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
P28874 UniProt NPD GO	KRE1_CANAL	Protein KRE1 precursor (Fragment)	0.03	-	end	2 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)				130
P40185 UniProt NPD GO	MMF1_YEAST	Protein MMF1, mitochondrial precursor (Maintenance of mitochondrial function 1) (Isoleucine biosynth ...	0.03	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA] mitochondrion [IDA]			145
Q9XFK7 UniProt NPD GO	MFT_ARATH	Protein MOTHER of FT and TF1	0.03	-	cyt	0	Cytoplasm (By similarity)				173
Q2KIN6 UniProt NPD GO	MPV17_BOVIN	Protein Mpv17	0.03	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				176
P39210 UniProt NPD GO	MPV17_HUMAN	Protein Mpv17	0.03	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to peroxisomal membrane [NAS] mitochondrial inner membrane [IDA]	251880		176
P19258 UniProt NPD GO	MPV17_MOUSE	Protein Mpv17 (Mpv-17)	0.03	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				176
P52920 UniProt NPD GO	NBP35_YEAST	Protein NBP35	0.03	-	cyt	0	Nucleus	nucleus [IDA]			328
Q5RAA9 UniProt NPD GO	NPS3A_PONPY	Protein NipSnap3A	0.03	-	mit	0	Cytoplasm; cytosol. May be part of some vesicular structure distinct from lysosomal vesicles (By sim ...				247
Q6CY85 UniProt NPD GO	PNS1_KLULA	Protein PNS1	0.03	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				553
P97361 UniProt NPD GO	PLUNC_MOUSE	Protein Plunc precursor (Palate lung and nasal epithelium clone protein)	0.03	-	cyt	0	Secreted protein (By similarity). Found in the nasal mucus (By similarity). Apical side of airway ep ...	extracellular region [ISS]			278
Q9NP55 UniProt NPD GO	PLUNC_HUMAN	Protein Plunc precursor (Palate lung and nasal epithelium clone protein) (Lung-specific protein X) ( ...	0.03	-	mit	0	Secreted protein (By similarity). Found in the nasal mucus (By similarity). Apical side of airway ep ...	extracellular region [IDA]	607412		256
P11634 UniProt NPD GO	QAX_NEUCR	Protein QA-X	0.03	-	mit	0					340
Q9HF51 UniProt NPD GO	RHO3_ASHGO	Protein RHO3	0.03	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				224
P08207 UniProt NPD GO	S10AA_MOUSE	Protein S100-A10 (S100 calcium-binding protein A10) (Calpactin-1 light chain) (Calpactin I light cha ...	0.03	-	cyt	1					96
P05943 UniProt NPD GO	S10AA_RAT	Protein S100-A10 (S100 calcium-binding protein A10) (Calpactin-1 light chain) (Calpactin I light cha ...	0.03	-	nuc	1					94
P79105 UniProt NPD GO	S10AC_BOVIN	Protein S100-A12 (S100 calcium-binding protein A12) (Calgranulin-C) (CAGC) (Calcium-binding protein ...	0.03	-	cyt	0					91
P06703 UniProt NPD GO	S10A6_HUMAN	Protein S100-A6 (S100 calcium-binding protein A6) (Calcyclin) (Prolactin receptor-associated protein ...	0.03	-	cyt	0		cytoplasm [TAS] nuclear envelope [NAS]	114110	1K9P	90
P27005 UniProt NPD GO	S10A8_MOUSE	Protein S100-A8 (S100 calcium-binding protein A8) (Calgranulin-A) (Migration inhibitory factor-relat ...	0.03	-	cyt	0					88
P82646 UniProt NPD GO	SCR27_ARATH	Protein SCRL27 precursor	0.03	-	cyt	0					93
Q6FXJ3 UniProt NPD GO	SYM1_CANGA	Protein SYM1	0.03	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				210
Q4P9K6 UniProt NPD GO	SYM1_USTMA	Protein SYM1	0.03	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				199
Q6CAW5 UniProt NPD GO	SYM1_YARLI	Protein SYM1	0.03	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				202
O74238 UniProt NPD GO	SNP1_PHANO	Protein SnodProt1 precursor	0.03	-	exc	0	Secreted protein (Potential)				136
P54006 UniProt NPD GO	TOXD_COCCA	Protein TOXD	0.03	-	cyt	0					297
P36227 UniProt NPD GO	USP2_PUCGR	Protein USP2 precursor	0.03	-	exc	2 *	Secreted protein (Probable)				113
Q6P6G5 UniProt NPD GO	YIPF1_RAT	Protein YIPF1 (YIP1 family member 1)	0.03	-	end	5	Membrane; multi-pass membrane protein (Potential)				306
Q5F384 UniProt NPD GO	YIPF3_CHICK	Protein YIPF3 (YIP1 family member 3)	0.03	-	end	5	Cell membrane; multi-pass membrane protein. Cytoplasm (By similarity)				336
