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
Q05359 UniProt NPD GO	ERP1_YEAST	Protein ERP1 precursor	0.05	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	ER to Golgi transport vesicle [IDA] mitochondrion [IDA]			219
Q8NFB2 UniProt NPD GO	FA11A_HUMAN	Protein FAM11A	0.05	-	end	8 *	Membrane; multi-pass membrane protein (Potential)		300483		350
Q5R8H8 UniProt NPD GO	FA11A_PONPY	Protein FAM11A	0.05	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				350
Q7TPG7 UniProt NPD GO	F19A2_MOUSE	Protein FAM19A2 precursor (Chemokine-like protein TAFA-2)	0.05	-	mit	0	Cytoplasm (By similarity)				131
Q8IU99 UniProt NPD GO	FA26C_HUMAN	Protein FAM26C	0.05	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				346
P48362 UniProt NPD GO	HGH1_YEAST	Protein HGH1	0.05	-	nuc	0		cytoplasm [IDA]			394
Q99181 UniProt NPD GO	HSH49_YEAST	Protein HSH49	0.05	-	nuc	0	Nucleus (Potential)	snRNP U2 [IDA]			213
Q5FVQ4 UniProt NPD GO	K0152_RAT	Protein KIAA0152 homolog precursor	0.05	-	end	1	Membrane; single-pass type I membrane protein (Potential)				291
Q6ZQI3 UniProt NPD GO	K0152_MOUSE	Protein KIAA0152 precursor	0.05	-	end	1	Membrane; single-pass type I membrane protein (Potential)				291
O15453 UniProt NPD GO	NBR2_HUMAN	Protein NBR2 (Next to BRCA1 gene 2 protein)	0.05	-	cyt	0					112
Q99PA5 UniProt NPD GO	NKG7_MOUSE	Protein NKG7 (Natural killer cell protein 7)	0.05	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				165
Q9UHT4 UniProt NPD GO	P1854_HUMAN	Protein PRO1854	0.05	-	cyt	0					67
Q00245 UniProt NPD GO	RHO3_YEAST	Protein RHO3	0.05	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	intracellular [TAS]			231
Q9P8J9 UniProt NPD GO	RHO3_SCHCO	Protein Rho3	0.05	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				206
P27003 UniProt NPD GO	S10AA_CHICK	Protein S100-A10 (S100 calcium-binding protein A10) (Calpactin-1 light chain) (Calpactin I light cha ...	0.05	-	cyt	1					96
P97352 UniProt NPD GO	S10AD_MOUSE	Protein S100-A13 (S100 calcium-binding protein A13)	0.05	-	cyt	0					98
P79342 UniProt NPD GO	S10AD_BOVIN	Protein S100-A13 (S100 calcium-binding protein A13) (8 kDa amlexanox-binding protein)	0.05	-	cyt	0					98
P33764 UniProt NPD GO	S10A3_HUMAN	Protein S100-A3 (S100 calcium-binding protein A3) (Protein S-100E)	0.05	-	cyt	0			176992	1KSO	101
Q2EN75 UniProt NPD GO	S10A6_PIG	Protein S100-A6 (S100 calcium-binding protein A6) (Calcyclin)	0.05	-	cyt	0					90
P02634 UniProt NPD GO	S100G_RAT	Protein S100-G (S100 calcium-binding protein G) (Vitamin D-dependent calcium-binding protein, intest ...	0.05	-	nuc	0					78
Q15513 UniProt NPD GO	SPHAR_HUMAN	Protein SPHAR (S-phase response protein)	0.05	-	mit	0					63
Q6BMY0 UniProt NPD GO	SYM1_DEBHA	Protein SYM1	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				206
Q6CIY7 UniProt NPD GO	SYM1_KLULA	Protein SYM1	0.05	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				195
Q969M1 UniProt NPD GO	TM40L_HUMAN	Protein TOMM40-like	0.05	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				308
P28115 UniProt NPD GO	WNT4_EPTST	Protein Wnt-4 (Fragment)	0.05	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				119
P31290 UniProt NPD GO	WNT7C_XENLA	Protein Wnt-7c (XWnt-7c) (Fragment)	0.05	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				135
P53039 UniProt NPD GO	YIP1_YEAST	Protein YIP1 (YPT-interacting protein 1)	0.05	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum membrane [IDA] ER to Golgi transport vesicle [IDA] integral to Golgi membrane [IDA]			248
