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
Q4P7M1 UniProt NPD GO	DBP9_USTMA	ATP-dependent RNA helicase DBP9 (EC 3.6.1.-)	0.66	+	nuc	0	Nucleus; nucleolus (By similarity)				686
Q5AZA6 UniProt NPD GO	DBP9_EMENI	ATP-dependent RNA helicase dbp9 (EC 3.6.1.-)	0.66	-	cyt	0	Nucleus; nucleolus (By similarity)				610
Q9V3R1 UniProt NPD GO	A36DE_DROME	Accessory gland protein Acp36DE precursor	0.66	-	nuc	0	Secreted protein (Probable)	extracellular region [TAS]			912
P45963 UniProt NPD GO	ACR7_CAEEL	Acetylcholine receptor subunit alpha-type acr-7 precursor	0.66	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				538
Q3V140 UniProt NPD GO	ACRBP_MOUSE	Acrosin-binding protein precursor (Proacrosin-binding protein sp32)	0.66	-	exc	0	Secreted protein (By similarity). Acrosome (By similarity). Colocalizes with proacrosin in the acros ...				540
Q6H8Q1 UniProt NPD GO	ABLM2_HUMAN	Actin-binding LIM protein 2 (Actin-binding LIM protein family member 2) (abLIM-2)	0.66	-	nuc	0	Cytoplasm (Probable)	cytoplasm [NAS]		1WIG	611
Q6BXN0 UniProt NPD GO	ARP4_DEBHA	Actin-like protein ARP4	0.66	-	nuc	0	Nucleus (By similarity)				492
Q5KM86 UniProt NPD GO	SPB1_CRYNE	AdoMet-dependent rRNA methyltransferase SPB1 (EC 2.1.1.-) (2'-O-ribose RNA methyltransferase) (S-ade ...	0.66	-	nuc	0	Nucleus; nucleolus (By similarity)				908
Q4FZR5 UniProt NPD GO	ACD_RAT	Adrenocortical dysplasia protein homolog	0.66	-	nuc	0	Nucleus (Potential)				417
Q38836 UniProt NPD GO	AGL11_ARATH	Agamous-like MADS-box protein AGL11	0.66	-	nuc	0	Nucleus (By similarity)				230
Q1XGV1 UniProt NPD GO	ASIP_CERAE	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.66	-	nuc	1 *	Secreted protein (By similarity)				132
Q1XGU9 UniProt NPD GO	ASIP_CERMI	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.66	-	nuc	1 *	Secreted protein (By similarity)				132
Q1XGV0 UniProt NPD GO	ASIP_ERYPA	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.66	-	nuc	1 *	Secreted protein (By similarity)				132
Q1XGV2 UniProt NPD GO	ASIP_MACRA	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.66	-	exc	0	Secreted protein (By similarity)				132
Q1XGU6 UniProt NPD GO	ASIP_TRACR	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.66	-	nuc	1 *	Secreted protein (By similarity)				132
Q1XGU7 UniProt NPD GO	ASIP_TRAOB	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.66	-	nuc	1 *	Secreted protein (By similarity)				132
Q9QXQ0 UniProt NPD GO	ACTN4_RAT	Alpha-actinin-4 (Non-muscle alpha-actinin 4) (F-actin cross linking protein)	0.66	-	cyt	0	Cytoplasm	cytoplasm [IDA]			911
Q5BIW4 UniProt NPD GO	ALS2_PANTR	Alsin (Amyotrophic lateral sclerosis protein 2 homolog)	0.66	-	nuc	0					1657
O93279 UniProt NPD GO	A4_FUGRU	Amyloid beta A4 protein precursor (APP) (ABPP) (Alzheimer disease amyloid A4 A4 protein homolog) [Co ...	0.66	-	nuc	1	Membrane; single-pass type I membrane protein				737
P51693 UniProt NPD GO	APLP1_HUMAN	Amyloid-like protein 1 precursor (APLP) (APLP-1) [Contains: C30]	0.66	-	mit	1	Cell membrane; single-pass type I membrane protein. C30: Cytoplasm. C-terminally processed in the Go ...	basement membrane [TAS]	104775		650
Q8R1Q3 UniProt NPD GO	ANGL7_MOUSE	Angiopoietin-related protein 7 precursor (Angiopoietin-like 7)	0.66	-	mit	0	Secreted protein (Probable)				337
P34552 UniProt NPD GO	ALX1_CAEEL	Apoptosis-linked gene 2-interacting protein X 1 (Protein pqn-58) (Protein YNK1)	0.66	-	nuc	0					882
P04931 UniProt NPD GO	ARP_PLAFA	Asparagine-rich protein (Ag319) (ARP) (Fragment)	0.66	+	nuc	0					537
P25345 UniProt NPD GO	SYNM_YEAST	Asparaginyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.22) (Asparagine--tRNA ligase) (AsnRS) ...	0.66	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			492
Q4WVH5 UniProt NPD GO	ATG16_ASPFU	Autophagy protein 16	0.66	-	nuc	0	Vacuole (By similarity). Cytoplasmic vesicle (By similarity). Vesicular and vacuolar. Found in punct ...				172
Q6CUD5 UniProt NPD GO	ATG12_KLULA	Autophagy-related protein 12 (Autophagy-related ubiquitin-like modifier ATG12)	0.66	-	nuc	0	Cytoplasm (By similarity)				189
