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
P54776 UniProt NPD GO	PRS6A_LYCES	26S protease regulatory subunit 6A homolog (TAT-binding protein homolog 1) (TBP-1) (Mg(2+)-dependent ...	0.31	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				423
P46507 UniProt NPD GO	PRS6B_MANSE	26S protease regulatory subunit 6B (ATPase MS73)	0.31	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				415
P19682 UniProt NPD GO	ROC3_NICSY	28 kDa ribonucleoprotein, chloroplast precursor (28RNP)	0.31	-	mit	0	Plastid; chloroplast				276
P54397 UniProt NPD GO	FKB39_DROME	39 kDa FK506-binding nuclear protein (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Ro ...	0.31	-	nuc	0	Nucleus (Probable)				357
Q9BZE1 UniProt NPD GO	RM37_HUMAN	39S ribosomal protein L37, mitochondrial precursor (L37mt) (MRP-L37)	0.31	-	cyt	0	Mitochondrion	mitochondrial ribosome [NAS]			423
Q56JX8 UniProt NPD GO	RS13_BOVIN	40S ribosomal protein S13	0.31	-	nuc	0					150
Q6ITC7 UniProt NPD GO	RS13_CHICK	40S ribosomal protein S13	0.31	-	nuc	0					150
P62277 UniProt NPD GO	RS13_HUMAN	40S ribosomal protein S13	0.31	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	180476		150
P62301 UniProt NPD GO	RS13_MOUSE	40S ribosomal protein S13	0.31	-	nuc	0					150
P62278 UniProt NPD GO	RS13_RAT	40S ribosomal protein S13	0.31	-	nuc	0					150
P19951 UniProt NPD GO	RS142_MAIZE	40S ribosomal protein S14 (Clone MCH2)	0.31	-	nuc	0					150
Q9SIH0 UniProt NPD GO	RS141_ARATH	40S ribosomal protein S14-1	0.31	-	mit	0	Cytoplasm				150
Q9CAX6 UniProt NPD GO	RS142_ARATH	40S ribosomal protein S14-2	0.31	-	cyt	0	Cytoplasm				150
Q42340 UniProt NPD GO	RS16_ARATH	40S ribosomal protein S16	0.31	-	cyt	0	Cytoplasm				146
Q962R2 UniProt NPD GO	RS17_SPOFR	40S ribosomal protein S17	0.31	-	nuc	0					132
Q3T0R1 UniProt NPD GO	RS18_BOVIN	40S ribosomal protein S18	0.31	-	mit	0	Cytoplasm				152
Q5TJE9 UniProt NPD GO	RS18_CANFA	40S ribosomal protein S18	0.31	-	mit	0	Cytoplasm				152
P62272 UniProt NPD GO	RS18_PIG	40S ribosomal protein S18	0.31	-	mit	0	Cytoplasm				152
P62271 UniProt NPD GO	RS18_RAT	40S ribosomal protein S18	0.31	-	mit	0	Cytoplasm				152
P62269 UniProt NPD GO	RS18_HUMAN	40S ribosomal protein S18 (Ke-3) (Ke3)	0.31	-	mit	0	Cytoplasm	cytosolic small ribosomal subunit (sensu Eu... [IDA]	180473		152
P62270 UniProt NPD GO	RS18_MOUSE	40S ribosomal protein S18 (Ke-3) (Ke3)	0.31	-	mit	0	Cytoplasm				152
P48153 UniProt NPD GO	RS3_MANSE	40S ribosomal protein S3	0.31	-	cyt	0					243
Q6DV02 UniProt NPD GO	RS3A_GECJA	40S ribosomal protein S3a	0.31	+	nuc	0					263
Q4R4Z6 UniProt NPD GO	RS3A_MACFA	40S ribosomal protein S3a	0.31	+	nuc	0					263
P97351 UniProt NPD GO	RS3A_MOUSE	40S ribosomal protein S3a	0.31	+	nuc	0		cytosol [IDA] nucleus [IDA] ribosome [NAS]			263
Q642T2 UniProt NPD GO	RS3A_XENTR	40S ribosomal protein S3a	0.31	+	nuc	0					263
P02362 UniProt NPD GO	RS7_XENLA	40S ribosomal protein S7 (S8)	0.31	-	nuc	0					194
P12672 UniProt NPD GO	RAPSN_MOUSE	43 kDa receptor-associated protein of the synapse (RAPsyn) (Acetylcholine receptor-associated 43 kDa ...	0.31	-	cyt	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic surface of postsynaptic me ...	Golgi apparatus [IDA] plasma membrane [IDA]			411
