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
Q6GLM9 UniProt NPD GO	CSN5_XENLA	COP9 signalosome complex subunit 5 (EC 3.4.-.-) (Signalosome subunit 5)	0.05	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				332
Q6P635 UniProt NPD GO	CSN5_XENTR	COP9 signalosome complex subunit 5 (EC 3.4.-.-) (Signalosome subunit 5)	0.05	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				334
Q6FU69 UniProt NPD GO	CSN9_CANGA	COP9 signalosome complex subunit 9	0.05	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				146
Q9SLP8 UniProt NPD GO	CAMT_CITNA	Caffeoyl-CoA O-methyltransferase (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase) (CCoAMT) ...	0.05	-	cyt	0					232
O04854 UniProt NPD GO	CAMT_EUCGU	Caffeoyl-CoA O-methyltransferase (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase) (CCoAMT) ...	0.05	-	cyt	0					249
P63099 UniProt NPD GO	CANB1_BOVIN	Calcineurin subunit B isoform 1 (Protein phosphatase 2B regulatory subunit 1) (Protein phosphatase 3 ...	0.05	-	cyt	0				1TCO	169
P63098 UniProt NPD GO	CANB1_HUMAN	Calcineurin subunit B isoform 1 (Protein phosphatase 2B regulatory subunit 1) (Protein phosphatase 3 ...	0.05	-	cyt	0		calcineurin complex [NAS]	601302	1MF8	169
Q63810 UniProt NPD GO	CANB1_MOUSE	Calcineurin subunit B isoform 1 (Protein phosphatase 2B regulatory subunit 1) (Protein phosphatase 3 ...	0.05	-	cyt	0					169
P63100 UniProt NPD GO	CANB1_RAT	Calcineurin subunit B isoform 1 (Protein phosphatase 2B regulatory subunit 1) (Protein phosphatase 3 ...	0.05	-	cyt	0					169
P28470 UniProt NPD GO	CANB2_RAT	Calcineurin subunit B isoform 2 (Protein phosphatase 2B regulatory subunit 2) (Protein phosphatase 3 ...	0.05	-	cyt	0					175
P25117 UniProt NPD GO	CALCR_PIG	Calcitonin receptor precursor (CT-R)	0.05	-	end	7	Membrane; multi-pass membrane protein				498
O01305 UniProt NPD GO	CAVP_BRAFL	Calcium vector protein (CAVP)	0.05	-	cyt	0	Cytoplasm (By similarity)				161
P04573 UniProt NPD GO	CAVP_BRALA	Calcium vector protein (CAVP)	0.05	-	cyt	0	Cytoplasm			1J7R	161
P38505 UniProt NPD GO	CALBP_ENTHI	Calcium-binding protein (CABP)	0.05	-	cyt	0				2EV7	134
P97391 UniProt NPD GO	PA2G5_MOUSE	Calcium-dependent phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (PLA ...	0.05	-	cyt	0	Secreted protein. Membrane. Also associated with various membranous organelles including the Golgi a ...				137
P25618 UniProt NPD GO	CWH43_YEAST	Calcofluor white hypersensitive protein precursor	0.05	-	end	19 *	Cell membrane; multi-pass membrane protein. Concentrates to the bud tip of small budded cells and to ...	bud neck [IDA] bud tip [IDA] integral to plasma membrane [IDA]			953
Q3SB10 UniProt NPD GO	CALGL_HOPST	Calglandulin	0.05	-	cyt	0	Cytoplasm (Probable). Not found in venom (By similarity)				156
Q3SB12 UniProt NPD GO	CALGL_NOTSC	Calglandulin	0.05	-	cyt	0	Cytoplasm (Probable). Not found in venom (By similarity)				156
Q3SB14 UniProt NPD GO	CALGL_OXYMI	Calglandulin	0.05	-	cyt	0	Cytoplasm (Probable). Not found in venom (By similarity)				156