Q872W1 UniProt NPD GO	ATG17_NEUCR	Autophagy-related protein 17	0.66	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Cytoplasmic and pu ...				568
Q5AI22 UniProt NPD GO	ATG21_CANAL	Autophagy-related protein 21	0.66	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Vacuole; vacuolar ...				529
O95999 UniProt NPD GO	BCL10_HUMAN	B-cell lymphoma/leukemia 10 (B-cell CLL/lymphoma 10) (Bcl-10) (CED-3/ICH-1 prodomain homologous E10- ...	0.66	-	nuc	0	Cytoplasm; perinuclear region. Appears to have a perinuclear, compact and filamentous pattern of exp ...		603517		233
Q9Z0H7 UniProt NPD GO	BCL10_MOUSE	B-cell lymphoma/leukemia 10 (B-cell CLL/lymphoma 10) (Bcl-10) (CED-3/ICH-1 prodomain homologous E10- ...	0.66	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [IDA] lipid raft [IDA]			233
Q5F486 UniProt NPD GO	BAG5_CHICK	BAG family molecular chaperone regulator 5 (BCL2-associated athanogene 5) (BAG-5)	0.66	-	nuc	0					450
Q12983 UniProt NPD GO	BNIP3_HUMAN	BCL2/adenovirus E1B 19 kDa protein-interacting protein 3	0.66	-	cyt	1	Mitochondrion. Coexpression with the EIB 19-kDa protein results in a shift in NIP3 localization patt ...	cytoplasm [ISS] dendrite [ISS] integral to mitochondrial outer membrane [IDA] mitochondrial membrane [IDA] mitochondrion [IDA] nuclear envelope [IDA] nucleoplasm [ISS] nucleus [ISS]	603293		194
P26818 UniProt NPD GO	ARBK2_BOVIN	Beta-adrenergic receptor kinase 2 (EC 2.7.11.15) (Beta-ARK-2) (G-protein-coupled receptor kinase 3)	0.66	-	cyt	0					688
Q8WYA6 UniProt NPD GO	CTBL1_HUMAN	Beta-catenin-like protein 1 (Nuclear-associated protein) (NAP) (Protein NYD-SP19)	0.66	+	nuc	0	Nucleus				563
P49001 UniProt NPD GO	BMP2_RAT	Bone morphogenetic protein 2 precursor (BMP-2) (BMP-2A)	0.66	+	exc	1 *	Secreted protein (By similarity)				393
P55107 UniProt NPD GO	BMP3B_HUMAN	Bone morphogenetic protein 3b precursor (BMP-3b) (Growth/differentiation factor 10) (GDF-10) (Bone-i ...	0.66	-	exc	0	Secreted protein		601361		478
P12644 UniProt NPD GO	BMP4_HUMAN	Bone morphogenetic protein 4 precursor (BMP-4) (BMP-2B)	0.66	-	exc	0	Secreted protein; extracellular space; extracellular matrix		112262		408
P79351 UniProt NPD GO	RNBR_CAPCA	Brain ribonuclease (EC 3.1.27.-) (BRB)	0.66	-	nuc	0	Secreted protein				151
Q8GUQ5 UniProt NPD GO	BRI1_LYCES	Brassinosteroid LRR receptor kinase precursor (EC 2.7.11.1) (tBRI1) (Altered brassinolide sensitivit ...	0.66	+	nuc	2 *	Cell membrane; single-pass type I membrane protein				1207
Q24206 UniProt NPD GO	BRC4_DROME	Broad-complex core-protein isoform 6	0.66	+	nuc	0	Nucleus				880
O60108 UniProt NPD GO	CBH2_SCHPO	CENP-B homolog protein 2 (CBHP-2)	0.66	-	mit	0	Nucleus				514
Q9HCU4 UniProt NPD GO	CELR2_HUMAN	Cadherin EGF LAG seven-pass G-type receptor 2 precursor (Epidermal growth factor-like 2) (Multiple e ...	0.66	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [NAS]	604265		2923
P34616 UniProt NPD GO	CAD3_CAEEL	Cadherin-3 precursor	0.66	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)	cytoplasm [IDA] plasma membrane [IDA]			3343
P43368 UniProt NPD GO	CAN3_PIG	Calpain-3 (EC 3.4.22.-) (Calpain L3) (Calpain p94) (Calcium-activated neutral proteinase 3) (CANP 3) ...	0.66	-	cyt	0	Cytoplasm				821
Q6CKY3 UniProt NPD GO	PALB_KLULA	Calpain-like protease palB/RIM13 (EC 3.4.22.-) (Cysteine protease RIM13)	0.66	-	cyt	0					685
O75052 UniProt NPD GO	CAPON_HUMAN	Carboxyl-terminal PDZ ligand of neuronal nitric oxide synthase protein (C--terminal PDZ ligand of ne ...	0.66	+	nuc	0		cytoplasm [ISS]	605551		506
P40234 UniProt NPD GO	CKI2_SCHPO	Casein kinase I homolog 2 (EC 2.7.11.1)	0.66	-	nuc	0	Cytoplasm	cytoplasm [IDA]			435
P78368 UniProt NPD GO	KC1G2_HUMAN	Casein kinase I isoform gamma-2 (EC 2.7.11.1) (CKI-gamma 2)	0.66	-	nuc	0	Cytoplasm		602214	2C47	415
P51878 UniProt NPD GO	CASP5_HUMAN	Caspase-5 precursor (EC 3.4.22.-) (CASP-5) (ICH-3 protease) (TY protease) (ICE(rel)-III) [Contains: ...	0.66	+	nuc	0			602665		418
P27636 UniProt NPD GO	CDC15_YEAST	Cell division control protein 15 (EC 2.7.11.1)	0.66	-	nuc	0		bud neck [TAS] spindle pole body [IDA]			974

You are viewing entries 15651 to 15700 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.