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
Q9H8X3 UniProt NPD GO	CF208_HUMAN	Protein C6orf208	0.11	-	nuc	0					128
Q9NU53 UniProt NPD GO	CF072_HUMAN	Protein C6orf72 precursor	0.11	-	end	1	Membrane; single-pass type I membrane protein (Potential)				330
Q6DFW0 UniProt NPD GO	CI072_MOUSE	Protein C9orf72 homolog	0.11	-	cyt	0					420
P32460 UniProt NPD GO	DCG1_YEAST	Protein DCG1	0.11	-	cyt	0					244
Q8R3R5 UniProt NPD GO	FA11B_MOUSE	Protein FAM11B	0.11	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				350
Q7TPG8 UniProt NPD GO	F19A1_MOUSE	Protein FAM19A1 precursor (Chemokine-like protein TAFA-1)	0.11	-	nuc	1 *	Secreted protein (By similarity)				133
Q8VCS3 UniProt NPD GO	FA20B_MOUSE	Protein FAM20B precursor	0.11	-	end	1 *	Secreted protein (Potential)				409
Q9D309 UniProt NPD GO	FAM3B_MOUSE	Protein FAM3B precursor (Cytokine-like protein 2-21)	0.11	-	mit	1 *	Secreted protein (By similarity)	extracellular region [NAS]			235
Q9DCL2 UniProt NPD GO	FA96A_MOUSE	Protein FAM96A	0.11	-	mit	0					160
Q8WUJ3 UniProt NPD GO	K1199_HUMAN	Protein KIAA1199 precursor	0.11	-	mit	0			608366		1361
Q7TPY9 UniProt NPD GO	LDOC1_MOUSE	Protein LDOC1	0.11	-	cyt	0	Nucleus (By similarity)				151
Q24434 UniProt NPD GO	ORD_DROME	Protein ORD (Orientation disrupter protein)	0.11	-	end	0	Nucleus. In male meiosis it assembles onto chromosomes in late G2 of the meiotic cell cycle. It rema ...	cohesin complex [IDA] female germ cell nucleus [IDA] male germ cell nucleus [IDA]			479
P38958 UniProt NPD GO	PT100_YEAST	Protein PET100, mitochondrial precursor	0.11	-	cyt	0	Mitochondrion	mitochondrial inner membrane [IDA]			111
P25362 UniProt NPD GO	PET18_YEAST	Protein PET18	0.11	-	cyt	0					215
Q4PIP8 UniProt NPD GO	PNS1_USTMA	Protein PNS1	0.11	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				602
P62818 UniProt NPD GO	S10A3_MOUSE	Protein S100-A3 (S100 calcium-binding protein A3) (Protein S-100E)	0.11	-	nuc	0					101
P62819 UniProt NPD GO	S10A3_RAT	Protein S100-A3 (S100 calcium-binding protein A3) (Protein S-100E)	0.11	-	nuc	0					101
P23833 UniProt NPD GO	SCO1_YEAST	Protein SCO1, mitochondrial precursor	0.11	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA]		2B7K	295
Q8K0G5 UniProt NPD GO	TSCC1_MOUSE	Protein TSSC1	0.11	-	cyt	0					386
Q5PPK9 UniProt NPD GO	TSSC1_RAT	Protein TSSC1	0.11	-	cyt	0					386
Q8NEX5 UniProt NPD GO	WFDC9_HUMAN	Protein WFDC9 precursor	0.11	-	cyt	1 *	Secreted protein (Potential)				89
P53845 UniProt NPD GO	YIF1_YEAST	Protein YIF1 (YIP1-interacting factor 1)	0.11	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum membrane [IPI] ER to Golgi transport vesicle [IDA] integral to Golgi membrane [IDA]			314
Q8BR70 UniProt NPD GO	YIPF6_MOUSE	Protein YIPF6 (YIP1 family member 6)	0.11	-	end	5	Membrane; multi-pass membrane protein (Potential)				236
Q62975 UniProt NPD GO	ZPI_RAT	Protein Z-dependent protease inhibitor precursor (PZ-dependent protease inhibitor) (PZI) (Serpin A10 ...	0.11	-	end	0	Secreted protein				436
P15364 UniProt NPD GO	AMAL_DROME	Protein amalgam precursor	0.11	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	plasma membrane [IDA]			333
Q6PAK3 UniProt NPD GO	ANM8_MOUSE	Protein arginine N-methyltransferase 8 (EC 2.1.1.-) (Heterogeneous nuclear ribonucleoprotein methylt ...	0.11	-	mit	0		plasma membrane [ISS]			394
O77682 UniProt NPD GO	CT004_RABIT	Protein c20orf4 homolog	0.11	-	cyt	0					337
