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
Q9GLF3 UniProt NPD GO	CLC5A_PIG	C-type lectin domain family 5 member A (C-type lectin superfamily member 5) (Myeloid DAP12-associati ...	0.03	-	end	1 *	Membrane; single-pass type II membrane protein (Probable)				185
Q4PRC6 UniProt NPD GO	CLEC7_DABRU	C-type lectin-like protein subunit 7 precursor	0.03	-	exc	0	Secreted protein (Potential)				150
Q9TUE1 UniProt NPD GO	C5AR_RABIT	C5a anaphylatoxin chemotactic receptor (C5a-R) (C5aR) (CD88 antigen) (Fragment)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				350
P58020 UniProt NPD GO	CD59_SHEEP	CD59 glycoprotein (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory protein) (MAC- ...	0.03	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				27
Q8WMQ3 UniProt NPD GO	CD9_PIG	CD9 antigen	0.03	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS]			225
P30409 UniProt NPD GO	CD9_CERAE	CD9 antigen (27 kDa diphtheria toxin receptor-associated protein) (DRAP27)	0.03	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS]			227
P21926 UniProt NPD GO	CD9_HUMAN	CD9 antigen (p24) (Leukocyte antigen MIC3) (Motility-related protein) (MRP-1) (Tetraspanin-29) (Tspa ...	0.03	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [NAS] plasma membrane [NAS]	143030		227
P18467 UniProt NPD GO	2DOB_PANTR	CHLA class II histocompatibility antigen, DO beta chain precursor (MHC class II antigen DOB)	0.03	-	nuc	1	Membrane; single-pass type I membrane protein				273
Q8CJ61 UniProt NPD GO	CKLF4_MOUSE	CKLF-like MARVEL transmembrane domain-containing protein 4 (Chemokine-like factor superfamily member ...	0.03	-	end	4	Membrane; multi-pass membrane protein				208
Q11203 UniProt NPD GO	SIAT6_HUMAN	CMP-N-acetylneuraminate-beta-1,4-galactoside alpha-2,3-sialyltransferase (EC 2.4.99.6) (N-acetyllact ...	0.03	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...		606494		375
P61132 UniProt NPD GO	SIAT6_PANTR	CMP-N-acetylneuraminate-beta-1,4-galactoside alpha-2,3-sialyltransferase (EC 2.4.99.6) (N-acetyllact ...	0.03	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				375
Q5KAB0 UniProt NPD GO	CSN5_CRYNE	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	0.03	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				371
Q6CQC6 UniProt NPD GO	CSN9_KLULA	COP9 signalosome complex subunit 9	0.03	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				158
P93711 UniProt NPD GO	CAMT_POPKI	Caffeoyl-CoA O-methyltransferase (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase) (CCoAMT) ...	0.03	-	cyt	0					235
Q43161 UniProt NPD GO	CAMT_STELP	Caffeoyl-CoA O-methyltransferase (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase) (CCoAMT) ...	0.03	-	cyt	0					241
O81185 UniProt NPD GO	CAMT1_EUCGL	Caffeoyl-CoA O-methyltransferase 1 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase 1) (CCoA ...	0.03	-	cyt	0					246
Q9XGD5 UniProt NPD GO	CAMT2_MAIZE	Caffeoyl-CoA O-methyltransferase 2 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase 2) (CCoA ...	0.03	-	cyt	0					264
O65922 UniProt NPD GO	CAMT2_POPTR	Caffeoyl-CoA O-methyltransferase 2 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase 2) (CCoA ...	0.03	-	cyt	0					247
Q8LAS7 UniProt NPD GO	CNBL2_ARATH	Calcineurin B-like protein 2 (SOS3-like calcium-binding protein 1)	0.03	-	cyt	0				1UHN	226
