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
Q10129 UniProt NPD GO	RT16_CAEEL	Probable mitochondrial 28S ribosomal protein S16 (MRP-S16)	0.06	-	mit	0	Mitochondrion (By similarity)				147
Q75Q40 UniProt NPD GO	TOM40_RAT	Probable mitochondrial import receptor subunit TOM40 homolog (Translocase of outer membrane 40 kDa s ...	0.06	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				361
O96008 UniProt NPD GO	TOM40_HUMAN	Probable mitochondrial import receptor subunit TOM40 homolog (Translocase of outer membrane 40 kDa s ...	0.06	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)	mitochondrial outer membrane [NAS]	608061		361
Q9C7X5 UniProt NPD GO	NAS4_ARATH	Probable nicotianamine synthase 4 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-a ...	0.06	-	cyt	0					324
Q17819 UniProt NPD GO	ORN_CAEEL	Probable oligoribonuclease (EC 3.1.-.-)	0.06	-	cyt	0					193
Q9SZ83 UniProt NPD GO	Y4967_ARATH	Probable oxidoreductase At4g09670 (EC 1.-.-.-)	0.06	-	cyt	0				1YDW	362
Q4R690 UniProt NPD GO	ZDH13_MACFA	Probable palmitoyltransferase ZDHHC13 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 13) ( ...	0.06	-	end	7	Membrane; multi-pass membrane protein (Potential)				622
Q9BAC5 UniProt NPD GO	RRP3_EUGGA	Probable plastid-specific 30S ribosomal protein 3 (PSRP-3)	0.06	-	mit	0	Plastid; chloroplast				103
Q9BAC2 UniProt NPD GO	RRP3_EUGMY	Probable plastid-specific 30S ribosomal protein 3 (PSRP-3)	0.06	-	cyt	0	Plastid; chloroplast				101
Q652J4 UniProt NPD GO	HAK13_ORYSA	Probable potassium transporter 13 (OsHAK13)	0.06	-	end	11 *	Membrane; multi-pass membrane protein (By similarity)				778
Q9VRL3 UniProt NPD GO	PFD4_DROME	Probable prefoldin subunit 4	0.06	-	cyt	0					138
P34329 UniProt NPD GO	PDIA4_CAEEL	Probable protein disulfide-isomerase A4 precursor (EC 5.3.4.1) (ERp-72 homolog)	0.06	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				618
Q9LPG6 UniProt NPD GO	RHM2_ARATH	Probable rhamnose biosynthetic enzyme 2 (EC 4.2.1.-) (EC 1.1.1.-) (RHAMNOSE BIOSYNTHESIS 2 protein) ...	0.06	-	cyt	0					667
Q92979 UniProt NPD GO	NEP1_HUMAN	Probable ribosome biogenesis protein NEP1 (Nucleolar protein EMG1 homolog) (Protein C2f)	0.06	-	nuc	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [ISS]			243
O35130 UniProt NPD GO	NEP1_MOUSE	Probable ribosome biogenesis protein NEP1 (Nucleolar protein EMG1 homolog) (Protein C2f)	0.06	-	nuc	0	Nucleus; nucleolus (By similarity)				244
Q10104 UniProt NPD GO	GLYC_SCHPO	Probable serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) (Serine methylase) (Glycine hydroxy ...	0.06	-	cyt	0	Cytoplasm (Potential)				472
O13972 UniProt NPD GO	GLYD_SCHPO	Probable serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) (Serine methylase) (Glycine hydroxy ...	0.06	-	cyt	0	Cytoplasm (Potential)				467
Q60MW2 UniProt NPD GO	SPCS3_CAEBR	Probable signal peptidase complex subunit 3 (EC 3.4.-.-) (Microsomal signal peptidase 22 kDa subunit ...	0.06	-	cyt	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (Potential)				180
Q9TLX6 UniProt NPD GO	TRME_CYACA	Probable tRNA modification GTPase trmE	0.06	-	cyt	0	Plastid; chloroplast				465
P15808 UniProt NPD GO	THY1_DICDI	Probable thymidylate synthase thy1 (EC 2.1.1.148) (TS) (TSase)	0.06	-	cyt	0					260
Q6CBE4 UniProt NPD GO	ETR1_YARLI	Probable trans-2-enoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.38)	0.06	-	mit	0	Mitochondrion (By similarity)				376
Q9YGI2 UniProt NPD GO	TXW1_NAJAT	Probable weak neurotoxin NNAM1 precursor	0.06	-	nuc	1 *	Secreted protein				86
Q9FI31 UniProt NPD GO	XTH20_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 20 precursor (EC 2.4.1.207) (At-XTH20) (X ...	0.06	-	mit	0	Secreted protein; extracellular space; apoplast (Probable)				282
Q8LER3 UniProt NPD GO	XTH7_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 7 precursor (EC 2.4.1.207) (At-XTH7) (XTH ...	0.06	-	vac	0	Secreted protein; extracellular space; apoplast (Probable)				293
Q8L9A9 UniProt NPD GO	XTH8_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 8 precursor (EC 2.4.1.207) (At-XTH8) (XTH ...	0.06	-	exc	0	Secreted protein; extracellular space; apoplast (Probable)				292
Q9U6R6 UniProt NPD GO	PROC_TRIPT	Procalin precursor (Allergen Tria p 1)	0.06	-	exc	0	Secreted protein				169
