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
P93962 UniProt NPD GO	RPOA_PSAST	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.49	-	cyt	0	Plastid; chloroplast				339
P92439 UniProt NPD GO	RPOA_THIBE	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.49	-	cyt	0	Plastid; chloroplast				339
Q3V542 UniProt NPD GO	RPOB_ACOCL	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.49	-	nuc	0	Plastid; chloroplast				1083
Q9MTM5 UniProt NPD GO	RPOB_OENHO	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.49	-	nuc	0	Plastid; chloroplast				1072
P23580 UniProt NPD GO	RPOC1_EUGGR	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.49	-	cyt	0	Plastid; chloroplast				586
Q33C47 UniProt NPD GO	RPOC1_NICTO	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.49	-	cyt	0	Plastid; chloroplast				681
P50712 UniProt NPD GO	DEF14_MOUSE	Defensin-related cryptdin 14 precursor (Fragment)	0.49	-	exc	0	Secreted protein				85
Q8CFD1 UniProt NPD GO	DRBP1_RAT	Developmentally-regulated RNA-binding protein 1	0.49	-	cyt	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). May shuttle between cytoplasm and ...	cytoplasm [ISS] nucleus [ISS]			476
Q8IUH3 UniProt NPD GO	DRBP1_HUMAN	Developmentally-regulated RNA-binding protein 1 (RB-1)	0.49	-	nuc	0	Cytoplasm. Predominantly. Nucleus. May shuttle between cytoplasm and nucleus	cytoplasm [IDA] nucleus [IDA]	608888		476
Q5R9A4 UniProt NPD GO	DNJB9_PONPY	DnaJ homolog subfamily B member 9	0.49	-	nuc	1 *	Cytoplasm (By similarity). Nucleus (By similarity). Stress induces its translocation to the nucleus ...				223
Q9R022 UniProt NPD GO	DJC12_MOUSE	DnaJ homolog subfamily C member 12 (J domain-containing protein 1)	0.49	-	nuc	0					198
Q93ZL5 UniProt NPD GO	DOF52_ARATH	Dof zinc finger protein DOF5.2 (AtDOF5.2)	0.49	-	nuc	0	Nucleus (Probable)				457
Q9HCR9 UniProt NPD GO	PDE11_HUMAN	Dual 3',5'-cyclic-AMP and -GMP phosphodiesterase 11A (EC 3.1.4.17) (EC 3.1.4.35) (cAMP and cGMP phos ...	0.49	-	end	0	Cytoplasm; cytosol		604961		934
Q90891 UniProt NPD GO	MP2K2_CHICK	Dual specificity mitogen-activated protein kinase kinase 2 (EC 2.7.12.2) (MAP kinase kinase 2) (MAPK ...	0.49	-	cyt	0					398
Q99078 UniProt NPD GO	FUZ7_USTMA	Dual specificity protein kinase FUZ7 (EC 2.7.12.2)	0.49	+	nuc	0					435
Q8CHY3 UniProt NPD GO	DYM_MOUSE	Dymeclin	0.49	-	end	0	Membrane; multi-pass membrane protein (Potential)				669
Q5RAW5 UniProt NPD GO	DYM_PONPY	Dymeclin	0.49	-	end	0	Membrane; multi-pass membrane protein (Potential)				669
Q7RTS9 UniProt NPD GO	DYM_HUMAN	Dymeclin (Dyggve-Melchior-Clausen syndrome protein)	0.49	-	end	0	Membrane; multi-pass membrane protein (Potential)		607461		669
Q8S3C9 UniProt NPD GO	DRP1D_ARATH	Dynamin-related protein 1D (Dynamin-like protein D) (Dynamin-like protein DLP3)	0.49	-	mit	0	Cytoplasm (By similarity). Microtubule-associated (By similarity)				612
O18738 UniProt NPD GO	DAG1_BOVIN	Dystroglycan precursor (Dystrophin-associated glycoprotein 1) [Contains: Alpha-dystroglycan (Alpha-D ...	0.49	-	exc	1	Alpha-dystroglycan: Secreted protein; extracellular space. Beta-dystroglycan: Cell membrane; single- ...				895
Q9TSZ6 UniProt NPD GO	DAG1_CANFA	Dystroglycan precursor (Dystrophin-associated glycoprotein 1) [Contains: Alpha-dystroglycan (Alpha-D ...	0.49	-	exc	1	Alpha-dystroglycan: Secreted protein; extracellular space. Beta-dystroglycan: Cell membrane; single- ...				892
Q9D4J1 UniProt NPD GO	EFHD1_MOUSE	EF-hand domain-containing protein 1 (Swiprosin-2)	0.49	-	nuc	0		mitochondrial inner membrane [IDA]			240
Q9D8Y0 UniProt NPD GO	EFHD2_MOUSE	EF-hand domain-containing protein 2 (Swiprosin-1)	0.49	-	cyt	0					240
P41163 UniProt NPD GO	ETV2_MOUSE	ETS translocation variant 2 (Ets-related protein 71)	0.49	+	nuc	0	Nucleus				335
P51023 UniProt NPD GO	PNT2_DROME	ETS-like protein pointed, isoform P2 (D-ETS-2)	0.49	+	nuc	0	Nucleus (Potential)				718
Q76CA2 UniProt NPD GO	ACTP2_CYMEC	Echotoxin-2 precursor (Echt 2)	0.49	-	exc	0	Secreted protein				276
Q8VHX2 UniProt NPD GO	EDAD_MOUSE	Ectodysplasin A receptor-associated adapter protein (EDAR-associated death domain protein) (Crinkled ...	0.49	-	nuc	0	Cytoplasm (Probable)	cytoplasm [NAS]			208
