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
P27518 UniProt NPD GO	CB21_GOSHI	Chlorophyll a-b binding protein 151, chloroplast precursor (LHCII type II CAB-151) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
P27492 UniProt NPD GO	CB21_TOBAC	Chlorophyll a-b binding protein 16, chloroplast precursor (LHCII type I CAB-16) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				266
P04777 UniProt NPD GO	CB21_ARATH	Chlorophyll a-b binding protein 165/180, chloroplast precursor (LHCII type I CAB-165/180)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				267
P24006 UniProt NPD GO	CB2A_PYRPY	Chlorophyll a-b binding protein 1A, chloroplast precursor (LHCII type II CAB-1A) (LHCP)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				278
P10707 UniProt NPD GO	CB2D_LYCES	Chlorophyll a-b binding protein 1D (LHCII type I CAB-1D) (LHCP) (Fragment)	0.01	-	vac	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				116
P04778 UniProt NPD GO	CB22_ARATH	Chlorophyll a-b binding protein 2, chloroplast precursor (LHCII type I CAB-2) (CAB-140) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				267
P08963 UniProt NPD GO	CB22_HORVU	Chlorophyll a-b binding protein 2, chloroplast precursor (LHCII type I CAB-2) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				264
P12331 UniProt NPD GO	CB22_ORYSA	Chlorophyll a-b binding protein 2, chloroplast precursor (LHCII type I CAB-2) (LHCP)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				261
P09755 UniProt NPD GO	CB22_SOYBN	Chlorophyll a-b binding protein 2, chloroplast precursor (LHCII type I CAB-2) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				256
P27493 UniProt NPD GO	CB22_TOBAC	Chlorophyll a-b binding protein 21, chloroplast precursor (LHCII type I CAB-21) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
P04780 UniProt NPD GO	CB22_PETSP	Chlorophyll a-b binding protein 22L, chloroplast precursor (LHCII type I CAB-22L) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				267
P04781 UniProt NPD GO	CB23_PETSP	Chlorophyll a-b binding protein 22R, chloroplast precursor (LHCII type I CAB-22R) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				267
P04782 UniProt NPD GO	CB24_PETSP	Chlorophyll a-b binding protein 25, chloroplast precursor (LHCII type I CAB-25) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				266
P27494 UniProt NPD GO	CB23_TOBAC	Chlorophyll a-b binding protein 36, chloroplast precursor (LHCII type I CAB-36) (LHCP)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
P12062 UniProt NPD GO	CB26_PETSP	Chlorophyll a-b binding protein 37, chloroplast precursor (LHCII type I CAB-37) (LHCP)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
P14276 UniProt NPD GO	CB2E_LYCES	Chlorophyll a-b binding protein 3A, chloroplast precursor (LHCII type I CAB-3A) (LHCP) (Fragments)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				267
P14277 UniProt NPD GO	CB2F_LYCES	Chlorophyll a-b binding protein 3B, chloroplast precursor (LHCII type I CAB-3B) (LHCP) (Fragments)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				267
P07369 UniProt NPD GO	CB2G_LYCES	Chlorophyll a-b binding protein 3C, chloroplast precursor (LHCII type I CAB-3C) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				267
P14278 UniProt NPD GO	CB24_LYCES	Chlorophyll a-b binding protein 4, chloroplast precursor (LHCII type I CAB-4) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
P27495 UniProt NPD GO	CB24_TOBAC	Chlorophyll a-b binding protein 40, chloroplast precursor (LHCII type I CAB-40) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				267
P14279 UniProt NPD GO	CB25_LYCES	Chlorophyll a-b binding protein 5, chloroplast precursor (LHCII type I CAB-5) (LHCP) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				237
P27496 UniProt NPD GO	CB25_TOBAC	Chlorophyll a-b binding protein 50, chloroplast precursor (LHCII type I CAB-50) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				267
P10708 UniProt NPD GO	CB12_LYCES	Chlorophyll a-b binding protein 7, chloroplast precursor (LHCI type II CAB-7)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				270
P27491 UniProt NPD GO	CB27_TOBAC	Chlorophyll a-b binding protein 7, chloroplast precursor (LHCII type I CAB-7) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				267
