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
O78435 UniProt NPD GO	MINE_GUITH	Putative cell division topological specificity factor	0.31	-	cyt	0	Plastid; chloroplast				88
O64789 UniProt NPD GO	DRL18_ARATH	Putative disease resistance protein At1g61310	0.31	-	nuc	0					925
Q21230 UniProt NPD GO	IF2B_CAEEL	Putative eukaryotic translation initiation factor 2 subunit beta (eIF-2-beta)	0.31	+	cyt	0					250
P58961 UniProt NPD GO	GR47B_DROME	Putative gustatory receptor 47b	0.31	-	mit	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			414
P38205 UniProt NPD GO	NCL1_YEAST	Putative methyltransferase NCL1 (EC 2.1.1.-)	0.31	-	mit	0	Nucleus; nucleolus	nucleus [IDA]			684
P40556 UniProt NPD GO	YIA6_YEAST	Putative mitochondrial carrier YIL006W	0.31	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			373
Q09535 UniProt NPD GO	PCH2_CAEEL	Putative pachytene checkpoint protein 2	0.31	-	nuc	0					424
P48460 UniProt NPD GO	YY06_CAEEL	Putative serine/threonine-protein phosphatase C27B7.6 in chromosome IV (EC 3.1.3.16)	0.31	-	mit	0					415
P48727 UniProt NPD GO	YMEX_CAEEL	Putative serine/threonine-protein phosphatase F56C9.1 in chromosome III (EC 3.1.3.16)	0.31	-	cyt	0					333
Q9SRV7 UniProt NPD GO	SY131_ARATH	Putative syntaxin-131 (AtSYP131)	0.31	-	cyt	1	Membrane; single-pass type IV membrane protein (By similarity)				306
O60908 UniProt NPD GO	YG02_HUMAN	Putative uncharacterized protein A-363E6.1	0.31	-	nuc	0					56
Q94IN5 UniProt NPD GO	PNO_EUGGR	Pyruvate dehydrogenase [NADP+], mitochondrial precursor (EC 1.2.1.51) (EC 1.16.1.5) (Pyruvate:NADP+ ...	0.31	-	nuc	0	Mitochondrion	mitochondrion [IDA]			1803
Q63484 UniProt NPD GO	AKT3_RAT	RAC-gamma serine/threonine-protein kinase (EC 2.7.11.1) (RAC-PK-gamma) (Protein kinase Akt-3) (Prote ...	0.31	-	cyt	0					454
Q8IV61 UniProt NPD GO	GRP3_HUMAN	RAS guanyl-releasing protein 3 (Calcium and DAG-regulated guanine nucleotide exchange factor III) (G ...	0.31	-	nuc	0		integral to plasma membrane [NAS]	609531		690
Q6NW40 UniProt NPD GO	RGMB_HUMAN	RGM domain family member B precursor	0.31	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				437
Q3U9F6 UniProt NPD GO	RN166_MOUSE	RING finger protein 166	0.31	-	nuc	0					237
Q6J1I7 UniProt NPD GO	RN166_RAT	RING finger protein 166	0.31	-	nuc	0					237
Q920M2 UniProt NPD GO	RNF39_RAT	RING finger protein 39 (LTP-induced RING finger protein)	0.31	-	nuc	0	Cytoplasm				352
O22255 UniProt NPD GO	ATL2N_ARATH	RING-H2 finger protein ATL2N	0.31	+	nuc	1 *					227
Q7X843 UniProt NPD GO	ATL3I_ARATH	RING-H2 finger protein ATL3I (YGHL1-C3HC4 RING fusion protein)	0.31	-	end	3 *					349
Q99278 UniProt NPD GO	MED11_YEAST	RNA polymerase II mediator complex subunit 11	0.31	-	nuc	0	Nucleus	mediator complex [IDA]			131
O94376 UniProt NPD GO	MED21_SCHPO	RNA polymerase II mediator complex subunit 21 (Suppressor of RNA polymerase B 7)	0.31	-	nuc	0	Nucleus (Potential)	mediator complex [IDA]			138
Q8VE92 UniProt NPD GO	RBM4B_MOUSE	RNA-binding protein 4B (RNA-binding motif protein 4B) (RNA-binding protein 30) (RNA-binding motif pr ...	0.31	-	nuc	0	Nucleus; nucleolus (By similarity)				357
Q9CWY9 UniProt NPD GO	RIP_MOUSE	RPA-interacting protein	0.31	-	nuc	0	Nucleus (By similarity)				219
Q4G2Y1 UniProt NPD GO	RIP_RAT	RPA-interacting protein	0.31	-	nuc	0	Nucleus (By similarity)				219
Q68Y52 UniProt NPD GO	RAC2_ORYSA	Rac-like GTP-binding protein 2 (OsRac2)	0.31	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				214
Q6FVF9 UniProt NPD GO	ERFD_CANGA	Ras modification protein ERF4	0.31	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				290
Q10182 UniProt NPD GO	ERFD_SCHPO	Ras modification protein erf4	0.31	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				172