Q96LZ3 UniProt NPD GO	CANB2_HUMAN	Calcineurin subunit B isoform 2 (Protein phosphatase 2B regulatory subunit 2) (Protein phosphatase 3 ...	0.03	-	cyt	0					169
P01262 UniProt NPD GO	CALC_ANGJA	Calcitonin	0.03	-	nuc	0	Secreted protein			1BZB	32
Q06389 UniProt NPD GO	NCS1_YEAST	Calcium-binding protein NCS-1	0.03	-	cyt	0	Peripheral membrane protein. Buds and bud scars			1FPW	189
P41859 UniProt NPD GO	FAR4_CALVO	CalliFMRFamide-4	0.03	-		0	Secreted protein				9
P41860 UniProt NPD GO	FAR5_CALVO	CalliFMRFamide-5	0.03	-		0	Secreted protein				9
P41862 UniProt NPD GO	FAR7_CALVO	CalliFMRFamide-7	0.03	-		0	Secreted protein				9
P41864 UniProt NPD GO	FAR9_CALVO	CalliFMRFamide-9	0.03	-		0	Secreted protein				11
P84339 UniProt NPD GO	CALM_AGABI	Calmodulin (CaM)	0.03	-	cyt	0					148
P02599 UniProt NPD GO	CALM_DICDI	Calmodulin (CaM)	0.03	-	cyt	0					151
P02594 UniProt NPD GO	CALM_ELEEL	Calmodulin (CaM)	0.03	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]			148
Q95NI4 UniProt NPD GO	CALM_HALOK	Calmodulin (CaM)	0.03	-	cyt	0					148
P62162 UniProt NPD GO	CALM_HORVU	Calmodulin (CaM)	0.03	-	cyt	0					148
P41040 UniProt NPD GO	CALM_MAIZE	Calmodulin (CaM)	0.03	-	cyt	0					148
P04464 UniProt NPD GO	CALM_WHEAT	Calmodulin (CaM)	0.03	-	cyt	0					148
P06787 UniProt NPD GO	CALM_YEAST	Calmodulin (CaM)	0.03	-	cyt	0		bud neck [IDA] bud tip [IDA] central plaque of spindle pole body [IDA] cytoplasm [TAS] incipient bud site [IDA] mating projection tip [IDA]		1LKJ	147
O02367 UniProt NPD GO	CALM_CIOIN	Calmodulin (CaM) (Ci-CaM)	0.03	-	cyt	0					148
Q7F8I8 UniProt NPD GO	CALM1_ORYSA	Calmodulin-1 (CaM-1)	0.03	-	cyt	0					148
P25854 UniProt NPD GO	CALM1_ARATH	Calmodulin-1/4 (CaM-1/4)	0.03	-	cyt	0					148
Q9XZP2 UniProt NPD GO	CALM2_BRAFL	Calmodulin-2 (CaM 2)	0.03	-	cyt	0					148
Q9UB37 UniProt NPD GO	CALM2_BRALA	Calmodulin-2 (CaM 2)	0.03	-	cyt	0					148
P62163 UniProt NPD GO	CALM2_SOYBN	Calmodulin-2 (CaM-2)	0.03	-	cyt	0					148
Q9SDJ0 UniProt NPD GO	CALM3_ORYSA	Calmodulin-3 (CaM-3)	0.03	-	cyt	0					148
Q03509 UniProt NPD GO	CALM6_ARATH	Calmodulin-6 (CaM-6)	0.03	-	cyt	0					148
P62150 UniProt NPD GO	CALM_ORYLA	Calmodulin-A (CaM A) (Fragment)	0.03	-	cyt	0					136
P83631 UniProt NPD GO	CPRM_PINNO	Calprismin (Fragment)	0.03	-	nuc	0					61
Q9STD3 UniProt NPD GO	CALR_CHLRE	Calreticulin precursor	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				420
P12637 UniProt NPD GO	CASQ2_CANFA	Calsequestrin-2 precursor (Calsequestrin, cardiac muscle isoform)	0.03	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen. This isoform of calsequestrin occurs in the sa ...			1SJI	410
O14958 UniProt NPD GO	CASQ2_HUMAN	Calsequestrin-2 precursor (Calsequestrin, cardiac muscle isoform)	0.03	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen. This isoform of calsequestrin occurs in the sa ...		604772		399
Q5RAN9 UniProt NPD GO	CASQ2_PONPY	Calsequestrin-2 precursor (Calsequestrin, cardiac muscle isoform)	0.03	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen (By similarity). This isoform of calsequestrin ...				400
O02777 UniProt NPD GO	CNR1_FELCA	Cannabinoid receptor 1 (CB1) (CB-R)	0.03	-	end	7	Membrane; multi-pass membrane protein				472
Q333S9 UniProt NPD GO	CNR1_RANES	Cannabinoid receptor 1 (CB1) (CB-R)	0.03	-	end	7	Membrane; multi-pass membrane protein (By similarity)				462

You are viewing entries 79301 to 79350 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.