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
P51675 UniProt NPD GO	CCR1_MOUSE	C-C chemokine receptor type 1 (C-C CKR-1) (CC-CKR-1) (CCR-1) (CCR1) (Macrophage inflammatory protein ...	0.02	-	end	7 *	Membrane; multi-pass membrane protein	plasma membrane [ISS]			355
P51679 UniProt NPD GO	CCR4_HUMAN	C-C chemokine receptor type 4 (C-C CKR-4) (CC-CKR-4) (CCR-4) (CCR4) (K5-5)	0.02	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	604836		360
P47774 UniProt NPD GO	CCR7_MOUSE	C-C chemokine receptor type 7 precursor (C-C CKR-7) (CC-CKR-7) (CCR-7) (MIP-3 beta receptor) (EBV-in ...	0.02	-	end	6	Membrane; multi-pass membrane protein				378
Q9JII9 UniProt NPD GO	CXCR3_RAT	C-X-C chemokine receptor type 3 (CXC-R3) (CXCR-3) (Interferon-inducible protein 10 receptor) (IP-10 ...	0.02	-	end	7	Membrane; multi-pass membrane protein (By similarity)				367
P48199 UniProt NPD GO	CRP_RAT	C-reactive protein precursor	0.02	-	end	0	Secreted protein				230
Q4PRC9 UniProt NPD GO	CLEC4_DABRU	C-type lectin-like protein subunit 4 precursor	0.02	-	end	0	Secreted protein (Potential)				146
P21805 UniProt NPD GO	ANFC_CHICK	C-type natriuretic peptide (CNP)	0.02	-	nuc	0	Secreted protein				22
Q9C8S6 UniProt NPD GO	Y1322_ARATH	C2 domain protein At1g63220	0.02	-	cyt	0				1WFJ	147
Q17345 UniProt NPD GO	CNOT7_CAEEL	CCR4-NOT transcription complex subunit 7 (CCR4-associated factor 1) (CAF1)	0.02	-	cyt	0	Nucleus (By similarity)				310
Q9QZA6 UniProt NPD GO	CD151_RAT	CD151 antigen (Platelet-endothelial tetraspan antigen 3) (PETA-3)	0.02	-	end	4 *	Membrane; multi-pass membrane protein				253
O35566 UniProt NPD GO	CD151_MOUSE	CD151 antigen (Platelet-endothelial tetraspan antigen 3) (PETA-3) (GP27) (Membrane glycoprotein SFA- ...	0.02	-	end	4 *	Membrane; multi-pass membrane protein				253
Q28785 UniProt NPD GO	CD59_PAPSP	CD59 glycoprotein precursor (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory prot ...	0.02	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				126
Q5R510 UniProt NPD GO	CD59_PONPY	CD59 glycoprotein precursor (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory prot ...	0.02	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				128
P41731 UniProt NPD GO	CD63_MOUSE	CD63 antigen	0.02	-	end	4 *	Lysosome; lysosomal membrane; multi-pass membrane protein	late endosome [IDA] lysosome [IDA]			237
P30932 UniProt NPD GO	CD9_BOVIN	CD9 antigen	0.02	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS]			225
Q99LJ5 UniProt NPD GO	CKLF3_MOUSE	CKLF-like MARVEL transmembrane domain-containing protein 3 (Chemokine-like factor superfamily member ...	0.02	-	end	3	Membrane; multi-pass membrane protein				184
Q96DZ9 UniProt NPD GO	CKLF5_HUMAN	CKLF-like MARVEL transmembrane domain-containing protein 5 (Chemokine-like factor superfamily member ...	0.02	-	end	4 *	Membrane; multi-pass membrane protein		607888		223
Q11205 UniProt NPD GO	SIA4B_RAT	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.-) (Beta-galactosi ...	0.02	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				350
Q16842 UniProt NPD GO	SIA4B_HUMAN	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.-) (Beta-galactosi ...	0.02	-	end	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...		607188		350
Q6KB58 UniProt NPD GO	SIA4B_PANTR	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.-) (Beta-galactosi ...	0.02	-	end	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				350
P25923 UniProt NPD GO	CYC02_CATRO	CYC02 protein	0.02	-	exc	1 *					101
