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
P30426 UniProt NPD GO	BPP8_BOTIN	Bradykinin-potentiating peptide S5,1 (Angiotensin-converting enzyme inhibitor)	0.01	-		0					10
P81754 UniProt NPD GO	BP37_LEUMA	Brain peptide 37F3	0.01	-		0					13
O95563 UniProt NPD GO	BR44_HUMAN	Brain protein 44	0.01	-	cyt	0					127
P24288 UniProt NPD GO	BCAT1_MOUSE	Branched-chain-amino-acid aminotransferase, cytosolic (EC 2.6.1.42) (BCAT(c)) (ECA39 protein)	0.01	-	cyt	0	Cytoplasm	cytosol [IDA]			386
O14370 UniProt NPD GO	BCA1_SCHPO	Branched-chain-amino-acid aminotransferase, mitochondrial precursor (EC 2.6.1.42) (BCAT)	0.01	-	cyt	0	Mitochondrion (Potential)	mitochondrial matrix [IGI]			380
P84111 UniProt NPD GO	BR1YA_RANBO	Brevinin-1BYa	0.01	-	cyt	0	Secreted protein				24
P84112 UniProt NPD GO	BR1YB_RANBO	Brevinin-1BYb	0.01	-	cyt	0	Secreted protein				24
P84113 UniProt NPD GO	BR1YC_RANBO	Brevinin-1BYc	0.01	-	mit	0	Secreted protein				24
P82825 UniProt NPD GO	BR1LA_RANLU	Brevinin-1La	0.01	-	nuc	0	Secreted protein				24
P82826 UniProt NPD GO	BR1LB_RANLU	Brevinin-1Lb	0.01	-	nuc	0	Secreted protein				24
Q8QFQ5 UniProt NPD GO	BR1PB_RANPI	Brevinin-1Pb precursor	0.01	-	end	0	Secreted protein (Probable)				69
P82232 UniProt NPD GO	BR1T_RANTE	Brevinin-1T	0.01	-		0	Secreted protein				20
P32424 UniProt NPD GO	BR2_RANBP	Brevinin-2	0.01	-	nuc	0	Secreted protein				33
P40837 UniProt NPD GO	BR2EA_RANES	Brevinin-2Ea	0.01	-	nuc	0	Secreted protein				33
P14518 UniProt NPD GO	BROM2_ANACO	Bromelain, stem (EC 3.4.22.32)	0.01	-	cyt	0					212
P82815 UniProt NPD GO	SCBK_MESMA	Bukatoxin	0.01	-	cyt	0	Secreted protein (By similarity)				65
O59933 UniProt NPD GO	ERG25_CANAL	C-4 methylsterol oxidase (EC 1.14.13.72) (Methylsterol monooxygenase)	0.01	-	nuc	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Probable)				308
O35532 UniProt NPD GO	ERG25_RAT	C-4 methylsterol oxidase (EC 1.14.13.72) (Methylsterol monooxygenase) (Neuropep 1) (RANP-1)	0.01	-	nuc	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				293
Q92254 UniProt NPD GO	ERG2_NEUCR	C-8 sterol isomerase (Delta-8--delta-7 sterol isomerase)	0.01	-	mit	1 *	Endoplasmic reticulum				256
P51680 UniProt NPD GO	CCR4_MOUSE	C-C chemokine receptor type 4 (C-C CKR-4) (CC-CKR-4) (CCR-4) (CCR4)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				360
Q28553 UniProt NPD GO	CXCR4_SHEEP	C-X-C chemokine receptor type 4 (CXC-R4) (CXCR-4) (SDF-1 receptor) (Stromal cell-derived factor 1 re ...	0.01	-	end	4 *	Membrane; multi-pass membrane protein				192
O18983 UniProt NPD GO	CXCR6_CERAE	C-X-C chemokine receptor type 6 (CXC-R6) (CXCR-6) (G-protein coupled receptor bonzo)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				342
P05731 UniProt NPD GO	PHCB_CYAPA	C-phycocyanin beta chain	0.01	-	mit	0	Plastid; cyanelle				172
P06205 UniProt NPD GO	CRP1_LIMPO	C-reactive protein 1.1 precursor	0.01	-	exc	0	Secreted protein			1LIM	242
P06207 UniProt NPD GO	CRP3_LIMPO	C-reactive protein 3.3 precursor	0.01	-	exc	0	Secreted protein				242
Q4PRC8 UniProt NPD GO	CLEC5_DABRU	C-type lectin-like protein subunit 5 precursor	0.01	-	end	0	Secreted protein (Potential)				148
O75973 UniProt NPD GO	C1QRF_HUMAN	C1q-related factor precursor (Complement component 1 Q subcomponent-like 1)	0.01	-	exc	0	Secreted protein				258
O88992 UniProt NPD GO	C1QRF_MOUSE	C1q-related factor precursor (Complement component 1 Q subcomponent-like 1)	0.01	-	exc	0	Secreted protein	cytoplasm [IDA]			258
P20851 UniProt NPD GO	C4BB_HUMAN	C4b-binding protein beta chain precursor	0.01	-	mit	0		extracellular region [NAS]	120831		252
Q6UWJ8 UniProt NPD GO	C16L2_HUMAN	CD164 sialomucin-like 2 protein precursor	0.01	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				174
Q9D6W7 UniProt NPD GO	C16L2_MOUSE	CD164 sialomucin-like 2 protein precursor	0.01	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				172