P21902 UniProt NPD GO	PCE_TACTR	Proclotting enzyme precursor (EC 3.4.21.86) [Contains: Proclotting enzyme light chain; Proclotting e ...	0.06	-	vac	0	Secreted protein. Secreted in hemolymph				375
Q811A3 UniProt NPD GO	PLOD2_RAT	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 precursor (EC 1.14.11.4) (Lysyl hydroxylase 2) (LH ...	0.06	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum cisterna; peripheral ...				737
Q20679 UniProt NPD GO	PLOD_CAEEL	Procollagen-lysine,2-oxoglutarate 5-dioxygenase precursor (EC 1.14.11.4) (Lysyl hydroxylase) (LH) (L ...	0.06	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum cisterna; peripheral ...				730
Q2NKT1 UniProt NPD GO	PROF4_BOVIN	Profilin-4	0.06	-	cyt	0					129
Q9DGC8 UniProt NPD GO	GON1_ORYLA	Progonadoliberin-1 precursor (Progonadoliberin I) (Medaka-type gonadotropin-releasing hormone) (mdGn ...	0.06	-	exc	0	Secreted protein	extracellular region [ISS]			91
P60988 UniProt NPD GO	PIP_MACFU	Prolactin-inducible protein homolog precursor	0.06	-	end	0	Secreted protein (By similarity)				146
Q9W644 UniProt NPD GO	PCNA_ANGJA	Proliferating cell nuclear antigen (PCNA)	0.06	-	cyt	0	Nucleus (By similarity)				260
Q43124 UniProt NPD GO	PCNA_BRANA	Proliferating cell nuclear antigen (PCNA)	0.06	-	mit	0	Nucleus				263
Q9M7Q7 UniProt NPD GO	PCNA1_ARATH	Proliferating cellular nuclear antigen 1 (PCNA 1)	0.06	-	cyt	0	Nucleus				263
Q9XTA2 UniProt NPD GO	PPCE_BOVIN	Prolyl endopeptidase (EC 3.4.21.26) (Post-proline cleaving enzyme) (PE)	0.06	-	nuc	0	Cytoplasm				710
P23687 UniProt NPD GO	PPCE_PIG	Prolyl endopeptidase (EC 3.4.21.26) (Post-proline cleaving enzyme) (PE)	0.06	-	nuc	0	Cytoplasm			1VZ3	710
Q7ZUC7 UniProt NPD GO	PGES2_BRARE	Prostaglandin E synthase 2 (EC 5.3.99.3) (Microsomal prostaglandin E synthase 2) (mPGES-2)	0.06	-	mit	0	Membrane; single-pass membrane protein				377
P43088 UniProt NPD GO	PF2R_HUMAN	Prostaglandin F2-alpha receptor (Prostanoid FP receptor) (PGF receptor) (PGF2 alpha receptor)	0.06	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600563		359
Q9ES87 UniProt NPD GO	PRSS8_RAT	Prostasin precursor (EC 3.4.21.-) [Contains: Prostasin light chain; Prostasin heavy chain]	0.06	-	exc	0	Prostasin: Cell membrane; single-pass membrane protein (By similarity). Prostasin light chain, prost ...				342
Q9D9N8 UniProt NPD GO	PAP21_MOUSE	Protease-associated domain-containing protein of 21 kDa precursor	0.06	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS]			188
P97372 UniProt NPD GO	PSME2_MOUSE	Proteasome activator complex subunit 2 (Proteasome activator 28-subunit beta) (PA28beta) (PA28b) (Ac ...	0.06	-	cyt	0					238
Q63798 UniProt NPD GO	PSME2_RAT	Proteasome activator complex subunit 2 (Proteasome activator 28-subunit beta) (PA28beta) (PA28b) (Ac ...	0.06	-	cyt	0					237
P21243 UniProt NPD GO	PSA6_YEAST	Proteasome component C7-alpha (EC 3.4.25.1) (Macropain subunit C7-alpha) (Proteinase YSCE subunit 7) ...	0.06	-	cyt	0	Cytoplasm. Nucleus	mitochondrion [IDA] proteasome core complex, alpha-subunit comp... [IPI]		2FNY	252
O96788 UniProt NPD GO	PSA1_TRYBR	Proteasome subunit alpha type 1 (EC 3.4.25.1) (20S proteasome subunit alpha-6)	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				266
Q9GU37 UniProt NPD GO	PSA1_TRYBB	Proteasome subunit alpha type 1 (EC 3.4.25.1) (20SPA1)	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				266
Q95008 UniProt NPD GO	PSA5_CAEEL	Proteasome subunit alpha type 5 (EC 3.4.25.1) (Proteasome subunit alpha 5)	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				248
Q9QUM9 UniProt NPD GO	PSA6_MOUSE	Proteasome subunit alpha type 6 (EC 3.4.25.1) (Proteasome iota chain) (Macropain iota chain) (Multic ...	0.06	-	cyt	0	Cytoplasm. Nucleus				246
P60901 UniProt NPD GO	PSA6_RAT	Proteasome subunit alpha type 6 (EC 3.4.25.1) (Proteasome iota chain) (Macropain iota chain) (Multic ...	0.06	-	cyt	0	Cytoplasm. Nucleus	proteasome core complex (sensu Eukaryota) [ISS]			246
P60900 UniProt NPD GO	PSA6_HUMAN	Proteasome subunit alpha type 6 (EC 3.4.25.1) (Proteasome iota chain) (Macropain iota chain) (Multic ...	0.06	-	cyt	0	Cytoplasm. Nucleus	proteasome core complex (sensu Eukaryota) [NAS]	602855		246

You are viewing entries 72901 to 72950 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.