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
Q8CAQ8 UniProt NPD GO	IMMT_MOUSE	Mitochondrial inner membrane protein (Mitofilin)	0.85	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)	mitochondrial inner membrane [ISS] mitochondrion [IDA]			757
Q5Z9J0 UniProt NPD GO	MPK12_ORYSA	Mitogen-activated protein kinase 12 (EC 2.7.11.24) (MAP kinase 12) (OsBWMK1) (Blast- and wound-induc ...	0.85	-	nuc	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation (Probable)				580
Q9WUL6 UniProt NPD GO	M3K14_MOUSE	Mitogen-activated protein kinase kinase kinase 14 (EC 2.7.11.25) (NF-kappa beta-inducing kinase) (Se ...	0.85	+	nuc	0	Cytoplasm				942
O60566 UniProt NPD GO	BUB1B_HUMAN	Mitotic checkpoint serine/threonine-protein kinase BUB1 beta (EC 2.7.11.1) (hBUBR1) (MAD3/BUB1-relat ...	0.85	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic in interphase cells. Bound to BUB3 or CENP-E, it can be localized to ...	anaphase-promoting complex [TAS] spindle midzone [NAS]	602860		1050
Q9WTX8 UniProt NPD GO	MD1L1_MOUSE	Mitotic spindle assembly checkpoint protein MAD1 (Mitotic arrest deficient-like protein 1) (MAD1-lik ...	0.85	-	nuc	0	Nucleus (By similarity). From the beginning to the end of mitosis, it is seen to move from a diffuse ...				717
Q58DU0 UniProt NPD GO	MMTA2_BOVIN	Multiple myeloma tumor-associated protein 2 homolog	0.85	+	nuc	0					235
Q9N2A2 UniProt NPD GO	ACM3_PONPY	Muscarinic acetylcholine receptor M3	0.85	+	vac	7	Membrane; multi-pass membrane protein				590
Q9S7G7 UniProt NPD GO	MB3R1_ARATH	Myb-related protein 3R-1 (Plant c-MYB-like protein 1) (Protein PC-MYB1) (PC-MYB1)	0.85	+	nuc	0	Nucleus (By similarity)				776
P52551 UniProt NPD GO	MYBB_XENLA	Myb-related protein B (B-Myb) (Myb-related protein 1) (XMYB1)	0.85	-	nuc	0	Nucleus				743
Q03414 UniProt NPD GO	MEF2A_XENLA	Myocyte-specific enhancer factor 2A homolog (Serum response factor-like protein 2) (SL-2)	0.85	-	nuc	0	Nucleus				516
P24699 UniProt NPD GO	MYF5_MOUSE	Myogenic factor 5 (Myf-5)	0.85	+	nuc	0	Nucleus	nucleus [TAS]			255
P23409 UniProt NPD GO	MYF6_HUMAN	Myogenic factor 6 (Myf-6)	0.85	+	nuc	0	Nucleus	nucleus [TAS]	160150		242
P15375 UniProt NPD GO	MYF6_MOUSE	Myogenic factor 6 (Myf-6) (Herculin)	0.85	+	nuc	0	Nucleus	nucleus [TAS]			242
Q7YS80 UniProt NPD GO	MYF6_BOVIN	Myogenic factor 6 (Myf-6) (Muscle-specific regulatory factor 4)	0.85	+	nuc	0	Nucleus (By similarity)				242
Q01795 UniProt NPD GO	MYF6_CHICK	Myogenic factor 6 (Myf-6) (Muscle-specific regulatory factor 4)	0.85	+	nuc	0	Nucleus				242
P19335 UniProt NPD GO	MYF6_RAT	Myogenic factor 6 (Myf-6) (Muscle-specific regulatory factor 4)	0.85	+	nuc	0	Nucleus				242
Q875X3 UniProt NPD GO	MYO2A_SACCA	Myosin-2A (Class V unconventional myosin MYO2A) (Type V myosin heavy chain MYO2A) (Myosin V MYO2A)	0.85	-	nuc	0					1567