Q3SB15 UniProt NPD GO	CALGL_OXYSC	Calglandulin	0.05	-	cyt	0	Cytoplasm (Probable). Not found in venom (By similarity)				156
Q3SB09 UniProt NPD GO	CALGL_PSEAU	Calglandulin	0.05	-	cyt	0	Cytoplasm (Probable). Not found in venom (By similarity)				156
Q3SB08 UniProt NPD GO	CALGL_PSEPO	Calglandulin	0.05	-	cyt	0	Cytoplasm (Probable). Not found in venom (By similarity)				156
Q3SB13 UniProt NPD GO	CALGL_PSETE	Calglandulin	0.05	-	cyt	0	Cytoplasm (Probable). Not found in venom (By similarity)				156
Q3SB11 UniProt NPD GO	CALGL_TROCA	Calglandulin	0.05	-	cyt	0	Cytoplasm (Probable). Not found in venom (By similarity)				156
P41865 UniProt NPD GO	FARA_CALVO	CalliFMRFamide-10	0.05	-		0	Secreted protein				9
P41869 UniProt NPD GO	FARI_CALVO	CalliMIRFamide-1	0.05	-		0	Secreted protein				12
P15094 UniProt NPD GO	CALM_ACHKL	Calmodulin (CaM)	0.05	-	cyt	0					148
P62144 UniProt NPD GO	CALM_ANAPL	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]			148
P62145 UniProt NPD GO	CALM_APLCA	Calmodulin (CaM)	0.05	-	cyt	0					148
P62157 UniProt NPD GO	CALM_BOVIN	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]		2F2P	148
Q6PI52 UniProt NPD GO	CALM_BRARE	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]			148
O16305 UniProt NPD GO	CALM_CAEEL	Calmodulin (CaM)	0.05	-	cyt	0				1OOJ	148
P62149 UniProt NPD GO	CALM_CHICK	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]		2BKI	148
Q6IT78 UniProt NPD GO	CALM_CTEID	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]			148
P62152 UniProt NPD GO	CALM_DROME	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [IDA] rhabdomere [IDA]		4CLN	148
Q7T3T2 UniProt NPD GO	CALM_EPIAK	Calmodulin (CaM)	0.05	-	cyt	0					148
Q5EHV7 UniProt NPD GO	CALM_GECJA	Calmodulin (CaM)	0.05	-	cyt	0					148
P62158 UniProt NPD GO	CALM_HUMAN	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [TAS] plasma membrane [TAS]	114180	2F3Z	148
O60041 UniProt NPD GO	CALM_KLULA	Calmodulin (CaM)	0.05	-	cyt	0					147
P62154 UniProt NPD GO	CALM_LOCMI	Calmodulin (CaM)	0.05	-	cyt	0					148
Q9GRJ1 UniProt NPD GO	CALM_LUMRU	Calmodulin (CaM)	0.05	-	cyt	0					148
Q40302 UniProt NPD GO	CALM_MACPY	Calmodulin (CaM)	0.05	-	cyt	0					148
Q95NR9 UniProt NPD GO	CALM_METSE	Calmodulin (CaM)	0.05	-	cyt	0					148
P62204 UniProt NPD GO	CALM_MOUSE	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]		2DFS	148
Q9U6D3 UniProt NPD GO	CALM_MYXGL	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]			148
P62156 UniProt NPD GO	CALM_ONCSP	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]			148
Q6R520 UniProt NPD GO	CALM_OREMO	Calmodulin (CaM)	0.05	-	cyt	0					148
P02595 UniProt NPD GO	CALM_PATSP	Calmodulin (CaM)	0.05	-	cyt	0					148
Q71UH6 UniProt NPD GO	CALM_PERFV	Calmodulin (CaM)	0.05	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]			148
P27165 UniProt NPD GO	CALM_PHYIN	Calmodulin (CaM)	0.05	-	cyt	0					148

You are viewing entries 73951 to 74000 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.