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
Q9P4C1 UniProt NPD GO	RT09_KLUMA	40S ribosomal protein S9, mitochondrial precursor	0.73	-	nuc	0	Mitochondrion (Potential)				292
P38120 UniProt NPD GO	RT09_YEAST	40S ribosomal protein S9, mitochondrial precursor	0.73	-	nuc	0	Mitochondrion (Potential)	mitochondrial small ribosomal subunit [IDA]			278
P40383 UniProt NPD GO	XRN1_SCHPO	5'-3' exoribonuclease 1 (EC 3.1.11.-) (Exonuclease 2) (Exonuclease II) (Exo II) (p140)	0.73	-	nuc	0	Nucleus				1328
P47963 UniProt NPD GO	RL13_MOUSE	60S ribosomal protein L13 (A52)	0.73	-	nuc	0					210
O17445 UniProt NPD GO	RL15_DROME	60S ribosomal protein L15	0.73	-	nuc	0					204
Q6F444 UniProt NPD GO	RL24_PLUXY	60S ribosomal protein L24	0.73	-	nuc	0					155
P61485 UniProt NPD GO	RL36A_BRARE	60S ribosomal protein L36a	0.73	-	nuc	0	Cytoplasm				105
P61487 UniProt NPD GO	RL36A_ICTPU	60S ribosomal protein L36a	0.73	-	nuc	0	Cytoplasm				105
P61486 UniProt NPD GO	RL36A_FUGRU	60S ribosomal protein L36a (60S ribosomal protein L44)	0.73	-	nuc	0	Cytoplasm				105
P02385 UniProt NPD GO	RL4B_XENLA	60S ribosomal protein L4-B (L1B) (Fragment)	0.73	+	nuc	0					396
Q26789 UniProt NPD GO	PFR2_TRYBB	73 kDa paraflagellar rod protein (73 kDa PFR protein) (PFR-C/PFR-D)	0.73	-	nuc	0					595
P38682 UniProt NPD GO	GLO3_YEAST	ADP-ribosylation factor GTPase-activating protein GLO3	0.73	-	nuc	0		COPI vesicle coat [IPI] COPI-coated vesicle [IDA] ER-Golgi intermediate compartment [IPI]			493
Q00776 UniProt NPD GO	AP1M1_YEAST	AP-1 complex subunit mu-1 (Mu(1)-adaptin) (Clathrin assembly protein complex 1 medium chain) (Clathr ...	0.73	-	nuc	0	Coated vesicle	AP-1 adaptor complex [IPI]			475
O00203 UniProt NPD GO	AP3B1_HUMAN	AP-3 complex subunit beta-1 (Adapter-related protein complex 3 beta-1 subunit) (Beta3A-adaptin) (Ada ...	0.73	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	Golgi apparatus [TAS]	608233		1094
P26309 UniProt NPD GO	CDC20_YEAST	APC/C activator protein CDC20 (Cell division control protein 20)	0.73	+	nuc	0	Nucleus	anaphase-promoting complex [TAS]			610
Q39295 UniProt NPD GO	AGL15_BRANA	Agamous-like MADS-box protein AGL15	0.73	-	nuc	0	Nucleus (By similarity)				264
Q29414 UniProt NPD GO	ASIP_BOVIN	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.73	+	exc	0	Secreted protein (By similarity)				133
Q5UK76 UniProt NPD GO	ASIP_CANFA	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.73	-	exc	0	Secreted protein (By similarity)				131
P79407 UniProt NPD GO	ASIP_VULVU	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.73	-	exc	0	Secreted protein (By similarity)				131
Q9XTT4 UniProt NPD GO	ANI1_CAEEL	Anillin-like protein 1	0.73	-	nuc	0					1159
P23348 UniProt NPD GO	B3A3_RAT	Anion exchange protein 3 (Neuronal band 3-like protein) (Solute carrier family 4 member 3)	0.73	+	end	11	Membrane; multi-pass membrane protein	integral to membrane [IEP]			1227
Q9WV06 UniProt NPD GO	ANKR2_MOUSE	Ankyrin repeat domain-containing protein 2 (Skeletal muscle ankyrin repeat protein) (mArpp)	0.73	+	cyt	0		nucleus [NAS] sarcomere [IDA]			328
Q07936 UniProt NPD GO	ANXA2_RAT	Annexin A2 (Annexin II) (Lipocortin II) (Calpactin I heavy chain) (Chromobindin-8) (p36) (Protein I) ...	0.73	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. In the lamina beneat ...	cytoplasm [IDA] perinuclear region [IDA] plasma membrane [IDA]			338
Q5QJC2 UniProt NPD GO	DCR1C_CHICK	Artemis protein (EC 3.1.-.-) (DNA cross-link repair 1C protein) (chSNM1C) (SNM1-like protein)	0.73	-	nuc	0	Nucleus (By similarity)				714
Q6FX35 UniProt NPD GO	ATG14_CANGA	Autophagy-related protein 14	0.73	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				364
Q75B65 UniProt NPD GO	ATG20_ASHGO	Autophagy-related protein 20	0.73	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				577