Q99104 UniProt NPD GO	MYO5A_MOUSE	Myosin-5A (Myosin Va) (Dilute myosin heavy chain, non-muscle)	0.85	-	nuc	0		myosin [IDA]			1853
Q02440 UniProt NPD GO	MYO5A_CHICK	Myosin-5A (Myosin Va) (Dilute myosin heavy chain, non-muscle) (Myosin heavy chain p190) (Myosin-V)	0.85	-	nuc	0	Golgi apparatus; Golgi membrane (Potential)			2DFS	1829
O14357 UniProt NPD GO	GPI1_SCHPO	N-acetylglucosaminyl-phosphatidylinositol biosynthetic protein gpi1	0.85	-	end	6	Membrane; multi-pass membrane protein (Potential)				653
O88522 UniProt NPD GO	NEMO_MOUSE	NF-kappa-B essential modulator (NEMO) (NF-kappa-B essential modifier) (Inhibitor of nuclear factor k ...	0.85	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [IDA]			412
Q95ZE9 UniProt NPD GO	NELFE_DROVI	Negative elongation factor E	0.85	-	nuc	0	Nucleus (By similarity). Associates with polytene chromosomes. Associates with the hsp70 promoter wh ...	transcriptional repressor complex [ISS]			281
Q61043 UniProt NPD GO	NIN_MOUSE	Ninein	0.85	+	nuc	0	Centrosome. Component of the core centrosome. Arranged in a tubular conformation with an open and a ...	centrosome [ISS]			2035
P29473 UniProt NPD GO	NOS3_BOVIN	Nitric-oxide synthase, endothelial (EC 1.14.13.39) (EC-NOS) (NOS type III) (NOSIII) (Endothelial NOS ...	0.85	+	cyt	0				9NSE	1204
P22211 UniProt NPD GO	NPR1_YEAST	Nitrogen permease reactivator protein (EC 2.7.11.1)	0.85	-	nuc	0		cytoplasm [TAS]			790
Q9U1H9 UniProt NPD GO	NXF1_DROME	Nuclear RNA export factor 1 (Protein tip-associating) (Protein small bristles) (DmNXF1)	0.85	-	nuc	0	Nucleus; nucleoplasm. Cytoplasm. Localized in the nucleoplasm and at both the nucleoplasmic and cyto ...	nuclear envelope [IDA] nucleoplasm [IDA]			672
O77638 UniProt NPD GO	NFAC1_PIG	Nuclear factor of activated T-cells, cytoplasmic 1 (NFAT transcription complex cytosolic component) ...	0.85	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic for the phosphorylated form and nuclear after activation that is con ...				822
Q9HCD5 UniProt NPD GO	NCOA5_HUMAN	Nuclear receptor coactivator 5 (NCoA-5) (Coactivator independent of AF-2) (CIA)	0.85	-	nuc	0	Nucleus			1V95	579
P38934 UniProt NPD GO	BFR1_YEAST	Nuclear segregation protein BFR1 (Brefeldin A resistance protein 1)	0.85	-	nuc	0		nuclear envelope-endoplasmic reticulum network [IDA] polysome [IDA]			470
Q945M9 UniProt NPD GO	NFYA9_ARATH	Nuclear transcription factor Y subunit A-9 (AtNF-YA-9)	0.85	-	nuc	0	Nucleus (Probable)				303
Q99LH1 UniProt NPD GO	NOG2_MOUSE	Nucleolar GTP-binding protein 2	0.85	-	nuc	0	Nucleus; nucleolus (By similarity)				728
Q9WV70 UniProt NPD GO	NOC2L_MOUSE	Nucleolar complex protein 2 homolog (Protein NOC2 homolog) (NOC2-like)	0.85	-	nuc	0	Nucleus; nucleolus (By similarity)				747
