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
P17814 UniProt NPD GO	4CL1_ORYSA	4-coumarate--CoA ligase 1 (EC 6.2.1.12) (4CL 1) (4-coumaroyl-CoA synthase 1)	0.04	-	cyt	0					564
Q42524 UniProt NPD GO	4CL1_ARATH	4-coumarate--CoA ligase 1 (EC 6.2.1.12) (4CL 1) (At4CL1) (4-coumaroyl-CoA synthase 1)	0.04	-	nuc	0					561
Q9LU36 UniProt NPD GO	4CL4_ARATH	4-coumarate--CoA ligase 4 (EC 6.2.1.12) (4CL 4) (At4CL4) (4-coumaroyl-CoA synthase 4) (4-coumarate C ...	0.04	-	nuc	0					570
Q00472 UniProt NPD GO	PNPP_SCHPO	4-nitrophenylphosphatase (EC 3.1.3.41) (PNPPase)	0.04	-	cyt	0					298
Q9VWG3 UniProt NPD GO	RS10B_DROME	40S ribosomal protein S10b	0.04	-	cyt	0	Cytoplasm (By similarity)				160
Q03253 UniProt NPD GO	RS12_TRYBB	40S ribosomal protein S12	0.04	-	cyt	0					143
Q759L8 UniProt NPD GO	RS16_ASHGO	40S ribosomal protein S16	0.04	-	cyt	0					143
Q6FR56 UniProt NPD GO	RS16_CANGA	40S ribosomal protein S16	0.04	-	cyt	0					143
O43992 UniProt NPD GO	RS2_LEIAM	40S ribosomal protein S2	0.04	+	cyt	0					265
P31009 UniProt NPD GO	RS2_DROME	40S ribosomal protein S2 (Protein strings of pearls)	0.04	+	cyt	0					267
P27685 UniProt NPD GO	RS2_DICDI	40S ribosomal protein S2 (S4) (LLRep3 protein)	0.04	-	nuc	0					265
P49200 UniProt NPD GO	RS20_ARATH	40S ribosomal protein S20	0.04	-	cyt	0					124
Q32PB8 UniProt NPD GO	RS21_BOVIN	40S ribosomal protein S21	0.04	-	cyt	0					83
P63220 UniProt NPD GO	RS21_HUMAN	40S ribosomal protein S21	0.04	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	180477		83
P63221 UniProt NPD GO	RS21_PIG	40S ribosomal protein S21	0.04	-	cyt	0		ribosome [ISS]			83
Q752J5 UniProt NPD GO	RS22_ASHGO	40S ribosomal protein S22	0.04	-	cyt	0					129
Q19877 UniProt NPD GO	RS23_CAEEL	40S ribosomal protein S23	0.04	-	nuc	0					143
Q9GRJ3 UniProt NPD GO	RS23_LUMRU	40S ribosomal protein S23	0.04	-	nuc	0					143
P83328 UniProt NPD GO	RS30_ONCMY	40S ribosomal protein S30 (Fragment)	0.04	-		0					11
O59950 UniProt NPD GO	RS4_YARLI	40S ribosomal protein S4 (S7)	0.04	-	mit	0					260
O62739 UniProt NPD GO	RS4Y1_MONDO	40S ribosomal protein S4, Y isoform 1	0.04	-	mit	0					262
Q757H6 UniProt NPD GO	RIB7_ASHGO	5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193) (HTP reductase)	0.04	-	cyt	0					246
Q16950 UniProt NPD GO	5HTB1_APLCA	5-hydroxytryptamine 1 receptor (5-HTB1) (Serotonin receptor 1)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				453
P35382 UniProt NPD GO	5HT2A_CAVPO	5-hydroxytryptamine 2A receptor (5-HT-2A) (Serotonin receptor 2A) (5-HT-2) (Fragment)	0.04	-	end	5 *	Cell membrane; multi-pass membrane protein. Localizes to the post-synaptic thickening of axo-dendrit ...				247
P24929 UniProt NPD GO	RK12_TOBAC	50S ribosomal protein L12, chloroplast precursor (CL12)	0.04	-	mit	0	Plastid; chloroplast				186
