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
O14682 UniProt NPD GO	ENC1_HUMAN	Ectoderm-neural cortex 1 protein (ENC-1) (p53-induced protein 10) (Nuclear matrix protein NRP/B)	0.40	-	mit	0	Nucleus; nuclear matrix	nucleus [TAS]	605173		589
Q91375 UniProt NPD GO	EF1GB_XENLA	Elongation factor 1-gamma-B (EF-1-gamma-B) (eEF-1B gamma-B) (p47)	0.40	+	cyt	0					437
O00418 UniProt NPD GO	EF2K_HUMAN	Elongation factor 2 kinase (EC 2.7.11.20) (eEF-2 kinase) (eEF-2K) (Calcium/calmodulin-dependent euka ...	0.40	-	nuc	0		cytoplasm [TAS]	606968		725
Q40864 UniProt NPD GO	EML_PICGL	Em-like protein	0.40	-	nuc	0					91
O60344 UniProt NPD GO	ECE2_HUMAN	Endothelin-converting enzyme 2 (EC 3.4.24.71) (ECE-2)	0.40	-	mit	1	Membrane; single-pass type II membrane protein	cytoplasmic vesicle membrane [IDA]			787
O95672 UniProt NPD GO	ECEL1_HUMAN	Endothelin-converting enzyme-like 1 (EC 3.4.24.-) (Xce protein)	0.40	-	cyt	1	Membrane; single-pass type II membrane protein (By similarity)	integral to plasma membrane [TAS]	605896		775
P70709 UniProt NPD GO	ECP_RAT	Eosinophil cationic protein precursor (EC 3.1.27.-) (ECP) (Ribonuclease 3) (RNase 3) (Eosinophil sec ...	0.40	-	exc	0	Matrix of eosinophil's large specific granule (By similarity)				155
Q02748 UniProt NPD GO	IF4A_DROME	Eukaryotic initiation factor 4A (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A) (eIF-4A)	0.40	-	cyt	0		nucleus [IC]			403
Q40465 UniProt NPD GO	IF411_TOBAC	Eukaryotic initiation factor 4A-11 (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-11) (eIF-4A-11)	0.40	-	cyt	0					413
P41381 UniProt NPD GO	IF4A8_TOBAC	Eukaryotic initiation factor 4A-8 (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-8) (eIF-4A-8)	0.40	-	cyt	0					413
P55871 UniProt NPD GO	IF2B_MALDO	Eukaryotic translation initiation factor 2 subunit beta (eIF-2-beta)	0.40	+	cyt	0					271
P48240 UniProt NPD GO	MTR3_YEAST	Exosome complex exonuclease MTR3 (EC 3.1.13.-) (mRNA transport regulator 3)	0.40	-	nuc	0	Cytoplasm. Nucleus; nucleolus	cytoplasmic exosome (RNase complex) [IDA] nuclear exosome (RNase complex) [IDA]			250
P70428 UniProt NPD GO	EXT2_MOUSE	Exostosin-2 (EC 2.4.1.224) (EC 2.4.1.225) (Glucuronosyl-N-acetylglucosaminyl-proteoglycan/N-acetylgl ...	0.40	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...				718
Q9TVM2 UniProt NPD GO	XPO1_DROME	Exportin-1 (Chromosome region maintenance 1 protein) (Protein embargoed)	0.40	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex; nucleoplasmic side	nuclear pore [IMP]			1063
Q99252 UniProt NPD GO	ECM3_YEAST	Extracellular matrix protein 3	0.40	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			613
P79136 UniProt NPD GO	CAPZB_BOVIN	F-actin capping protein subunit beta (CapZ beta)	0.40	-	mit	0	Calyx. Sperm head cytoskeletal structure tightly associated to the nucleus				301
Q6P3S6 UniProt NPD GO	FBX42_HUMAN	F-box only protein 42	0.40	-	nuc	0			609109		717
Q9UKC9 UniProt NPD GO	FBXL2_HUMAN	F-box/LRR-repeat protein 2 (F-box and leucine-rich repeat protein 2) (F-box protein FBL2/FBL3)	0.40	-	nuc	0		cytoplasm [TAS]	605652		423
Q61160 UniProt NPD GO	FADD_MOUSE	FADD protein (FAS-associating death domain-containing protein) (Mediator of receptor induced toxicit ...	0.40	-	nuc	0				1FAD	205
Q8VII0 UniProt NPD GO	FRMD6_RAT	FERM domain-containing protein 6 (FERM domain-containing protein 163SCII) (Fragment)	0.40	-	nuc	0					327
O23305 UniProt NPD GO	Y4449_ARATH	FHA domain-containing protein At4g14490	0.40	-	nuc	0				1UHT	386
Q92235 UniProt NPD GO	FPPS_GIBFU	Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes ...	0.40	-	cyt	0	Cytoplasm				347
Q96RD9 UniProt NPD GO	FCRL5_HUMAN	Fc receptor-like protein 5 precursor (Immunoglobulin receptor translocation-associated gene 2 protei ...	0.40	-	exc	1	Membrane; single-pass type I membrane protein (Potential)		605877		977
Q8N4E7 UniProt NPD GO	FTMT_HUMAN	Ferritin, mitochondrial precursor (EC 1.16.3.1)	0.40	-	mit	0	Mitochondrion		608847	1R03	242