Q61112 UniProt NPD GO	CAB45_MOUSE	45 kDa calcium-binding protein precursor (Cab45) (Stromal cell-derived factor 4) (SDF-4)	0.31	-	vac	1 *	Golgi apparatus; Golgi lumen				361
Q91ZS3 UniProt NPD GO	CAB45_RAT	45 kDa calcium-binding protein precursor (Cab45) (Stromal cell-derived factor 4) (SDF-4)	0.31	-	mit	1 *	Golgi apparatus; Golgi lumen (By similarity)				361
P54646 UniProt NPD GO	AAPK2_HUMAN	5'-AMP-activated protein kinase catalytic subunit alpha-2 (EC 2.7.11.1) (AMPK alpha-2 chain)	0.31	-	cyt	0			600497		552
P43090 UniProt NPD GO	HEM0_OPSTA	5-aminolevulinate synthase, erythroid-specific, mitochondrial precursor (EC 2.3.1.37) (5-aminolevuli ...	0.31	-	mit	0	Mitochondrion; mitochondrial matrix				582
P43091 UniProt NPD GO	HEM1_OPSTA	5-aminolevulinate synthase, nonspecific, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic aci ...	0.31	-	mit	0	Mitochondrion; mitochondrial matrix				627
Q9D110 UniProt NPD GO	MTHFS_MOUSE	5-formyltetrahydrofolate cyclo-ligase (EC 6.3.3.2) (5,10-methenyl-tetrahydrofolate synthetase) (Meth ...	0.31	-	mit	0	Cytoplasm (By similarity)				202
P23979 UniProt NPD GO	5HT3R_MOUSE	5-hydroxytryptamine 3 receptor precursor (5-HT-3) (Serotonin-gated ion channel receptor) (5-HT3R)	0.31	-	end	4	Membrane; multi-pass membrane protein				487
P20905 UniProt NPD GO	5HT1R_DROME	5-hydroxytryptamine receptor 1 (5-HT receptor) (Serotonin receptor 1) (5HT-dro)	0.31	-	end	8 *	Membrane; multi-pass membrane protein				564
P47860 UniProt NPD GO	K6PP_RAT	6-phosphofructokinase type C (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phosphofruct ...	0.31	+	cyt	0					788
Q867C9 UniProt NPD GO	K6PF_HORSE	6-phosphofructokinase, muscle type (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phosph ...	0.31	-	cyt	0		6-phosphofructokinase complex [ISS]			779
P00511 UniProt NPD GO	K6PF_RABIT	6-phosphofructokinase, muscle type (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phosph ...	0.31	-	cyt	0		6-phosphofructokinase complex [ISS]			779
P47858 UniProt NPD GO	K6PF_RAT	6-phosphofructokinase, muscle type (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phosph ...	0.31	-	cyt	0		6-phosphofructokinase complex [ISS]			779
O95337 UniProt NPD GO	YZX3_HUMAN	6.2 kDa protein from clone 683	0.31	-	mit	0					59
Q8SR96 UniProt NPD GO	RL10_ENCCU	60S ribosomal protein L10	0.31	-	mit	0					219
O61231 UniProt NPD GO	RL10_DROME	60S ribosomal protein L10 (QM protein homolog) (dQM)	0.31	-	mit	0					218
Q9P720 UniProt NPD GO	RL16_NEUCR	60S ribosomal protein L16	0.31	+	cyt	0					202
P38653 UniProt NPD GO	RL21_ENTHI	60S ribosomal protein L21	0.31	-	nuc	0					166
Q9FDZ9 UniProt NPD GO	RL212_ARATH	60S ribosomal protein L21-2	0.31	-	cyt	0					164
P47198 UniProt NPD GO	RL22_RAT	60S ribosomal protein L22	0.31	-	nuc	0					127
P50886 UniProt NPD GO	RL22_XENLA	60S ribosomal protein L22	0.31	-	nuc	0					127
Q28IL6 UniProt NPD GO	RL22_XENTR	60S ribosomal protein L22	0.31	-	nuc	0					127
P05743 UniProt NPD GO	RL26A_YEAST	60S ribosomal protein L26-A (YL33)	0.31	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [IDA]		1K5Y	126

You are viewing entries 39101 to 39150 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.