Q91V98 UniProt NPD GO	CD248_MOUSE	Endosialin precursor (Tumor endothelial marker 1) (CD248 antigen)	0.49	-	exc	1	Membrane; single-pass type I membrane protein (Probable)	cytoplasm [IDA]			765
P29323 UniProt NPD GO	EPHB2_HUMAN	Ephrin type-B receptor 2 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EPH-3) (DRT) (Rec ...	0.49	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS] synapse [ISS]	600997	1F0M	1055
P05453 UniProt NPD GO	ERF2_YEAST	Eukaryotic peptide chain release factor GTP-binding subunit (ERF2) (Translation release factor 3) (P ...	0.49	-	nuc	0	Cytoplasm (Probable)	cytosol [TAS] translation release factor complex [IDA]		1YJP	685
Q66JS6 UniProt NPD GO	IF31_MOUSE	Eukaryotic translation initiation factor 3 subunit 1 (eIF-3 alpha)	0.49	-	cyt	0					263
Q7Z6M2 UniProt NPD GO	FBX33_HUMAN	F-box only protein 33	0.49	-	mit	0			609103		555
Q32LM4 UniProt NPD GO	FBX39_BOVIN	F-box only protein 39	0.49	-	cyt	0					443
Q6X9E4 UniProt NPD GO	FBW12_HUMAN	F-box/WD repeat protein 12 (F-box and WD-40 domain protein 12) (F-box only protein 35)	0.49	-	cyt	0			609075		464
P38911 UniProt NPD GO	FKBP3_YEAST	FK506-binding nuclear protein (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Proline r ...	0.49	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			411
O44185 UniProt NPD GO	FLP13_CAEEL	FMRFamide-like neuropeptide 13 precursor [Contains: AADGAPLIRF-amide 1; AADGAPLIRF-amide 2]	0.49	-	exc	0	Secreted protein	extracellular region [IC]			160
Q6SJP8 UniProt NPD GO	FG17B_BRARE	Fibroblast growth factor 17b precursor (FGF-17b)	0.49	-	nuc	0	Secreted protein (By similarity)	extracellular region [ISS]			215
P55075 UniProt NPD GO	FGF8_HUMAN	Fibroblast growth factor 8 precursor (FGF-8) (HBGF-8) (Androgen-induced growth factor) (AIGF)	0.49	-	exc	0	Secreted protein		600483	2FDB	233
Q9QY10 UniProt NPD GO	FGFP1_RAT	Fibroblast growth factor-binding protein 1 precursor (FGF-binding protein 1) (FGF-BP1) (FGFBP-1) (FG ...	0.49	-	exc	0	Secreted protein; extracellular space (Probable). Extracellular and plasma membrane-associated (By s ...				238
P25010 UniProt NPD GO	CCNAL_DAUCA	G2/mitotic-specific cyclin C13-1 (A-like cyclin) (Fragment)	0.49	+	cyt	0					341
Q8H1G0 UniProt NPD GO	GAT25_ARATH	GATA transcription factor 25 (ZIM-like 2 protein)	0.49	-	nuc	0	Nucleus (Probable)				302
O89100 UniProt NPD GO	GRAP2_MOUSE	GRB2-related adaptor protein 2 (GADS protein) (Growth factor receptor-binding protein) (GRBLG) (GRB- ...	0.49	-	cyt	0				2D0N	322
Q9H3Q3 UniProt NPD GO	G3ST2_HUMAN	Galactose-3-O-sulfotransferase 2 (EC 2.8.2.-) (Gal3ST-2) (Galbeta1-3GalNAc 3'-sulfotransferase 2) (B ...	0.49	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)	membrane [TAS]	608237		398
Q96RP7 UniProt NPD GO	G3ST4_HUMAN	Galactose-3-O-sulfotransferase 4 (EC 2.8.2.-) (Galbeta1-3GalNAc 3'-sulfotransferase) (Beta-galactose ...	0.49	-	nuc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)	integral to membrane [NAS] membrane fraction [IDA]	608235		486
O75899 UniProt NPD GO	GABR2_HUMAN	Gamma-aminobutyric acid type B receptor, subunit 2 precursor (GABA-B receptor 2) (GABA-B-R2) (Gb2) ( ...	0.49	-	end	7	Cell membrane; multi-pass membrane protein. Moreover coexpression of GABA-B-R1 and GABA-B-R2 appears ...	integral to plasma membrane [TAS]	607340		941
P50572 UniProt NPD GO	GBRR1_RAT	Gamma-aminobutyric-acid receptor rho-1 subunit precursor (GABA(A) receptor)	0.49	-	end	4	Membrane; multi-pass membrane protein				474
Q8VE33 UniProt NPD GO	GD1L1_MOUSE	Ganglioside-induced differentiation-associated protein 1-like 1 (GDAP1-L1)	0.49	-	nuc	1					370
Q9C6I4 UniProt NPD GO	G2OX7_ARATH	Gibberellin 2-beta-dioxygenase 7 (EC 1.14.11.13) (Gibberellin 2-beta-hydroxylase 7) (Gibberellin 2-o ...	0.49	-	cyt	0					336
P15505 UniProt NPD GO	GCSP_CHICK	Glycine dehydrogenase [decarboxylating], mitochondrial precursor (EC 1.4.4.2) (Glycine decarboxylase ...	0.49	-	mit	0	Mitochondrion				1004
Q7TNC8 UniProt NPD GO	GLRA2_MOUSE	Glycine receptor alpha-2 chain precursor	0.49	-	end	4	Membrane; multi-pass membrane protein				452

You are viewing entries 25551 to 25600 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.