Q9UN86 UniProt NPD GO	G3BP2_HUMAN	Ras-GTPase-activating protein-binding protein 2 (GAP SH3-domain-binding protein 2) (G3BP-2)	0.31	-	nuc	0	Cytoplasm	cytoplasm [NAS]			482
Q8R367 UniProt NPD GO	RERG_MOUSE	Ras-related and estrogen-regulated growth inhibitor	0.31	-	cyt	0	Cytoplasm (By similarity)				199
P61020 UniProt NPD GO	RAB5B_HUMAN	Ras-related protein Rab-5B	0.31	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side. Endosome; early endosome; early endosome membrane; li ...	endosome [IDA]	179514		215
P61021 UniProt NPD GO	RAB5B_MOUSE	Ras-related protein Rab-5B	0.31	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side. Endosome; early endosome; early endosome membrane; li ...	endocytic vesicle [IDA]			215
P18433 UniProt NPD GO	PTPRA_HUMAN	Receptor-type tyrosine-protein phosphatase alpha precursor (EC 3.1.3.48) (Protein-tyrosine phosphata ...	0.31	-	end	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	176884		802
Q03348 UniProt NPD GO	PTPRA_RAT	Receptor-type tyrosine-protein phosphatase alpha precursor (EC 3.1.3.48) (Protein-tyrosine phosphata ...	0.31	-	nuc	1	Membrane; single-pass type I membrane protein				796
P49799 UniProt NPD GO	RGS4_RAT	Regulator of G-protein signaling 4 (RGS4) (RGP4)	0.31	-	nuc	0				1EZY	205
O95758 UniProt NPD GO	ROD1_HUMAN	Regulator of differentiation 1 (Rod1)	0.31	-	nuc	0			607527		521
Q8QZY4 UniProt NPD GO	RTBDN_MOUSE	Retbindin precursor	0.31	-	nuc	1 *	Secreted protein (Potential)				247
Q9TVB8 UniProt NPD GO	RPE65_CANFA	Retinal pigment epithelium-specific 65 kDa protein	0.31	+	mit	0	Cytoplasm (By similarity). Cell membrane; lipid-anchor (By similarity). Attached to the membrane by ...				532
Q9XT71 UniProt NPD GO	RPE65_CERAE	Retinal pigment epithelium-specific 65 kDa protein	0.31	+	mit	0	Cytoplasm (By similarity). Cell membrane; lipid-anchor (By similarity). Attached to the membrane by ...				532
Q16518 UniProt NPD GO	RPE65_HUMAN	Retinal pigment epithelium-specific 65 kDa protein	0.31	+	mit	0	Cytoplasm (By similarity). Cell membrane; lipid-anchor (By similarity). Attached to the membrane by ...		204100		532
Q2HJ68 UniProt NPD GO	RND1_BOVIN	Rho-related GTP-binding protein Rho6 (Rho family GTPase 1) (Rnd1)	0.31	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				232
Q9D3G9 UniProt NPD GO	RHOH_MOUSE	Rho-related GTP-binding protein RhoH	0.31	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				191
O15974 UniProt NPD GO	OPSD2_PATYE	Rhodopsin, G0-coupled (G0-rhodopsin)	0.31	-	end	7 *	Membrane; multi-pass membrane protein				399
P00671 UniProt NPD GO	RNAS1_PIG	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.31	-	nuc	0	Secreted protein				124
Q9WTT5 UniProt NPD GO	RNAS1_ACOCA	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.31	-	exc	0	Secreted protein				149
P18653 UniProt NPD GO	KS6A1_MOUSE	Ribosomal protein S6 kinase alpha-1 (EC 2.7.11.1) (S6K-alpha 1) (90 kDa ribosomal protein S6 kinase ...	0.31	-	cyt	0		spindle [IDA]			724
Q9UK32 UniProt NPD GO	KS6A6_HUMAN	Ribosomal protein S6 kinase alpha-6 (EC 2.7.11.1) (S6K-alpha 6) (90 kDa ribosomal protein S6 kinase ...	0.31	-	cyt	0			300303		745
P24478 UniProt NPD GO	RIPS_TRIKI	Ribosome-inactivating protein karasurin-C precursor (EC 3.2.2.22) (rRNA N-glycosidase) [Contains: Ri ...	0.31	-	exc	0					289
P16499 UniProt NPD GO	PDE6A_HUMAN	Rod cGMP-specific 3',5'-cyclic phosphodiesterase alpha-subunit (EC 3.1.4.35) (GMP-PDE alpha) (PDE V- ...	0.31	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		268000		859
P32340 UniProt NPD GO	NDI1_YEAST	Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial precursor (EC 1.6.5.3) (Internal ...	0.31	-	mit	1	Mitochondrion; mitochondrial inner membrane. Bound to the mitochondrial inner membrane facing the ma ...	mitochondrial matrix [IDA]			513

You are viewing entries 39801 to 39850 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.