P53093 UniProt NPD GO	YIP4_YEAST	Protein YIP4 (YPT-interacting protein 4)	0.05	-	end	4	Membrane; multi-pass membrane protein (Potential)				235
Q9Y548 UniProt NPD GO	YIPF1_HUMAN	Protein YIPF1 (YIP1 family member 1)	0.05	-	end	5	Membrane; multi-pass membrane protein (Potential)				306
Q5RBL0 UniProt NPD GO	YIPF1_PONPY	Protein YIPF1 (YIP1 family member 1)	0.05	-	end	5	Membrane; multi-pass membrane protein (Potential)				306
Q99LP8 UniProt NPD GO	YIPF2_MOUSE	Protein YIPF2 (YIP1 family member 2)	0.05	-	end	5	Membrane; multi-pass membrane protein (Potential)				312
Q6P5I8 UniProt NPD GO	YIPF5_BRARE	Protein YIPF5 (YIP1 family member 5)	0.05	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				257
Q96EC8 UniProt NPD GO	YIPF6_HUMAN	Protein YIPF6 (YIP1 family member 6)	0.05	-	end	5	Membrane; multi-pass membrane protein (Potential)				236
P06293 UniProt NPD GO	PRTZ_HORVU	Protein Z (Z4) (Major endosperm albumin)	0.05	-	cyt	0					399
P29518 UniProt NPD GO	BT1_MAIZE	Protein brittle-1, chloroplast precursor	0.05	-	mit	0	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (Potential). Plastid; ...				436
P52588 UniProt NPD GO	PDI_MAIZE	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI)	0.05	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				513
P07237 UniProt NPD GO	PDIA1_HUMAN	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI) (Prolyl 4-hydroxylase subunit beta) (Cellul ...	0.05	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Highly abundant. In some cell types, seems to be ...	cell surface [IEP] endoplasmic reticulum [TAS] ER-Golgi intermediate compartment [IDA] extracellular region [NAS]	176790	2BJX	508
Q5R5B6 UniProt NPD GO	PDIA1_PONPY	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI) (Prolyl 4-hydroxylase subunit beta) (Cellul ...	0.05	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Highly abundant. In some cell types, seems to be ...				508
P49028 UniProt NPD GO	MGN_DROME	Protein mago nashi	0.05	-	cyt	0	Nucleus. Cytoplasm. Part of the EJC assembled on mRNAs in the nucleus and remains part of the comple ...	cytoplasm [IDA] nucleus [IDA]		1RK8	147
P49029 UniProt NPD GO	MGN_CAEEL	Protein mago nashi homolog (Ce-mago)	0.05	-	cyt	0	Nucleus (By similarity)				152
P23487 UniProt NPD GO	MEX1_DROME	Protein midgut expression 1	0.05	-	cyt	1 *					83
Q5ZL05 UniProt NPD GO	ORAI1_CHICK	Protein orai-1	0.05	-	mit	3 *	Cell membrane; multi-pass membrane protein (By similarity)				226
Q5ZLW2 UniProt NPD GO	ORAI2_CHICK	Protein orai-2	0.05	-	end	3	Membrane; multi-pass membrane protein (By similarity)				257
Q8BH10 UniProt NPD GO	ORAI2_MOUSE	Protein orai-2	0.05	-	end	4	Membrane; multi-pass membrane protein (By similarity)				250
Q6P8G8 UniProt NPD GO	ORAI3_MOUSE	Protein orai-3	0.05	-	end	3	Membrane; multi-pass membrane protein (By similarity)				290
Q6AXR8 UniProt NPD GO	ORAI3_RAT	Protein orai-3	0.05	-	end	3	Membrane; multi-pass membrane protein (By similarity)				290
P20650 UniProt NPD GO	PP2CA_RAT	Protein phosphatase 2C isoform alpha (EC 3.1.3.16) (PP2C-alpha) (IA) (Protein phosphatase 1A)	0.05	-	nuc	0					382
Q9V579 UniProt NPD GO	PREL_DROME	Protein preli-like	0.05	-	cyt	0	Mitochondrion	mitochondrion [IDA]			236
O13928 UniProt NPD GO	RHO3_SCHPO	Protein rho3	0.05	-	cyt	0	Cell membrane; lipid anchor. Found at the cell periphery and the growing tips of interphase cells. L ...				205
P21748 UniProt NPD GO	SALA_DROOR	Protein spalt-accessory precursor	0.05	-	cyt	0	Secreted protein (By similarity)				142

You are viewing entries 75401 to 75450 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.