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
Q05923 UniProt NPD GO	DUS2_HUMAN	Dual specificity protein phosphatase 2 (EC 3.1.3.48) (EC 3.1.3.16) (Dual specificity protein phospha ...	0.30	-	cyt	0	Nucleus	nucleus [TAS]	603068	1M3G	314
Q64346 UniProt NPD GO	DUS6_RAT	Dual specificity protein phosphatase 6 (EC 3.1.3.48) (EC 3.1.3.16) (Mitogen-activated protein kinase ...	0.30	-	nuc	0	Cytoplasm	cytoplasm [IDA]			381
Q9ESC1 UniProt NPD GO	ELTD1_RAT	EGF, latrophilin and seven transmembrane domain-containing protein 1 precursor (EGF-TM7-latrophilin- ...	0.30	-	end	7	Cell membrane; multi-pass membrane protein. Subunit alpha: Secreted protein; extracellular space. Cy ...				738
P19419 UniProt NPD GO	ELK1_HUMAN	ETS domain-containing protein Elk-1	0.30	+	nuc	0	Nucleus		311040	1DUX	428
P26635 UniProt NPD GO	EGR2_POERE	Early growth response protein 2 (EGR-2) (Krox-20 protein) (Fragment)	0.30	-	nuc	0	Nucleus				62
Q9Y227 UniProt NPD GO	ENP4_HUMAN	Ectonucleoside triphosphate diphosphohydrolase 4 (EC 3.6.1.6) (NTPDase4) (Uridine-diphosphatase) (UD ...	0.30	-	end	2 *	Membrane; multi-pass membrane protein (Potential). Localizes in the Golgi and autophagic vacuoles/ly ...	integral to Golgi membrane [IDA]	607577		616
Q10361 UniProt NPD GO	ETP1_SCHPO	Electron transfer protein 1, mitochondrial precursor	0.30	-	end	7	Mitochondrion; mitochondrial membrane; multi-pass membrane protein				631
P43896 UniProt NPD GO	EFTS_BOVIN	Elongation factor Ts, mitochondrial precursor (EF-Ts) (EF-TsMt)	0.30	-	mit	0	Mitochondrion			1XB2	338
Q02908 UniProt NPD GO	ELP3_YEAST	Elongator complex protein 3 (EC 2.3.1.48) (Gamma-toxin target 3)	0.30	-	mit	0	Cytoplasm. Nucleus	DNA-directed RNA polymerase II, holoenzyme [IDA] transcription elongation factor complex [IDA]			557
P22701 UniProt NPD GO	EM2_WHEAT	Em protein CS41	0.30	-	nuc	0					94
Q02973 UniProt NPD GO	EM6_ARATH	Em-like protein GEA6	0.30	-	nuc	0					92
Q39799 UniProt NPD GO	CHI1_GOSHI	Endochitinase 1 precursor (EC 3.2.1.14)	0.30	-	exc	0					324
Q969S2 UniProt NPD GO	NEIL2_HUMAN	Endonuclease VIII-like 2 (EC 3.2.2.-) (EC 4.2.99.18) (Nei-like 2) (DNA glycosylase/AP lyase Neil2) ( ...	0.30	-	cyt	0	Nucleus		608933	1VZP	331
Q03103 UniProt NPD GO	ERO1_YEAST	Endoplasmic oxidoreductin-1 precursor (EC 1.8.4.-) (Endoplasmic oxidoreductase protein 1)	0.30	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side	endoplasmic reticulum [IDA]		1RQ1	563
Q29092 UniProt NPD GO	ENPL_PIG	Endoplasmin precursor (Heat shock protein 90 kDa beta member 1) (94 kDa glucose-regulated protein) ( ...	0.30	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				804
Q6CEE7 UniProt NPD GO	PPN1_YARLI	Endopolyphosphatase (EC 3.6.1.10)	0.30	+	vac	0	Vacuole; vacuolar membrane; single-pass type II membrane protein				747
Q03145 UniProt NPD GO	EPHA2_MOUSE	Ephrin type-A receptor 2 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor ECK) (Epithelial ...	0.30	-	end	1 *	Membrane; single-pass type I membrane protein				977
Q62413 UniProt NPD GO	EPHA6_MOUSE	Ephrin type-A receptor 6 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EHK-2) (EPH homol ...	0.30	+	nuc	1	Membrane; single-pass type I membrane protein				1035
Q80VP1 UniProt NPD GO	EPN1_MOUSE	Epsin-1 (EPS-15-interacting protein 1) (Intersectin-EH-binding protein 1) (Ibp1)	0.30	-	nuc	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein (By similarity). Nucleus (By s ...				566
P29676 UniProt NPD GO	EPO_RAT	Erythropoietin precursor	0.30	-	exc	1 *	Secreted protein				192
Q13542 UniProt NPD GO	4EBP2_HUMAN	Eukaryotic translation initiation factor 4E-binding protein 2 (4E-BP2) (eIF4E-binding protein 2)	0.30	-	nuc	0			602224		120
Q9VXK6 UniProt NPD GO	IF5_DROME	Eukaryotic translation initiation factor 5 (eIF-5)	0.30	-	mit	0		cytosol [ISS]			464
Q06011 UniProt NPD GO	ECM19_YEAST	Extracellular matrix protein 19	0.30	-	nuc	1 *	Mitochondrion; mitochondrial membrane (Potential)				112
P41975 UniProt NPD GO	SODE_RABIT	Extracellular superoxide dismutase [Cu-Zn] precursor (EC 1.15.1.1) (EC-SOD)	0.30	-	exc	0	Secreted protein; extracellular space				244
