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
P26378 UniProt NPD GO	ELAV4_HUMAN	ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)	0.31	-	nuc	0			168360	1G2E	380
Q62902 UniProt NPD GO	LMAN1_RAT	ERGIC-53 protein precursor (ER-Golgi intermediate compartment 53 kDa protein) (Lectin, mannose-bindi ...	0.31	-	end	1	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...	endoplasmic reticulum [TAS] ER-Golgi intermediate compartment [TAS] Golgi apparatus [TAS]		1R1Z	517
O62845 UniProt NPD GO	ELAC_MACEU	Early lactation protein	0.31	-	nuc	0	Secreted protein				83
Q02918 UniProt NPD GO	NO36A_SOYBN	Early nodulin 36A	0.31	-	nuc	0					90
Q9T076 UniProt NPD GO	ENL2_ARATH	Early nodulin-like protein 2 precursor (Phytocyanin-like protein)	0.31	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			349
P29547 UniProt NPD GO	EF1G1_YEAST	Elongation factor 1-gamma 1 (EF-1-gamma 1) (Translation elongation factor 1B gamma 1) (Eukaryotic el ...	0.31	+	cyt	0	Cytoplasm. Nucleus	cytosolic ribosome (sensu Eukaryota) [IGI]		1NHY	415
P42755 UniProt NPD GO	EM4_WHEAT	Em protein H5	0.31	-	nuc	0					93
P07981 UniProt NPD GO	GUN1_TRIRE	Endoglucanase EG-1 precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Cellulase)	0.31	-	nuc	0	Secreted protein			1EG1	459
Q95M18 UniProt NPD GO	ENPL_BOVIN	Endoplasmin precursor (Heat shock protein 90 kDa beta member 1) (94 kDa glucose-regulated protein) ( ...	0.31	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				804
Q96319 UniProt NPD GO	ERH_ARATH	Enhancer of rudimentary homolog	0.31	-	mit	0					109
P13387 UniProt NPD GO	EGFR_CHICK	Epidermal growth factor receptor precursor (EC 2.7.10.1) (CER) (Fragment)	0.31	-	end	1	Membrane; single-pass type I membrane protein				703
Q07303 UniProt NPD GO	EPOR_RAT	Erythropoietin receptor precursor (EPO-R)	0.31	-	exc	1	Membrane; single-pass type I membrane protein				507
P93822 UniProt NPD GO	ERF14_ARATH	Ethylene-responsive transcription factor 14 (Ethylene-responsive element-binding factor 14) (EREBP-1 ...	0.31	-	nuc	0	Nucleus (Probable)				133
Q9FK59 UniProt NPD GO	IF4E3_ARATH	Eukaryotic translation initiation factor 4E type 3 (eIF4E type 3) (eIF-4E type 3) (mRNA cap-binding ...	0.31	-	cyt	0					221
P70445 UniProt NPD GO	4EBP2_MOUSE	Eukaryotic translation initiation factor 4E-binding protein 2 (4E-BP2) (eIF4E-binding protein 2) (Ph ...	0.31	-	nuc	0					120
P59325 UniProt NPD GO	IF5_MOUSE	Eukaryotic translation initiation factor 5 (eIF-5)	0.31	-	nuc	0					429
Q07205 UniProt NPD GO	IF5_RAT	Eukaryotic translation initiation factor 5 (eIF-5)	0.31	-	nuc	0					429
Q06200 UniProt NPD GO	ECM7_YEAST	Extracellular matrix protein 7 (Zinc-regulated gene 15 protein)	0.31	-	end	4 *	Membrane; multi-pass membrane protein				448
Q9UKT7 UniProt NPD GO	FBXL3_HUMAN	F-box/LRR-repeat protein 3 (F-box/LRR-repeat protein 3A) (F-box and leucine-rich repeat protein 3A)	0.31	-	mit	0	Nucleus. Predominantly. Cytoplasm	ubiquitin ligase complex [NAS]	605653		428
Q7RWW0 UniProt NPD GO	POB3_NEUCR	FACT complex subunit pob-3 (Facilitates chromatin transcription complex subunit pob-3)	0.31	-	mit	0	Nucleus (By similarity)				565
P08020 UniProt NPD GO	FMR1_APLCA	FMRFamide neuropeptides type FMRF-1 precursor [Contains: FMRFamide] (Fragment)	0.31	-	nuc	0	Secreted protein				309
P41855 UniProt NPD GO	FARP_CAEEL	FMRFamide-like neuropeptides precursor [Contains: PNFMRY-amide; AGSDPNFLRF-amide; SQPNFLRF-amide; AS ...	0.31	-	mit	0	Secreted protein				175
P10675 UniProt NPD GO	FAS1_SCHAM	Fasciclin-1 precursor (Fasciclin I) (FAS I) (FCN)	0.31	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				662
P05314 UniProt NPD GO	NIR_SPIOL	Ferredoxin--nitrite reductase, chloroplast precursor (EC 1.7.7.1)	0.31	-	mit	0	Plastid; chloroplast			2AKJ	594
P29389 UniProt NPD GO	FRIH_CRIGR	Ferritin heavy chain (EC 1.16.3.1) (Ferritin H subunit)	0.31	-	nuc	0		plasma membrane [ISS]			185