P04783 UniProt NPD GO	CB25_PETSP	Chlorophyll a-b binding protein 91R, chloroplast precursor (LHCII type I CAB-91R) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				267
P15773 UniProt NPD GO	CB2_MALDO	Chlorophyll a-b binding protein AB10, chloroplast precursor (LHCII type I CAB-AB10) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				268
P12469 UniProt NPD GO	CB23_NICPL	Chlorophyll a-b binding protein C, chloroplast precursor (LHCII type I CAB-C) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				267
P12470 UniProt NPD GO	CB25_NICPL	Chlorophyll a-b binding protein E, chloroplast precursor (LHCII type I CAB-E) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				266
P08222 UniProt NPD GO	CB22_CUCSA	Chlorophyll a-b binding protein of LHCII type 1 (Chlorophyll a-b binding protein of LHCII type I) (C ...	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				206
P22686 UniProt NPD GO	CB2_CHLMO	Chlorophyll a-b binding protein of LHCII type I, chloroplast precursor (CAB) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				256
P15193 UniProt NPD GO	CB2A_PINSY	Chlorophyll a-b binding protein type 2 member 1A, chloroplast precursor (Chlorophyll a-b binding pro ...	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				278
P15194 UniProt NPD GO	CB2B_PINSY	Chlorophyll a-b binding protein type 2 member 1B, chloroplast precursor (Chlorophyll a-b binding pro ...	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				274
P92919 UniProt NPD GO	CB23_APIGR	Chlorophyll a-b binding protein, chloroplast precursor (Allergen Api g 3)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				264
P27519 UniProt NPD GO	CB23_ORYSA	Chlorophyll a-b binding protein, chloroplast precursor (LHCII type I CAB) (LHCP)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein	thylakoid membrane (sensu Viridiplantae) [IEP]			263
P12333 UniProt NPD GO	CB2A_SPIOL	Chlorophyll a-b binding protein, chloroplast precursor (LHCII type I CAB) (LHCP)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein			1RWT	267
P59678 UniProt NPD GO	CLH2_CHEAL	Chlorophyllase type 2 (EC 3.1.1.14) (CaCLH2) (Chlorophyll-chlorophyllido hydrolase 2) (Chlase 2) (Fr ...	0.01	-	cyt	0					21
P59776 UniProt NPD GO	RR19_CHLRE	Chloroplast 30S ribosomal protein S19	0.01	-	nuc	0	Plastid; chloroplast				92
P51310 UniProt NPD GO	RR19_PORPU	Chloroplast 30S ribosomal protein S19	0.01	-	mit	0	Plastid; chloroplast				92
P49496 UniProt NPD GO	RR8_ODOSI	Chloroplast 30S ribosomal protein S8	0.01	-	nuc	0	Plastid; chloroplast				132
P49549 UniProt NPD GO	RK11_ODOSI	Chloroplast 50S ribosomal protein L11	0.01	-	nuc	0	Plastid; chloroplast				141
P31915 UniProt NPD GO	RK12_EUGGR	Chloroplast 50S ribosomal protein L12	0.01	-	cyt	0	Plastid; chloroplast				131
P49550 UniProt NPD GO	RK12_ODOSI	Chloroplast 50S ribosomal protein L12	0.01	-	cyt	0	Plastid; chloroplast				127
P21511 UniProt NPD GO	RK14_EUGGR	Chloroplast 50S ribosomal protein L14	0.01	-	cyt	0	Plastid; chloroplast				121
O46908 UniProt NPD GO	RK6_GUITH	Chloroplast 50S ribosomal protein L6	0.01	-	mit	0	Plastid; chloroplast				179
Q85FN1 UniProt NPD GO	ATPI_ADICA	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.01	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				248
Q00825 UniProt NPD GO	ATPI_ODOSI	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.01	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				242
P51247 UniProt NPD GO	ATPI_PORPU	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.01	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				248
P20864 UniProt NPD GO	CEMA_VICFA	Chloroplast envelope membrane protein (Fragment)	0.01	-	mit	0	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				76
Q5PRC0 UniProt NPD GO	C25HA_BRARE	Cholesterol 25-hydroxylase-like protein A (EC 1.14.99.-)	0.01	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				251
Q567X1 UniProt NPD GO	C25HB_BRARE	Cholesterol 25-hydroxylase-like protein B (EC 1.14.99.-)	0.01	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				282

You are viewing entries 87101 to 87150 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.