Q28216 UniProt NPD GO	CD59_CERAE	CD59 glycoprotein precursor (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory prot ...	0.01	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				128
Q8SQ46 UniProt NPD GO	CD59_MACFA	CD59 glycoprotein precursor (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory prot ...	0.01	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				128
O62680 UniProt NPD GO	CD59_PIG	CD59 glycoprotein precursor (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory prot ...	0.01	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor				123
P13987 UniProt NPD GO	CD59_HUMAN	CD59 glycoprotein precursor (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory prot ...	0.01	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	membrane fraction [TAS] plasma membrane [NAS]	107271	1ERH	128
Q9XSK2 UniProt NPD GO	CD63_BOVIN	CD63 antigen	0.01	-	end	4 *	Lysosome; lysosomal membrane; multi-pass membrane protein (By similarity)				236
Q76B49 UniProt NPD GO	CD63_FELCA	CD63 antigen	0.01	-	end	4 *	Lysosome; lysosomal membrane; multi-pass membrane protein (By similarity)				237
Q28709 UniProt NPD GO	CD63_RABIT	CD63 antigen	0.01	-	end	4 *	Lysosome; lysosomal membrane; multi-pass membrane protein (By similarity)				237
P28648 UniProt NPD GO	CD63_RAT	CD63 antigen (Mast cell antigen AD1)	0.01	-	end	4 *	Lysosome; lysosomal membrane; multi-pass membrane protein. Cell membrane; multi-pass membrane protei ...	integral to membrane [TAS] lysosome [IDA] plasma membrane [IDA]			237
P08962 UniProt NPD GO	CD63_HUMAN	CD63 antigen (Melanoma-associated antigen ME491) (Lysosome-associated membrane glycoprotein 3) (LAMP ...	0.01	-	end	4 *	Lysosome; lysosomal membrane; multi-pass membrane protein	endosome membrane [IDA] integral to plasma membrane [TAS] lysosomal membrane [TAS] plasma membrane [TAS]	155740		237
O70352 UniProt NPD GO	CD82_RAT	CD82 antigen (Metastasis suppressor homolog)	0.01	-	end	4 *	Membrane; multi-pass membrane protein				266
O14735 UniProt NPD GO	CDIPT_HUMAN	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (EC 2.7.8.11) (Phosphatidylinositol synthase) ...	0.01	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...		605893		213
P06197 UniProt NPD GO	PIS_YEAST	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (EC 2.7.8.11) (Phosphatidylinositol synthase) ...	0.01	-	mit	3 *	Microsome. Mitochondrion; mitochondrial outer membrane; peripheral membrane protein	microsome [IDA] mitochondrial outer membrane [IDA]			220
Q96MX0 UniProt NPD GO	CKLF3_HUMAN	CKLF-like MARVEL transmembrane domain-containing protein 3 (Chemokine-like factor superfamily member ...	0.01	-	end	3	Membrane; multi-pass membrane protein		607886		182
Q8IZV2 UniProt NPD GO	CKLF8_HUMAN	CKLF-like MARVEL transmembrane domain-containing protein 8 (Chemokine-like factor superfamily member ...	0.01	-	end	4 *	Membrane; multi-pass membrane protein		607891		173
Q9CZR4 UniProt NPD GO	CKLF8_MOUSE	CKLF-like MARVEL transmembrane domain-containing protein 8 (Chemokine-like factor superfamily member ...	0.01	-	end	4 *	Membrane; multi-pass membrane protein				173
Q11204 UniProt NPD GO	SIA4B_MOUSE	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.-) (Beta-galactosi ...	0.01	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				350
Q8VEH6 UniProt NPD GO	CBWD1_MOUSE	COBW domain-containing protein 1	0.01	-	cyt	0					393
Q99MB4 UniProt NPD GO	CBWD1_RAT	COBW domain-containing protein 1	0.01	-	cyt	0					394
P68396 UniProt NPD GO	CSN8_BRAOL	COP9 signalosome complex subunit 8 (CSN complex subunit 8) (Constitutive photomorphogenesis protein ...	0.01	-	cyt	0	Cytoplasm. Nucleus				23

You are viewing entries 86901 to 86950 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.