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
P22029 UniProt NPD GO	BOTA_BOTJA	Botrocetin, alpha chain (Platelet coagglutinin)	0.00	-	cyt	0	Secreted protein			1U0O	133
P31862 UniProt NPD GO	IBBWP_MAIZE	Bowman-Birk type wound-induced proteinase inhibitor WIP1 precursor	0.00	-	exc	1 *					102
P31351 UniProt NPD GO	BPP_VIPAS	Bradykinin-potentiating peptide (Angiotensin-converting enzyme inhibitor)	0.00	-		0					10
P30425 UniProt NPD GO	BPP7_BOTIN	Bradykinin-potentiating peptide S5,2 (5A) (Angiotensin-converting enzyme inhibitor)	0.00	-		0					5
Q9GKM4 UniProt NPD GO	BCAT1_SHEEP	Branched-chain-amino-acid aminotransferase, cytosolic (EC 2.6.1.42) (BCAT(c))	0.00	-	cyt	0	Cytoplasm				385
P32423 UniProt NPD GO	BR1_RANBP	Brevinin-1	0.00	-	nuc	0	Secreted protein				24
P82833 UniProt NPD GO	BR1BA_RANBE	Brevinin-1Ba	0.00	-	mit	0	Secreted protein				24
P82834 UniProt NPD GO	BR1BB_RANBE	Brevinin-1Bb	0.00	-	mit	0	Secreted protein				24
P82835 UniProt NPD GO	BR1BC_RANBE	Brevinin-1Bc	0.00	-	mit	0	Secreted protein				24
P82836 UniProt NPD GO	BR1BD_RANBE	Brevinin-1Bd	0.00	-	mit	0	Secreted protein				24
P82837 UniProt NPD GO	BR1BE_RANBE	Brevinin-1Be	0.00	-	nuc	0	Secreted protein				24
P82838 UniProt NPD GO	BR1BF_RANBE	Brevinin-1Bf	0.00	-	mit	0	Secreted protein				24
P40835 UniProt NPD GO	BR1EA_RANES	Brevinin-1Ea	0.00	-	mit	0	Secreted protein				24
P82841 UniProt NPD GO	BR1PA_RANPI	Brevinin-1Pa	0.00	-	nuc	0	Secreted protein				24
P82843 UniProt NPD GO	BR1PC_RANPI	Brevinin-1Pc	0.00	-	nuc	0	Secreted protein				24
P82844 UniProt NPD GO	BR1PD_RANPI	Brevinin-1Pd	0.00	-	nuc	0	Secreted protein				24
P82845 UniProt NPD GO	BR1PE_RANPI	Brevinin-1Pe	0.00	-	nuc	0	Secreted protein				24
P82871 UniProt NPD GO	BR1SY_RANSY	Brevinin-1SY	0.00	-	mit	0	Secreted protein				24
P82904 UniProt NPD GO	BR1SA_RANSP	Brevinin-1Sa	0.00	-	mit	0	Secreted protein				24
P82905 UniProt NPD GO	BR1SB_RANSP	Brevinin-1Sb	0.00	-	cyt	0	Secreted protein				24
P82906 UniProt NPD GO	BR1SC_RANSP	Brevinin-1Sc	0.00	-	cyt	0	Secreted protein				24
P40838 UniProt NPD GO	BR2EB_RANES	Brevinin-2Eb	0.00	-	nuc	0	Secreted protein				33
P40839 UniProt NPD GO	BR2EC_RANES	Brevinin-2Ec	0.00	-	nuc	0	Secreted protein				34
P84842 UniProt NPD GO	BR2EC_RANSA	Brevinin-2Ec	0.00	-	nuc	0	Secreted protein	extracellular region [IDA]			34
P40841 UniProt NPD GO	BR2EE_RANES	Brevinin-2Ee	0.00	-	nuc	0	Secreted protein				29
P82234 UniProt NPD GO	BR2TC_RANTE	Brevinin-2Tc	0.00	-	cyt	0	Secreted protein				29
P82235 UniProt NPD GO	BR2TD_RANTE	Brevinin-2Td	0.00	-	cyt	0	Secreted protein				29
P58803 UniProt NPD GO	BRHP_CONIM	Bromoheptapeptide Im	0.00	-		0	Secreted protein				7
P58804 UniProt NPD GO	CXBW_CONRA	Bromosleeper peptide	0.00	-	cyt	0	Secreted protein				33
P84118 UniProt NPD GO	BURS_PERAM	Bursicon (Bursicon subunit alpha) (Cuticle-tanning hormone) (Fragments)	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			81
P33281 UniProt NPD GO	ERG2_MAGGR	C-8 sterol isomerase (Delta-8--delta-7 sterol isomerase)	0.00	-	end	1 *	Endoplasmic reticulum				221
P32352 UniProt NPD GO	ERG2_YEAST	C-8 sterol isomerase (Delta-8--delta-7 sterol isomerase)	0.00	-	mit	1 *	Endoplasmic reticulum				222
