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
P53012 UniProt NPD GO	SCS3_YEAST	Protein SCS3	0.08	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			380
P33335 UniProt NPD GO	SGE1_YEAST	Protein SGE1 (Crystal violet resistance protein) (10-N-nonyl acridine orange resistance protein)	0.08	-	end	14 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			543
P53078 UniProt NPD GO	SSM1_YEAST	Protein SSM1	0.08	-	cyt	0					280
Q06563 UniProt NPD GO	SYM1_YEAST	Protein SYM1 (Stress-inducible yeast MPV17 protein 1)	0.08	+	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			197
Q9S7R5 UniProt NPD GO	TSF_ARATH	Protein TWIN SISTER of FT (TFL1-like protein)	0.08	-	cyt	0	Cytoplasm (By similarity)				175
Q8BPP5 UniProt NPD GO	U3023_MOUSE	Protein UNQ3023/PRO9821 precursor	0.08	-	nuc	0	Secreted protein (By similarity)				171
P28141 UniProt NPD GO	WNT1_SCEOC	Protein Wnt-1 (Fragment)	0.08	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				126
P47793 UniProt NPD GO	WNT4A_BRARE	Protein Wnt-4a precursor	0.08	-	end	1 *	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [NAS]			352
P28097 UniProt NPD GO	WNT6_STRPU	Protein Wnt-6 (Fragment)	0.08	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				117
P38616 UniProt NPD GO	YGP1_YEAST	Protein YGP1 precursor (GP38)	0.08	-	exc	0	Secreted protein	cell wall (sensu Fungi) [TAS]			354
Q7SXS2 UniProt NPD GO	YIPF5_XENLA	Protein YIPF5 (YIP1 family member 5)	0.08	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				256
Q5XID0 UniProt NPD GO	YIPF5_RAT	Protein YIPF5 (YIP1 family member 5) (YPT-interacting protein 1 A)	0.08	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				257
P38374 UniProt NPD GO	YSY6_YEAST	Protein YSY6	0.08	-	mit	1 *	Membrane; peripheral membrane protein	endoplasmic reticulum [IDA]			65
Q8VED2 UniProt NPD GO	CNO_MOUSE	Protein cappuccino	0.08	-	cyt	0	Cytoplasm				215
Q4WNS8 UniProt NPD GO	ECM33_ASPFU	Protein ecm33 precursor	0.08	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				398
O62829 UniProt NPD GO	PP2CA_BOVIN	Protein phosphatase 2C isoform alpha (EC 3.1.3.16) (PP2C-alpha)	0.08	-	nuc	0					382
P35813 UniProt NPD GO	PP2CA_HUMAN	Protein phosphatase 2C isoform alpha (EC 3.1.3.16) (PP2C-alpha) (IA) (Protein phosphatase 1A)	0.08	-	nuc	0			606108	1A6Q	382
Q4WDZ0 UniProt NPD GO	SYM1_ASPFU	Protein sym1	0.08	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				196
Q96TW8 UniProt NPD GO	SC61A_HANAN	Protein transport protein SEC61 subunit alpha	0.08	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				479
P78979 UniProt NPD GO	SC61A_YARLI	Protein transport protein SEC61 subunit alpha	0.08	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				471
Q9TSM6 UniProt NPD GO	TP4A1_MACFA	Protein tyrosine phosphatase type IVA protein 1 (EC 3.1.3.48) (Protein-tyrosine phosphatase 4a1) (Pr ...	0.08	-	mit	0	Cell membrane. Endosome; early endosome. Endoplasmic reticulum. Cytoplasm. And mitotic spindle				173
Q63739 UniProt NPD GO	TP4A1_MOUSE	Protein tyrosine phosphatase type IVA protein 1 (EC 3.1.3.48) (Protein-tyrosine phosphatase 4a1) (Pr ...	0.08	-	mit	0	Cell membrane. Endosome; early endosome. Endoplasmic reticulum. Cytoplasm. And mitotic spindle	endosome [TAS] plasma membrane [TAS]			173
Q78EG7 UniProt NPD GO	TP4A1_RAT	Protein tyrosine phosphatase type IVA protein 1 (EC 3.1.3.48) (Protein-tyrosine phosphatase 4a1) (Pr ...	0.08	-	mit	0	Cell membrane (By similarity). Endosome; early endosome (By similarity). Endoplasmic reticulum (By s ...	nucleus [IDA]		1ZCL	173
Q93096 UniProt NPD GO	TP4A1_HUMAN	Protein tyrosine phosphatase type IVA protein 1 (EC 3.1.3.48) (Protein-tyrosine phosphatase 4a1) (Pr ...	0.08	-	mit	0	Cell membrane. Endosome; early endosome. Endoplasmic reticulum. Cytoplasm. And mitotic spindle		601585	1XM2	173
O70274 UniProt NPD GO	TP4A2_MOUSE	Protein tyrosine phosphatase type IVA protein 2 (EC 3.1.3.48) (Protein-tyrosine phosphatase 4a2) (Pr ...	0.08	-	mit	0	Cell membrane. Endosome; early endosome. Cytoplasm				167