Q9NUP1 UniProt NPD GO	CNO_HUMAN	Protein cappuccino homolog	0.11	-	cyt	0	Cytoplasm (By similarity)		605695		217
Q96JJ7 UniProt NPD GO	TXD10_HUMAN	Protein disulfide-isomerase TXNDC10 precursor (EC 5.3.4.1) (Thioredoxin domain-containing protein 10 ...	0.11	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				454
P31505 UniProt NPD GO	HUNB_BITTE	Protein hunchback (Fragment)	0.11	-	nuc	0	Nucleus (Probable)				56
O75688 UniProt NPD GO	PP2CB_HUMAN	Protein phosphatase 2C isoform beta (EC 3.1.3.16) (PP2C-beta)	0.11	+	nuc	0			603770		479
Q5KBD8 UniProt NPD GO	PPME1_CRYNE	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.11	-	mit	0					422
Q9V3U9 UniProt NPD GO	SLMO_DROME	Protein slowmo	0.11	-	cyt	0	Mitochondrion	mitochondrion [IMP]			215
Q1MTR8 UniProt NPD GO	SVP26_SCHPO	Protein svp26	0.11	-	end	4 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein. Early Golgi (By similarity)				227
Q9P6K1 UniProt NPD GO	SFT2_SCHPO	Protein transport protein sft2	0.11	-	end	4	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				201
O02437 UniProt NPD GO	YELL_DROSU	Protein yellow precursor	0.11	-	mit	1 *	Secreted protein				568
Q9Z184 UniProt NPD GO	PADI3_MOUSE	Protein-arginine deiminase type-3 (EC 3.5.3.15) (Protein-arginine deiminase type III) (Peptidylargin ...	0.11	-	cyt	0	Cytoplasm (By similarity)				664
O02849 UniProt NPD GO	PADI3_SHEEP	Protein-arginine deiminase type-3 (EC 3.5.3.15) (Protein-arginine deiminase type III) (Peptidylargin ...	0.11	-	cyt	0	Cytoplasm (By similarity)				664
Q08189 UniProt NPD GO	TGM3_MOUSE	Protein-glutamine gamma-glutamyltransferase E precursor (EC 2.3.2.13) (TGase E) (TGE) (TG(E)) (Trans ...	0.11	-	cyt	0		cornified envelope [TAS] cytoplasm [ISS] extrinsic to internal side of plasma membrane [ISS]			693
P06302 UniProt NPD GO	PTMA_RAT	Prothymosin alpha [Contains: Thymosin alpha]	0.11	-	nuc	0	Nucleus				111
Q05876 UniProt NPD GO	FYN_CHICK	Proto-oncogene tyrosine-protein kinase Fyn (EC 2.7.10.2) (p59-Fyn)	0.11	-	nuc	0					533
P39688 UniProt NPD GO	FYN_MOUSE	Proto-oncogene tyrosine-protein kinase Fyn (EC 2.7.10.2) (p59-Fyn)	0.11	-	nuc	0	Cell membrane. Present and active in lipid rafts				533
P06241 UniProt NPD GO	FYN_HUMAN	Proto-oncogene tyrosine-protein kinase Fyn (EC 2.7.10.2) (p59-Fyn) (Protooncogene Syn) (SLK)	0.11	-	nuc	0	Cell membrane. Present and active in lipid rafts		137025	1ZBJ	536
P83421 UniProt NPD GO	PSYC_OIKKI	Psychimicin	0.11	-	nuc	0	Secreted protein				45
P11685 UniProt NPD GO	PSPC_RAT	Pulmonary surfactant-associated protein C precursor (SP-C) (Pulmonary surfactant-associated proteoli ...	0.11	-	gol	1 *	Secreted protein; extracellular space				194
Q8T634 UniProt NPD GO	CU36A_MANSE	Pupal cuticle protein 36a precursor (CP36a)	0.11	-	mit	0					280
Q9P7W2 UniProt NPD GO	FTHC_SCHPO	Putative 5-formyltetrahydrofolate cyclo-ligase (EC 6.3.3.2) (5,10-methenyl-tetrahydrofolate syntheta ...	0.11	-	nuc	0					204
Q9XWE6 UniProt NPD GO	MTHFS_CAEEL	Putative 5-formyltetrahydrofolate cyclo-ligase (EC 6.3.3.2) (5,10-methenyl-tetrahydrofolate syntheta ...	0.11	-	nuc	0					206
O04212 UniProt NPD GO	Y2090_ARATH	Putative ABC1 protein At2g40090 precursor	0.11	-	mit	1 *					538
Q19564 UniProt NPD GO	OXDA_CAEEL	Putative D-amino-acid oxidase (EC 1.4.3.3) (DAMOX) (DAO) (DAAO)	0.11	-	cyt	0					334

You are viewing entries 63351 to 63400 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.