O88566 UniProt NPD GO	AXN2_MOUSE	Axin-2 (Axis inhibition protein 2) (Conductin) (Axin-like protein) (Axil)	0.73	-	nuc	0	Cytoplasm (By similarity)				840
Q99PV8 UniProt NPD GO	BC11B_MOUSE	B-cell lymphoma/leukemia 11B (B-cell CLL/lymphoma 11B) (Radiation-induced tumor suppressor gene 1 pr ...	0.73	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			884
Q9BSF8 UniProt NPD GO	BTBDA_HUMAN	BTB/POZ domain-containing protein 10	0.73	-	nuc	0	Nucleus				475
Q5R585 UniProt NPD GO	BTBDA_PONPY	BTB/POZ domain-containing protein 10	0.73	-	nuc	0	Nucleus (By similarity)				475
Q8N3L3 UniProt NPD GO	TXLNB_HUMAN	Beta-taxilin (Muscle-derived protein 77) (hMDP77)	0.73	-	nuc	0					684
Q9JJ80 UniProt NPD GO	BXDC1_MOUSE	Brix domain-containing protein 1	0.73	+	nuc	0	Nucleus; nucleolus (By similarity)				306
O15519 UniProt NPD GO	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator precursor (Cellular FLICE-like inhibitory protein) (c-FLIP) ...	0.73	-	cyt	0			603599		480
Q5RD56 UniProt NPD GO	CFLAR_PONPY	CASP8 and FADD-like apoptosis regulator precursor [Contains: CASP8 and FADD-like apoptosis regulator ...	0.73	-	cyt	0					480
Q12468 UniProt NPD GO	CSN5_YEAST	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	0.73	-	nuc	0	Cytoplasm. Nucleus. The nuclear location requires the formation of the CSN complex	signalosome complex [IDA]			455
Q9HCP0 UniProt NPD GO	KC1G1_HUMAN	Casein kinase I isoform gamma-1 (EC 2.7.11.1) (CKI-gamma 1)	0.73	+	nuc	0	Cytoplasm		606274	2CMW	422
Q9HDV6 UniProt NPD GO	MOR2_SCHPO	Cell polarity protein mor2 (Morphological round protein 2)	0.73	-	end	0	Cytoplasm. Membrane; peripheral membrane protein. Found at the cell tips and at the site of septum f ...	site of polarized growth [IDA]			2196
P04637 UniProt NPD GO	P53_HUMAN	Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13)	0.73	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] insoluble fraction [IDA] mitochondrion [IDA] nuclear matrix [IDA] nucleolus [IDA] nucleoplasm [IDA] nucleus [IDA]	133239	3SAK	393
P35526 UniProt NPD GO	CLIC5_BOVIN	Chloride intracellular channel protein 5 (Chlorine channel protein p64)	0.73	-	nuc	0	Intracellular organelles	cytoplasmic membrane-bound vesicle [TAS] microsome [TAS] plasma membrane [TAS]			437
Q70XY4 UniProt NPD GO	RR18_AMBTC	Chloroplast 30S ribosomal protein S18	0.73	-	nuc	0	Plastid; chloroplast				101
P25459 UniProt NPD GO	RR18_MAIZE	Chloroplast 30S ribosomal protein S18	0.73	-	nuc	0	Plastid; chloroplast				170
Q6YXM4 UniProt NPD GO	RR18_PHYPA	Chloroplast 30S ribosomal protein S18	0.73	-	nuc	0	Plastid; chloroplast				79
Q6L379 UniProt NPD GO	RR18_SACHY	Chloroplast 30S ribosomal protein S18	0.73	-	nuc	0	Plastid; chloroplast				163
Q6ENU2 UniProt NPD GO	RR18_SACOF	Chloroplast 30S ribosomal protein S18	0.73	-	nuc	0	Plastid; chloroplast				163
Q9MUL8 UniProt NPD GO	RK32_MESVI	Chloroplast 50S ribosomal protein L32	0.73	-	nuc	0	Plastid; chloroplast				56
P49566 UniProt NPD GO	RK34_ODOSI	Chloroplast 50S ribosomal protein L34	0.73	+	mit	0	Plastid; chloroplast				48
Q7GUC8 UniProt NPD GO	RK36_PINKO	Chloroplast 50S ribosomal protein L36	0.73	-	mit	0	Plastid; chloroplast				37
P41631 UniProt NPD GO	RK36_PINTH	Chloroplast 50S ribosomal protein L36	0.73	-	mit	0	Plastid; chloroplast				37
P49584 UniProt NPD GO	PCY1A_CRIGR	Choline-phosphate cytidylyltransferase A (EC 2.7.7.15) (Phosphorylcholine transferase A) (CTP:phosph ...	0.73	+	nuc	0	Cytoplasm; cytosol (By similarity). Membrane; peripheral membrane protein (By similarity). It can in ...				367
Q9P2I0 UniProt NPD GO	CPSF2_HUMAN	Cleavage and polyadenylation specificity factor 100 kDa subunit (CPSF 100 kDa subunit)	0.73	-	cyt	0	Nucleus (Potential)		606028		782

You are viewing entries 12201 to 12250 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.