Q8K2K6 UniProt NPD GO	NUPL_MOUSE	Nucleoporin-like protein RIP (HIV-1 Rev-binding protein homolog)	0.85	-	nuc	0	Nucleus (By similarity). Cytoplasmic vesicle (By similarity). Associated with the cytosolic surface ...	cytoplasmic membrane-bound vesicle [IDA]			561
Q4KLH5 UniProt NPD GO	NUPL_RAT	Nucleoporin-like protein RIP (HIV-1 Rev-binding protein homolog)	0.85	-	nuc	0	Nucleus (By similarity). Cytoplasmic vesicle (By similarity)				561
P18751 UniProt NPD GO	ZO71_XENLA	Oocyte zinc finger protein XLCOF7.1 (Fragment)	0.85	-	nuc	0	Nucleus (Potential)				898
Q5QNQ6 UniProt NPD GO	OSBP2_MOUSE	Oxysterol-binding protein 2	0.85	+	nuc	0	Membrane; peripheral membrane protein (By similarity)				908
Q9ULD6 UniProt NPD GO	PDZD6_HUMAN	PDZ domain-containing protein 6	0.85	+	nuc	0					942
P31366 UniProt NPD GO	POU1_BRARE	POU domain protein 1 (ZFPOU1)	0.85	+	nuc	0	Nucleus				425
P79745 UniProt NPD GO	POU23_BRARE	POU domain protein ZP-23	0.85	+	nuc	0	Nucleus				443
Q60520 UniProt NPD GO	SIN3A_MOUSE	Paired amphipathic helix protein Sin3a (Transcriptional corepressor Sin3a) (Histone deacetylase comp ...	0.85	-	nuc	0	Nucleus	kinetochore [IDA] nucleus [IDA]		1S5R	1282
Q62141 UniProt NPD GO	SIN3B_MOUSE	Paired amphipathic helix protein Sin3b (Transcriptional corepressor Sin3b) (Histone deacetylase comp ...	0.85	-	nuc	0	Nucleus	nucleus [IDA]		2F05	1098
Q4WC37 UniProt NPD GO	PFA4_ASPFU	Palmitoyltransferase pfa4 (EC 2.3.1.-) (Protein fatty acyltransferase 4)	0.85	-	mit	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				402
Q6IMP4 UniProt NPD GO	PANX2_MOUSE	Pannexin-2	0.85	-	nuc	4 *	Membrane; multi-pass membrane protein (Potential)				607
Q86RN8 UniProt NPD GO	MYSP_BOOMI	Paramyosin	0.85	-	nuc	0	Thick filaments of the myofibrils				873
P35415 UniProt NPD GO	MYSP1_DROME	Paramyosin, long form	0.85	-	nuc	0	Thick filaments of the myofibrils				879
O42941 UniProt NPD GO	CYP7_SCHPO	Peptidylprolyl isomerase cyp7 (EC 5.2.1.8) (Cyclophilin 7) (Complexed with cdc5 protein 27)	0.85	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	spliceosome complex [IDA]			463
O15534 UniProt NPD GO	PER1_HUMAN	Period circadian protein 1 (Circadian pacemaker protein Rigui) (hPER)	0.85	-	nuc	0	Nucleus (By similarity)		602260		1290
Q5SW28 UniProt NPD GO	PI3R5_MOUSE	Phosphoinositide 3-kinase regulatory subunit 5 (PI3-kinase regulatory subunit 5) (PI3-kinase p101 su ...	0.85	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Membrane; peripheral membrane protein (By simila ...				871
P36126 UniProt NPD GO	SPO14_YEAST	Phospholipase D1 (EC 3.1.4.4) (PLD 1) (Choline phosphatase 1) (Phosphatidylcholine-hydrolyzing phosp ...	0.85	-	nuc	0		endosome [IDA] prospore membrane [IDA]			1380
Q99NA7 UniProt NPD GO	PITX1_RAT	Pituitary homeobox 1	0.85	+	nuc	0	Nucleus				315

You are viewing entries 6601 to 6650 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.