Q7SXA6 UniProt NPD GO	FRIH3_XENLA	Ferritin heavy chain, oocyte isoform (EC 1.16.3.1) (A-ferritin) (XeAF) (GV-HCH)	0.31	-	nuc	0					177
Q8VCM7 UniProt NPD GO	FIBG_MOUSE	Fibrinogen gamma chain precursor	0.31	-	exc	0	Secreted protein				436
Q60791 UniProt NPD GO	FBS1_MOUSE	Fibrosin-1 (Fragment)	0.31	-	mit	0	Secreted protein				71
P98095 UniProt NPD GO	FBLN2_HUMAN	Fibulin-2 precursor	0.31	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [TAS]	135821		1184
P14207 UniProt NPD GO	FOLR2_HUMAN	Folate receptor beta precursor (FR-beta) (Folate receptor 2) (Folate receptor, fetal/placental) (Pla ...	0.31	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Secreted protein (Probable)	membrane fraction [TAS]	136425		255
O62650 UniProt NPD GO	FST_HORSE	Follistatin precursor (FS) (Activin-binding protein)	0.31	-	exc	0	Secreted protein				344
Q08645 UniProt NPD GO	FOLE_YEAST	Folylpolyglutamate synthase (EC 6.3.2.17) (Folylpoly-gamma-glutamate synthetase) (FPGS) (Tetrahydrof ...	0.31	-	nuc	1 *	Mitochondrion. Cytoplasm	cytoplasm [IDA] mitochondrion [IDA]			548
P48542 UniProt NPD GO	IRK6_MOUSE	G protein-activated inward rectifier potassium channel 2 (GIRK2) (Potassium channel, inwardly rectif ...	0.31	-	end	2	Membrane; multi-pass membrane protein				425
P48550 UniProt NPD GO	IRK6_RAT	G protein-activated inward rectifier potassium channel 2 (GIRK2) (Potassium channel, inwardly rectif ...	0.31	-	end	2	Membrane; multi-pass membrane protein				425
Q10653 UniProt NPD GO	CCNB1_CAEEL	G2/mitotic-specific cyclin-B1	0.31	-	nuc	0					361
O77689 UniProt NPD GO	CCNB2_BOVIN	G2/mitotic-specific cyclin-B2	0.31	-	nuc	0					398
P30777 UniProt NPD GO	GPI10_YEAST	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Glycosylphosphati ...	0.31	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				616
O13774 UniProt NPD GO	GCH1_SCHPO	GTP cyclohydrolase I (EC 3.5.4.16) (GTP-CH-I)	0.31	-	cyt	0					235
P36864 UniProt NPD GO	YPTV5_VOLCA	GTP-binding protein yptV5	0.31	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				205
P18507 UniProt NPD GO	GBRG2_HUMAN	Gamma-aminobutyric-acid receptor gamma-2 subunit precursor (GABA(A) receptor)	0.31	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	607681		467
P18508 UniProt NPD GO	GBRG2_RAT	Gamma-aminobutyric-acid receptor gamma-2 subunit precursor (GABA(A) receptor)	0.31	-	end	4	Membrane; multi-pass membrane protein	cytoplasm [IEP]			466
P22933 UniProt NPD GO	GBRD_MOUSE	Gamma-aminobutyric-acid receptor subunit delta precursor (GABA(A) receptor)	0.31	-	nuc	4	Membrane; multi-pass membrane protein				449
O14194 UniProt NPD GO	GGT2_SCHPO	Gamma-glutamyltranspeptidase 2 precursor (EC 2.3.2.2) (Gamma-glutamyltransferase 2) [Contains: Gamma ...	0.31	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				611
Q29RK8 UniProt NPD GO	CXA12_BOVIN	Gap junction alpha-12 protein	0.31	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				429
P18719 UniProt NPD GO	ZG32_XENLA	Gastrula zinc finger protein XLCGF32.1 (Fragment)	0.31	-	nuc	0	Nucleus (Potential)				111
P18724 UniProt NPD GO	ZG49_XENLA	Gastrula zinc finger protein XLCGF49.1 (Fragment)	0.31	-	nuc	0	Nucleus (Potential)				140
P53610 UniProt NPD GO	PGT1_RAT	Geranylgeranyl transferase type-1 subunit beta (EC 2.5.1.59) (Geranylgeranyl transferase type I subu ...	0.31	-	nuc	0		CAAX-protein geranylgeranyltransferase complex [TAS]		1TNZ	377
P19389 UniProt NPD GO	GIA2_GIALA	Giardin alpha-2 subunit	0.31	+	nuc	0	Most likely in the edges of the ventral disk microribbons				296
Q9M8W7 UniProt NPD GO	GLR11_ARATH	Glutamate receptor 1.1 precursor (Ligand-gated ion channel 1.1) (AtGLR1)	0.31	-	end	4	Membrane; multi-pass membrane protein				808
Q9LFN8 UniProt NPD GO	GLR26_ARATH	Glutamate receptor 2.6 precursor (Ligand-gated ion channel 2.6)	0.31	-	end	4 *	Membrane; multi-pass membrane protein				967

You are viewing entries 39401 to 39450 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.