O18926 UniProt NPD GO	CADH3_PIG	Cadherin-3 (Placental-cadherin) (P-cadherin) (Fragment)	0.02	-	cyt	0	Membrane; single-pass type I membrane protein (Potential)				145
P56242 UniProt NPD GO	CR41_LITCE	Caerin-4.1	0.02	-	cyt	0	Secreted protein				23
P56243 UniProt NPD GO	CR42_LITCE	Caerin-4.2	0.02	-	cyt	0	Secreted protein				23
Q41086 UniProt NPD GO	COMT2_POPTM	Caffeic acid 3-O-methyltransferase 2 (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyl ...	0.02	-	cyt	0					364
O65162 UniProt NPD GO	CAMT_MESCR	Caffeoyl-CoA O-methyltransferase (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase) (CCoAMT) ...	0.02	-	cyt	0					254
Q9XGD6 UniProt NPD GO	CAMT1_MAIZE	Caffeoyl-CoA O-methyltransferase 1 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase 1) (CCoA ...	0.02	-	cyt	0					258
Q9SWB8 UniProt NPD GO	CAMT2_EUCGL	Caffeoyl-CoA O-methyltransferase 2 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase 2) (CCoA ...	0.02	-	cyt	0					247
O04899 UniProt NPD GO	CAMT5_TOBAC	Caffeoyl-CoA O-methyltransferase 5 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase 5) (CCoA ...	0.02	-	cyt	0					240
Q42945 UniProt NPD GO	CAMT6_TOBAC	Caffeoyl-CoA O-methyltransferase 6 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase 6) (CCoA ...	0.02	-	cyt	0					247
P01260 UniProt NPD GO	CALC_BOVIN	Calcitonin	0.02	-	nuc	0	Secreted protein				32
P31888 UniProt NPD GO	CALCR_RANRI	Calcitonin gene-related peptide (CGRP)	0.02	-	nuc	0					37
Q9R1W5 UniProt NPD GO	CALRL_MOUSE	Calcitonin gene-related peptide type 1 receptor precursor (CGRP type 1 receptor) (Calcitonin recepto ...	0.02	-	end	7	Membrane; multi-pass membrane protein				463
Q63118 UniProt NPD GO	CALRL_RAT	Calcitonin gene-related peptide type 1 receptor precursor (CGRP type 1 receptor) (Calcitonin recepto ...	0.02	-	end	8 *	Membrane; multi-pass membrane protein				464
O75838 UniProt NPD GO	KIP2_HUMAN	Calcium and integrin-binding protein 2 (Kinase-interacting protein 2) (KIP 2)	0.02	-	cyt	0			605564		187
Q9Z309 UniProt NPD GO	KIP2_MOUSE	Calcium and integrin-binding protein 2 (Kinase-interacting protein 2) (KIP 2)	0.02	-	cyt	0					187
Q86V35 UniProt NPD GO	CABP7_HUMAN	Calcium-binding protein 7 (CaBP7)	0.02	-	nuc	1					215
Q91ZM8 UniProt NPD GO	CABP7_MOUSE	Calcium-binding protein 7 (CaBP7)	0.02	-	nuc	1					215
Q866X0 UniProt NPD GO	CABP7_PAPAN	Calcium-binding protein 7 (CaBP7)	0.02	-	nuc	1					215
O42720 UniProt NPD GO	CBP1_AJECA	Calcium-binding protein precursor (CBP)	0.02	-	exc	0	Secreted protein; extracellular space				110
P41866 UniProt NPD GO	FARB_CALVO	CalliFMRFamide-11	0.02	-		0	Secreted protein				7
P41867 UniProt NPD GO	FARC_CALVO	CalliFMRFamide-12	0.02	-		0	Secreted protein				10
P41863 UniProt NPD GO	FAR8_CALVO	CalliFMRFamide-8	0.02	-		0	Secreted protein				8
P41517 UniProt NPD GO	TKC1_CALVO	Callitachykinin-1 (Callitachykinin I)	0.02	-		0	Secreted protein				9
P04352 UniProt NPD GO	CALM_CHLRE	Calmodulin (CaM)	0.02	-	cyt	0					162
P11118 UniProt NPD GO	CALM_EUGGR	Calmodulin (CaM)	0.02	-	cyt	0					148
P25069 UniProt NPD GO	CALM2_ARATH	Calmodulin-2/3/5 (CaM-2/3/5)	0.02	-	cyt	0					148
Q8TD86 UniProt NPD GO	CALL6_HUMAN	Calmodulin-like protein 6 (Calglandulin-like protein)	0.02	-	cyt	0	Cytoplasm. Nucleus				181
O23320 UniProt NPD GO	CML8_ARATH	Calmodulin-like protein 8 (AtCaM-8)	0.02	-	cyt	0					151
P31235 UniProt NPD GO	CASQ2_RABIT	Calsequestrin-2 precursor (Calsequestrin, cardiac muscle isoform)	0.02	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen. This isoform of calsequestrin occurs in the sa ...				409

You are viewing entries 82651 to 82700 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.