P16622 UniProt NPD GO	HEMH_YEAST	Ferrochelatase, mitochondrial precursor (EC 4.99.1.1) (Protoheme ferro-lyase) (Heme synthetase)	0.40	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side. It is bound t ...	mitochondrial inner membrane [TAS]		1LBQ	393
Q969F0 UniProt NPD GO	FATE1_HUMAN	Fetal and adult testis-expressed transcript protein (Protein BJ-HCC-2)	0.40	-	nuc	1			300450		183
Q9UGM5 UniProt NPD GO	FETUB_HUMAN	Fetuin-B precursor (Gugu) (IRL685) (16G2)	0.40	-	exc	0	Secreted protein (Potential)	extracellular region [NAS]	605954		382
P19477 UniProt NPD GO	FIBA_PARPA	Fibrinogen-like protein A precursor (FREP-A)	0.40	-	exc	0					282
Q91V87 UniProt NPD GO	FGRL1_MOUSE	Fibroblast growth factor receptor-like 1 precursor (FGF receptor-like protein 1) (Fibroblast growth ...	0.40	-	exc	1		plasma membrane [IDA]			529
Q9BYJ0 UniProt NPD GO	FGFP2_HUMAN	Fibroblast growth factor-binding protein 2 precursor (FGF-binding protein 2) (FGF-BP2) (FGFBP-2) (37 ...	0.40	-	exc	0	Secreted protein; extracellular space				223
P11722 UniProt NPD GO	FINC_CHICK	Fibronectin (FN) (Fragments)	0.40	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				1256
Q08879 UniProt NPD GO	FBLN1_MOUSE	Fibulin-1 precursor (Basement-membrane protein 90) (BM-90)	0.40	-	exc	0	Secreted protein; extracellular space; extracellular matrix	basement membrane [IDA]			705
Q06787 UniProt NPD GO	FMR1_HUMAN	Fragile X mental retardation 1 protein (Protein FMR-1) (FMRP)	0.40	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleolus [TAS] nucleoplasm [TAS] soluble fraction [TAS]	309550	2FMR	632
Q9TY03 UniProt NPD GO	FRDA_CAEEL	Frataxin homolog	0.40	-	mit	0					136
Q7Z2K8 UniProt NPD GO	GRIN1_HUMAN	G protein-regulated inducer of neurite outgrowth 1 (GRIN1)	0.40	-	nuc	0	Cell membrane; lipid-anchor (By similarity). Highly enriched in growth cone (By similarity)				1008
Q5R7U0 UniProt NPD GO	GASP2_PONPY	G-protein coupled receptor-associated sorting protein 2 (GASP-2)	0.40	-	nuc	0					838
P18063 UniProt NPD GO	CCNB_ASTPE	G2/mitotic-specific cyclin-B	0.40	-	mit	0					394
Q60FX9 UniProt NPD GO	CCNB2_ANGJA	G2/mitotic-specific cyclin-B2	0.40	-	cyt	0					394
Q39573 UniProt NPD GO	YPTC5_CHLRE	GTP-binding protein YPTC5	0.40	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				206
Q9UG22 UniProt NPD GO	GIMA2_HUMAN	GTPase, IMAP family member 2 (Immunity-associated protein 2) (hIMAP2)	0.40	-	end	2	Membrane; multi-pass membrane protein (Potential)		608085		337
P02529 UniProt NPD GO	CRGC_RAT	Gamma crystallin C (Gamma crystallin 2-1)	0.40	-	nuc	0					173
P23005 UniProt NPD GO	CRGF_BOVIN	Gamma crystallin F (Gamma crystallin IVA)	0.40	-	cyt	0				1M8U	173
P10044 UniProt NPD GO	CRGM2_CYPCA	Gamma crystallin M2 (Gamma-M2)	0.40	-	nuc	0					173
P24045 UniProt NPD GO	GBRB4_CHICK	Gamma-aminobutyric-acid receptor beta-4 subunit precursor (GABA(A) receptor)	0.40	+	end	4	Membrane; multi-pass membrane protein				488
Q9ES14 UniProt NPD GO	GBRE_RAT	Gamma-aminobutyric-acid receptor epsilon subunit precursor (GABA(A) receptor)	0.40	+	end	4	Membrane; multi-pass membrane protein				506
P06659 UniProt NPD GO	GDBB_WHEAT	Gamma-gliadin B precursor	0.40	-	nuc	0					291
P08453 UniProt NPD GO	GDB2_WHEAT	Gamma-gliadin precursor	0.40	-	nuc	0					327
Q9ESZ8 UniProt NPD GO	GTF2I_MOUSE	General transcription factor II-I (GTFII-I) (TFII-I) (Bruton tyrosine kinase-associated protein 135) ...	0.40	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)			1Q60	998
Q91189 UniProt NPD GO	GLUC2_ONCMY	Glucagon-2 precursor (Glucagon II) [Contains: Glicentin-related polypeptide 2 (GRPP 2); Glucagon-2; ...	0.40	-	exc	0	Secreted protein				178
P35547 UniProt NPD GO	GCR_SHEEP	Glucocorticoid receptor (GR) (Fragment)	0.40	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in the absence of ligand; nuclear af ...				314

You are viewing entries 31801 to 31850 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.