P36210 UniProt NPD GO	RK121_ARATH	50S ribosomal protein L12-1, chloroplast precursor (CL12-A)	0.04	-	mit	0	Plastid; chloroplast				191
P92959 UniProt NPD GO	RK24_ARATH	50S ribosomal protein L24, chloroplast precursor	0.04	-	mit	0	Plastid; chloroplast				198
P82248 UniProt NPD GO	RK29_SPIOL	50S ribosomal protein L29, chloroplast (Fragment)	0.04	-	nuc	0	Plastid; chloroplast				26
Q7XYP4 UniProt NPD GO	RK3_CHLS6	50S ribosomal protein L3, chloroplast precursor	0.04	-	mit	1 *	Plastid; chloroplast (Potential)				302
Q9TLZ1 UniProt NPD GO	CH60_CYACA	60 kDa chaperonin (Protein Cpn60) (groEL protein)	0.04	-	mit	0	Plastid; chloroplast				530
O02649 UniProt NPD GO	CH60_DROME	60 kDa heat shock protein, mitochondrial precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock p ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			573
Q94660 UniProt NPD GO	RLA0_PLAF8	60S acidic ribosomal protein P0	0.04	-	cyt	0					316
P14869 UniProt NPD GO	RLA0_MOUSE	60S acidic ribosomal protein P0 (L10E)	0.04	-	cyt	0					317
P29763 UniProt NPD GO	RLA1_CHLRE	60S acidic ribosomal protein P1	0.04	-	cyt	0					107
O01359 UniProt NPD GO	RLA1_OSCBR	60S acidic ribosomal protein P1 (Ribosomal protein RPL-21)	0.04	-	cyt	0					112
Q9UU78 UniProt NPD GO	RLA5_SCHPO	60S acidic ribosomal protein P1-alpha 5	0.04	-	cyt	0					109
Q29315 UniProt NPD GO	RLA2_PIG	60S acidic ribosomal protein P2	0.04	-	cyt	0					115
P42037 UniProt NPD GO	RLA2_ALTAL	60S acidic ribosomal protein P2 (Minor allergen Alt a 5) (Alt a 6) (Alt a VI)	0.04	-	exc	0					113
P42039 UniProt NPD GO	RLA4_CLAHE	60S acidic ribosomal protein P2 (Minor allergen Cla h 4) (Cla h IV)	0.04	-	exc	0					111
Q9HFQ4 UniProt NPD GO	RLA4_CANAL	60S acidic ribosomal protein P2-B (CaRP2B)	0.04	-	exc	0					111
Q9SVZ6 UniProt NPD GO	RLA31_ARATH	60S acidic ribosomal protein P3-1	0.04	-	cyt	0					119
O75000 UniProt NPD GO	RL12_SCHPO	60S ribosomal protein L12	0.04	-	cyt	0					165
P50883 UniProt NPD GO	RL121_ARATH	60S ribosomal protein L12-1	0.04	-	cyt	0					166
Q9LFH5 UniProt NPD GO	RL122_ARATH	60S ribosomal protein L12-2	0.04	-	cyt	0					166
P82454 UniProt NPD GO	RL13A_SPIOL	60S ribosomal protein L13a (Fragment)	0.04	-		0					15
O74391 UniProt NPD GO	RL25B_SCHPO	60S ribosomal protein L25-B	0.04	-	nuc	0					141
P38706 UniProt NPD GO	RL27_YEAST	60S ribosomal protein L27	0.04	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			136
Q9SKX8 UniProt NPD GO	RL271_ARATH	60S ribosomal protein L27-1	0.04	-	cyt	0					135
O14388 UniProt NPD GO	RL27A_SCHPO	60S ribosomal protein L27-A	0.04	-	mit	0					136
Q9USX4 UniProt NPD GO	RL33A_SCHPO	60S ribosomal protein L33-A (L37A)	0.04	-	cyt	0					108

You are viewing entries 76051 to 76100 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.