Q9QZN0 UniProt NPD GO	FBX15_MOUSE	F-box only protein 15	0.30	-	mit	0		SCF ubiquitin ligase complex [IDA]			433
Q9H469 UniProt NPD GO	FBX37_HUMAN	F-box only protein 37 (F-box/LRR-repeat protein 15)	0.30	-	cyt	0					296
Q9STX3 UniProt NPD GO	GID2_ARATH	F-box protein GID2 (Protein SLEEPY1)	0.30	-	nuc	0	Nucleus				151
Q5AYE3 UniProt NPD GO	POB3_EMENI	FACT complex subunit pob3 (Facilitates chromatin transcription complex subunit pob3)	0.30	-	cyt	0	Nucleus (By similarity)				589
Q9Y801 UniProt NPD GO	YFAS1_SCHPO	FAS1 domain-containing protein C146.10 precursor	0.30	-	exc	0	Membrane				189
Q8WMY2 UniProt NPD GO	FPPS_BOVIN	Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes ...	0.30	-	cyt	0	Cytoplasm (By similarity)				353
P34229 UniProt NPD GO	FAS1_YARLI	Fatty acid synthase subunit beta (EC 2.3.1.86) [Includes: 3-hydroxypalmitoyl-[acyl-carrier-protein] ...	0.30	-	nuc	0		fatty acid synthase complex [NAS]			2086
Q39161 UniProt NPD GO	NIR_ARATH	Ferredoxin--nitrite reductase, chloroplast precursor (EC 1.7.7.1) (NiR)	0.30	-	mit	0	Plastid; chloroplast	mitochondrion [IDA]			586
Q9T0P4 UniProt NPD GO	GLTB2_ARATH	Ferredoxin-dependent glutamate synthase 2, chloroplast precursor (EC 1.4.7.1) (Fd-GOGAT 2)	0.30	-	mit	0	Plastid; chloroplast; chloroplast stroma (By similarity)				1629
P41349 UniProt NPD GO	FTRC2_SPIOL	Ferredoxin-thioredoxin reductase catalytic chain, chloroplast precursor (EC 1.18.-.-) (FTR-C) (Ferre ...	0.30	-	mit	0	Plastid; chloroplast				148
O59786 UniProt NPD GO	HEMH_SCHPO	Ferrochelatase, mitochondrial precursor (EC 4.99.1.1) (Protoheme ferro-lyase) (Heme synthetase)	0.30	-	cyt	0	Mitochondrion; mitochondrial inner membrane. Bound to the mitochondrial inner membrane in eukaryotic ...				384
O35565 UniProt NPD GO	FGF10_MOUSE	Fibroblast growth factor 10 precursor (FGF-10) (Keratinocyte growth factor 2)	0.30	-	exc	1 *	Secreted protein (Potential)	cell surface [NAS] extracellular space [IDA] nucleus [IDA]			209
P23142 UniProt NPD GO	FBLN1_HUMAN	Fibulin-1 precursor	0.30	-	exc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [TAS] extracellular region [NAS] extracellular space [TAS] soluble fraction [TAS]	608180		703
Q8NFG4 UniProt NPD GO	FLCN_HUMAN	Folliculin (Birt-Hogg-Dube syndrome protein) (BHD skin lesion fibrofolliculoma protein)	0.30	-	cyt	0			607273		579
P50291 UniProt NPD GO	FST_BOVIN	Follistatin precursor (FS) (Activin-binding protein)	0.30	-	exc	0	Secreted protein				344
P47931 UniProt NPD GO	FST_MOUSE	Follistatin precursor (FS) (Activin-binding protein)	0.30	-	exc	0	Secreted protein				344
P21674 UniProt NPD GO	FST_RAT	Follistatin precursor (FS) (Activin-binding protein)	0.30	-	exc	0	Secreted protein			2ARP	344
O60829 UniProt NPD GO	GAGC1_HUMAN	G antigen family C member 1 (Prostate-associated gene 4 protein) (PAGE-4) (PAGE-1) (GAGE-9)	0.30	+	nuc	0			300287		102
Q5T6X5 UniProt NPD GO	GPC6A_HUMAN	G-protein coupled receptor family C group 6 member A precursor (hGPRC6A) (G-protein coupled receptor ...	0.30	-	end	7	Cell membrane; multi-pass membrane protein (By similarity)				926
Q5R6J5 UniProt NPD GO	CCND1_PONPY	G1/S-specific cyclin-D1	0.30	-	cyt	0					295
P24385 UniProt NPD GO	CCND1_HUMAN	G1/S-specific cyclin-D1 (PRAD1 oncogene) (BCL-1 oncogene)	0.30	-	cyt	0			168461		295
P46277 UniProt NPD GO	CCNB1_MEDVA	G2/mitotic-specific cyclin-1 (B-like cyclin) (CycMs1)	0.30	-	nuc	0					428
Q92162 UniProt NPD GO	CCNB_CARAU	G2/mitotic-specific cyclin-B	0.30	-	mit	0					397
P51987 UniProt NPD GO	CCNB_CHLVR	G2/mitotic-specific cyclin-B	0.30	-	nuc	0					392
P15206 UniProt NPD GO	CCNB_MARGL	G2/mitotic-specific cyclin-B	0.30	-	nuc	0					388
O95479 UniProt NPD GO	G6PE_HUMAN	GDH/6PGL endoplasmic bifunctional protein precursor [Includes: Glucose 1-dehydrogenase (EC 1.1.1.47) ...	0.30	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Microsomes, endoplasmic reticulum lumen		604931		791

You are viewing entries 40301 to 40350 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.)

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