Q3B8G4 UniProt NPD GO	YIPF3_XENLA	Protein YIPF3 (YIP1 family member 3)	0.03	-	end	5	Cell membrane; multi-pass membrane protein. Cytoplasm (By similarity)				341
Q9GZM5 UniProt NPD GO	YIPF3_HUMAN	Protein YIPF3 (YIP1 family member 3) (Killer lineage protein 1) (Natural killer cell-specific antige ...	0.03	-	end	5	Cell membrane; multi-pass membrane protein. Cytoplasm. Localization to the cytoplasm or to the cell ...		609775		350
Q5R6W5 UniProt NPD GO	YIPF5_PONPY	Protein YIPF5 (YIP1 family member 5)	0.03	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				257
Q969M3 UniProt NPD GO	YIPF5_HUMAN	Protein YIPF5 (YIP1 family member 5) (YPT-interacting protein 1 A) (Five-pass transmembrane protein ...	0.03	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				257
Q28CH8 UniProt NPD GO	YIPF6_XENTR	Protein YIPF6 (YIP1 family member 6)	0.03	-	end	5	Membrane; multi-pass membrane protein (Potential)				233
Q5KEZ1 UniProt NPD GO	YOP1_CRYNE	Protein YOP1	0.03	-	mit	2	Membrane; multi-pass membrane protein (Potential)				206
Q9JIF0 UniProt NPD GO	ANM1_MOUSE	Protein arginine N-methyltransferase 1 (EC 2.1.1.-)	0.03	-	cyt	0	Nucleus (By similarity)				371
Q63009 UniProt NPD GO	ANM1_RAT	Protein arginine N-methyltransferase 1 (EC 2.1.1.-)	0.03	-	cyt	0	Nucleus (By similarity)	nucleus [IDA]		1ORI	353
Q99873 UniProt NPD GO	ANM1_HUMAN	Protein arginine N-methyltransferase 1 (EC 2.1.1.-) (Interferon receptor 1-bound protein 4)	0.03	-	cyt	0	Nucleus	cytoplasm [TAS] nucleus [IDA]	602950		361
O60678 UniProt NPD GO	ANM3_HUMAN	Protein arginine N-methyltransferase 3 (EC 2.1.1.-) (Heterogeneous nuclear ribonucleoprotein methylt ...	0.03	-	cyt	0	Cytoplasm	cytoplasm [NAS]	603190	2FYT	531
Q01358 UniProt NPD GO	BLI3_NEUCR	Protein bli-3	0.03	-	nuc	0					209
Q5RCH2 UniProt NPD GO	PDIA2_PONPY	Protein disulfide-isomerase A2 precursor (EC 5.3.4.1)	0.03	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				525
Q63081 UniProt NPD GO	PDIA6_RAT	Protein disulfide-isomerase A6 precursor (EC 5.3.4.1) (Protein disulfide isomerase P5) (Calcium-bind ...	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	ER-Golgi intermediate compartment [TAS]			440
Q922R8 UniProt NPD GO	PDIA6_MOUSE	Protein disulfide-isomerase A6 precursor (EC 5.3.4.1) (Thioredoxin domain-containing protein 7)	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				440
Q92249 UniProt NPD GO	ERP38_NEUCR	Protein disulfide-isomerase erp38 precursor (EC 5.3.4.1) (ERp38)	0.03	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				369
Q9XF61 UniProt NPD GO	PDI_DATGL	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI)	0.03	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				507
P54399 UniProt NPD GO	PDI_DROME	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI)	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)	endoplasmic reticulum [IDA]			496
P04785 UniProt NPD GO	PDIA1_RAT	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI) (Prolyl 4-hydroxylase subunit beta) (Cellul ...	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Highly abundant. In some cell types, seems to be ...				509
Q8R4U2 UniProt NPD GO	PDIA1_CRIGR	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI) (Prolyl 4-hydroxylase subunit beta) (p58)	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Highly abundant. In some cell types, seems to be ...				509
P34413 UniProt NPD GO	DPY19_CAEEL	Protein dpy-19 (Protein dumpy-19)	0.03	-	end	10 *					683
P61326 UniProt NPD GO	MGN_HUMAN	Protein mago nashi homolog	0.03	-	cyt	0	Nucleus (By similarity)	nucleus [NAS]	602603	1P27	146
P61327 UniProt NPD GO	MGN_MOUSE	Protein mago nashi homolog	0.03	-	cyt	0	Nucleus (By similarity)	nucleus [NAS]			146
O42149 UniProt NPD GO	MGN_XENLA	Protein mago nashi homolog (Xl-mago)	0.03	-	cyt	0	Nucleus (By similarity)				146

You are viewing entries 81351 to 81400 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.