.5.1.58) (CAAX farnesyltransferase subunit beta) (RAS ...	0.10	-	cyt	0				3FTI	437
P24156 UniProt NPD GO	L2CC_DROME	Protein l(2)37Cc	0.10	-	cyt	0					276
Q09172 UniProt NPD GO	PP2C2_SCHPO	Protein phosphatase 2C homolog 2 (EC 3.1.3.16) (PP2C-2)	0.10	-	cyt	0					370
Q8BHN0 UniProt NPD GO	PP2CL_MOUSE	Protein phosphatase 2C isoform epsilon (EC 3.1.3.16) (PP2C-epsilon) (Protein phosphatase 1L) (Protei ...	0.10	-	mit	0	Membrane; single-pass type I membrane protein (Potential)				360
Q5ALW7 UniProt NPD GO	PPME1_CANAL	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.10	-	cyt	0					360
P34387 UniProt NPD GO	TG198_CAEEL	Protein tag-198 precursor (EC 3.1.-.-)	0.10	-	mit	0					367
Q64697 UniProt NPD GO	PTCA_MOUSE	Protein tyrosine phosphatase receptor type C-associated protein (PTPRC-associated protein) (CD45-ass ...	0.10	-	exc	1 *					197
Q9D658 UniProt NPD GO	TP4A3_MOUSE	Protein tyrosine phosphatase type IVA protein 3 (EC 3.1.3.48) (Protein-tyrosine phosphatase 4a3) (Pr ...	0.10	-	mit	0	Cell membrane. Endosome; early endosome				173
Q9XZF0 UniProt NPD GO	YIPP_DROME	Protein yippee	0.10	-	mit	0					121
O44440 UniProt NPD GO	YPL2_CAEEL	Protein yippee-like B0546.4	0.10	-	nuc	0					161
P51176 UniProt NPD GO	TGM2_BOVIN	Protein-glutamine gamma-glutamyltransferase 2 (EC 2.3.2.13) (Tissue transglutaminase) (TGase C) (TGC ...	0.10	-	mit	0					687
Q86BN8 UniProt NPD GO	PTPM1_DROME	Protein-tyrosine phosphatase mitochondrial 1-like protein, mitochondrial precursor (EC 3.1.3.48) (EC ...	0.10	-	nuc	0	Mitochondrion (Potential)				200
P01252 UniProt NPD GO	PTMA_BOVIN	Prothymosin alpha [Contains: Thymosin alpha-1]	0.10	+	nuc	0	Nucleus				109
P06454 UniProt NPD GO	PTMA_HUMAN	Prothymosin alpha [Contains: Thymosin alpha-1]	0.10	+	nuc	0	Nucleus	nucleus [TAS]	188390		110
Q5R790 UniProt NPD GO	PTMA_PONPY	Prothymosin alpha [Contains: Thymosin alpha]	0.10	+	nuc	0	Nucleus (By similarity)				109
Q8BIZ0 UniProt NPD GO	PCD20_MOUSE	Protocadherin-20 precursor	0.10	-	mit	1 *	Membrane; single-pass type I membrane protein (By similarity)				925
P13495 UniProt NPD GO	NXLB_PSETE	Pseudonajatoxin b (Long neurotoxin B)	0.10	-	nuc	0	Secreted protein				71
P21841 UniProt NPD GO	PSPC_MOUSE	Pulmonary surfactant-associated protein C precursor (SP-C) (SP5) (Pulmonary surfactant-associated pr ...	0.10	-	gol	1 *	Secreted protein; extracellular space				193
Q9STT7 UniProt NPD GO	ATH4_ARATH	Putative ABC2 homolog 4	0.10	-	end	3	Membrane; multi-pass membrane protein (Potential)				664
Q9XTQ7 UniProt NPD GO	KE4L_CAEEL	Putative Ke4-like protein tag-148	0.10	-	end	7	Membrane; multi-pass membrane protein (Probable)				462
Q10217 UniProt NPD GO	ACPM_SCHPO	Putative acyl carrier protein, mitochondrial precursor (ACP) (NADH-ubiquinone oxidoreductase 9.6 kDa ...	0.10	-	mit	0	Mitochondrion (By similarity)				112
P47182 UniProt NPD GO	AAD10_YEAST	Putative aryl-alcohol dehydrogenase AAD10 (EC 1.1.1.-)	0.10	-	cyt	0					288
Q9FNE0 UniProt NPD GO	CX5C4_ARATH	Putative cytochrome c oxidase polypeptide Vc-4 (EC 1.9.3.1) (Cytochrome c oxidase subunit 5c-4)	0.10	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				65
Q12288 UniProt NPD GO	YL126_YEAST	Putative glutamine amidotransferase YLR126C (EC 6.3.5.-)	0.10	-	cyt	0	Cytoplasm	cytoplasm [IDA]			251
Q9P7Q9 UniProt NPD GO	YFV5_SCHPO	Putative glycosyl transferase C1834.05 in chromosome I precursor (EC 2.-.-.-)	0.10	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				577
Q9C947 UniProt NPD GO	LCR66_ARATH	Putative low-molecular-weight cysteine-rich protein LCR66 precursor	0.10	-	exc	1 *	Secreted protein (Potential)				76
Q9FFP8 UniProt NPD GO	LCR74_ARATH	Putative low-molecular-weight cysteine-rich protein LCR74 precursor	0.10	-	vac	0	Secreted protein (Potential)				73
P82723 UniProt NPD GO	LCR8_ARATH	Putative low-molecular-weight cysteine-rich protein LCR8 precursor	0.10	-	mit	0					73
P82724 UniProt NPD GO	LCR9_ARATH	Putative low-molecular-weight cysteine-rich protein LCR9 precursor	0.10	-	exc	1 *					78
Q09758 UniProt NPD GO	YA71_SCHPO	Putative membrane-bound O-acyltransferase C24H6.01c (EC 2.3.1.-)	0.10	-	end	9	Membrane; multi-pass membrane protein (Potential)				588
Q9M271 UniProt NPD GO	MTPA1_ARATH	Putative metal tolerance protein A1 (AtMTPa1) (AtMTP2)	0.10	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				334
P38921 UniProt NPD GO	PET8_YEAST	Putative mitochondrial carrier protein PET8	0.10	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			284
Q9V637 UniProt NPD GO	PSMF1_DROME	Putative proteasome inhibitor	0.10	-	cyt	0					270
P57056 UniProt NPD GO	CU032_HUMAN	Putative protein C21orf32	0.10	-	mit	0					206
Q9VEP1 UniProt NPD GO	RRMJ1_DROME	Putative ribosomal RNA methyltransferase CG5220 (EC 2.1.1.-) (rRNA (uridine-2'-O-)-methyltransferase ...	0.10	-	nuc	0					302
P90893 UniProt NPD GO	YM9I_CAEEL	Putative serine protease F56F10.1 precursor (EC 3.4.-.-)	0.10	-	exc	0					540
P34676 UniProt NPD GO	YO26_CAEEL	Putative serine protease Z688.6 precursor (EC 3.4.-.-)	0.10	-	exc	0					507

You are viewing entries 65101 to 65150 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.