P19094 UniProt NPD GO	CRP_MUSCA	C-reactive protein (Fragment)	0.00	-		0	Secreted protein				20
P12245 UniProt NPD GO	CRP_PLEPL	C-reactive protein (Fragment)	0.00	-	cyt	0	Secreted protein				32
Q4PRD0 UniProt NPD GO	CLEC3_DABRU	C-type lectin-like protein subunit 3 precursor	0.00	-	exc	0	Secreted protein (Potential)				148
P05548 UniProt NPD GO	CAVPT_BRALA	CAVP-target protein (CAVPT)	0.00	-	cyt	0					243
O97703 UniProt NPD GO	CD81_CERAE	CD81 antigen	0.00	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS]			236
P35762 UniProt NPD GO	CD81_MOUSE	CD81 antigen (26 kDa cell surface protein TAPA-1) (Target of the antiproliferative antibody 1)	0.00	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS]			236
P60034 UniProt NPD GO	CD81_PANTR	CD81 antigen (26 kDa cell surface protein TAPA-1) (Target of the antiproliferative antibody 1)	0.00	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS]			236
Q62745 UniProt NPD GO	CD81_RAT	CD81 antigen (26 kDa cell surface protein TAPA-1) (Target of the antiproliferative antibody 1)	0.00	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS]			236
P60033 UniProt NPD GO	CD81_HUMAN	CD81 antigen (26 kDa cell surface protein TAPA-1) (Target of the antiproliferative antibody 1) (Tetr ...	0.00	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]	186845	1IV5	236
Q9N0J9 UniProt NPD GO	CD81_SAGOE	CD81 protein	0.00	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS]			236
P40237 UniProt NPD GO	CD82_MOUSE	CD82 antigen (Inducible membrane protein R2) (C33 antigen) (IA4)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				266
P27701 UniProt NPD GO	CD82_HUMAN	CD82 antigen (Inducible membrane protein R2) (C33 antigen) (IA4) (Metastasis suppressor Kangai 1) (S ...	0.00	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	600623		267
Q8VDP6 UniProt NPD GO	CDIPT_MOUSE	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (EC 2.7.8.11) (Phosphatidylinositol synthase) ...	0.00	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				213
P70500 UniProt NPD GO	CDIPT_RAT	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (EC 2.7.8.11) (Phosphatidylinositol synthase) ...	0.00	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				213
Q9D6G9 UniProt NPD GO	CKLF5_MOUSE	CKLF-like MARVEL transmembrane domain-containing protein 5 (Chemokine-like factor superfamily member ...	0.00	-	end	4 *	Membrane; multi-pass membrane protein				156
Q9CZ69 UniProt NPD GO	CKLF6_MOUSE	CKLF-like MARVEL transmembrane domain-containing protein 6 (Chemokine-like factor superfamily member ...	0.00	-	end	3	Membrane; multi-pass membrane protein				183
Q96FZ5 UniProt NPD GO	CKLF7_HUMAN	CKLF-like MARVEL transmembrane domain-containing protein 7 (Chemokine-like factor superfamily member ...	0.00	-	end	4 *	Membrane; multi-pass membrane protein		607890		175
Q9ESD6 UniProt NPD GO	CKLF7_MOUSE	CKLF-like MARVEL transmembrane domain-containing protein 7 (Chemokine-like factor superfamily member ...	0.00	-	end	4 *	Membrane; multi-pass membrane protein				167

You are viewing entries 92901 to 92950 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.