Q6P9X4 UniProt NPD GO	TP4A2_RAT	Protein tyrosine phosphatase type IVA protein 2 (EC 3.1.3.48) (Protein-tyrosine phosphatase 4a2) (Pr ...	0.08	-	mit	0	Cell membrane (By similarity). Endosome; early endosome (By similarity). Cytoplasm (By similarity)				167
Q12974 UniProt NPD GO	TP4A2_HUMAN	Protein tyrosine phosphatase type IVA protein 2 (EC 3.1.3.48) (Protein-tyrosine phosphatase 4a2) (Pr ...	0.08	-	mit	0	Cell membrane. Endosome; early endosome. Cytoplasm		601584		167
O75365 UniProt NPD GO	TP4A3_HUMAN	Protein tyrosine phosphatase type IVA protein 3 (EC 3.1.3.48) (Protein-tyrosine phosphatase 4a3) (Pr ...	0.08	-	mit	0	Cell membrane. Endosome; early endosome		606449	1V3A	173
Q9GP81 UniProt NPD GO	YELL_DROGU	Protein yellow precursor	0.08	-	mit	1 *	Secreted protein				568
Q9D0U3 UniProt NPD GO	YPEL6_MOUSE	Protein yippee-like 6	0.08	-	mit	0					119
Q9FN32 UniProt NPD GO	YIPL6_ARATH	Protein yippee-like At5g53940	0.08	-	cyt	0					129
Q9Z185 UniProt NPD GO	PADI1_MOUSE	Protein-arginine deiminase type-1 (EC 3.5.3.15) (Protein-arginine deiminase type I) (Peptidylarginin ...	0.08	-	cyt	0	Cytoplasm (By similarity)				662
O77081 UniProt NPD GO	TPSA_CAEEL	Protein-tyrosine sulfotransferase A (EC 2.8.2.20) (Tyrosylprotein sulfotransferase-A) (TPST-A)	0.08	-	pox	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				380
P01078 UniProt NPD GO	IPR_SOLME	Proteinase inhibitor	0.08	-	nuc	0	Secreted protein				52
Q03198 UniProt NPD GO	IPIA_TOBAC	Proteinase inhibitor I-A precursor (PI-IA) (Inhibitor of microbial serine proteinases minor isoform) ...	0.08	-	exc	0	Secreted protein (Potential)				107
P83241 UniProt NPD GO	IP23_CAPAN	Proteinase inhibitor PSI-1.2	0.08	-	nuc	0					52
Q90ZK2 UniProt NPD GO	PTMA_RANES	Prothymosin alpha (Prot-alpha)	0.08	-	nuc	0	Nucleus (By similarity)				109
Q68F55 UniProt NPD GO	PTMAB_XENLA	Prothymosin alpha-B	0.08	-	cyt	0	Nucleus (By similarity)				112
Q9BYE9 UniProt NPD GO	PCDLK_HUMAN	Protocadherin LKC precursor (PC-LKC)	0.08	-	end	1	Cell membrane; apical cell membrane; single-pass type I membrane protein. Cell membrane; cell-cell j ...	integral to membrane [IDA]			1310
Q8N6Y1 UniProt NPD GO	PCD20_HUMAN	Protocadherin-20 precursor (Protocadherin-13)	0.08	-	mit	1 *	Membrane; single-pass type I membrane protein (By similarity)				924
P60245 UniProt NPD GO	CXP3F_CONPU	Psi-conotoxin PIIIF	0.08	-	nuc	0	Secreted protein			1JLP	24
Q9TT06 UniProt NPD GO	SFTPA_SHEEP	Pulmonary surfactant-associated protein A precursor (SP-A) (PSP-A) (PSAP)	0.08	-	vac	0	Secreted protein; extracellular space (By similarity)				248
Q8IWL2 UniProt NPD GO	SFTA1_HUMAN	Pulmonary surfactant-associated protein A1 precursor (SP-A1) (SP-A) (PSP-A) (PSPA) (Alveolar protein ...	0.08	-	mit	0	Secreted protein; extracellular space		178630		248
Q8IWL1 UniProt NPD GO	SFTA2_HUMAN	Pulmonary surfactant-associated protein A2 precursor (SP-A2) (SP-A) (PSP-A) (PSPA) (Alveolar protein ...	0.08	-	mit	0	Secreted protein; extracellular space		178642		248
P27779 UniProt NPD GO	CUP7_DROME	Pupal cuticle protein Edg-78E precursor	0.08	-	exc	0					122
P40039 UniProt NPD GO	FCY21_YEAST	Purine-cytosine permease FCY21 (PCP FCY21) (Cytosine/purine transport protein FCY21) (Fluorocytosine ...	0.08	-	end	10	Membrane; multi-pass membrane protein (Probable)				528
Q9C5W1 UniProt NPD GO	OPRL2_ARATH	Putative 12-oxophytodienoate reductase-like protein 2 (EC 1.3.1.-)	0.08	-	mit	0					269
Q751Q6 UniProt NPD GO	ATP8L_ASHGO	Putative ATP synthase protein 8-like protein	0.08	-	vac	1 *	Membrane; single-pass membrane protein				48
Q3EAS6 UniProt NPD GO	RECA4_ARATH	Putative DNA repair protein recA homolog 4 (Recombinase A homolog 4)	0.08	-	cyt	0	Cytoplasm (By similarity)				229
P91917 UniProt NPD GO	YCHF_CAEEL	Putative GTP-binding protein W08E3.3	0.08	-	cyt	0					395

You are viewing entries 68851 to 68900 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.