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
Q7YQM2 UniProt NPD GO	AFF2_PANTR	AF4/FMR2 family member 2 (Fragile X mental retardation protein 2 homolog) (Protein FMR-2)	0.96	-	nuc	0					1272
Q7YQM1 UniProt NPD GO	AFF2_PONPY	AF4/FMR2 family member 2 (Fragile X mental retardation protein 2 homolog) (Protein FMR-2)	0.96	-	nuc	0					1272
O55112 UniProt NPD GO	AFF2_MOUSE	AF4/FMR2 family member 2 (Fragile X mental retardation protein 2 homolog) (Protein FMR-2) (FMR2P) (P ...	0.96	-	nuc	0					1272
Q9UHB7 UniProt NPD GO	AFF4_HUMAN	AF4/FMR2 family member 4 (ALL1-fused gene from chromosome 5q31) (Major CDK9 elongation factor-associ ...	0.96	-	nuc	0	Nucleus		604417		1163
Q5ANB2 UniProt NPD GO	DBP10_CANAL	ATP-dependent RNA helicase DBP10 (EC 3.6.1.-)	0.96	+	nuc	0	Nucleus; nucleolus (By similarity)				908
Q12389 UniProt NPD GO	DBP10_YEAST	ATP-dependent RNA helicase DBP10 (EC 3.6.1.-) (DEAD box protein 10)	0.96	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			995
Q6FPT7 UniProt NPD GO	DBP4_CANGA	ATP-dependent RNA helicase DBP4 (EC 3.6.1.-)	0.96	-	nuc	0	Nucleus; nucleolus (By similarity)				765
Q9ESV0 UniProt NPD GO	DDX24_MOUSE	ATP-dependent RNA helicase DDX24 (EC 3.6.1.-) (DEAD box protein 24)	0.96	+	nuc	0					857
Q4WM60 UniProt NPD GO	DBP4_ASPFU	ATP-dependent RNA helicase dbp4 (EC 3.6.1.-)	0.96	+	nuc	0	Nucleus; nucleolus (By similarity)				787
Q9UTK5 UniProt NPD GO	ALM1_SCHPO	Abnormal long morphology protein 1 (Sp8)	0.96	-	nuc	0	Cytoplasm	medial ring [IDA]			1727
Q06157 UniProt NPD GO	AMDR_ASPOR	Acetamidase regulatory protein	0.96	-	nuc	0	Nucleus				775
Q9H1I8 UniProt NPD GO	ASCC2_HUMAN	Activating signal cointegrator 1 complex subunit 2 (ASC-1 complex subunit p100) (Trip4 complex subun ...	0.96	-	nuc	0					757
P08678 UniProt NPD GO	CYAA_YEAST	Adenylate cyclase (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase)	0.96	-	nuc	0		mitochondrion [IDA] plasma membrane [IDA]			2026
P46589 UniProt NPD GO	ADF1_CANAL	Adherence factor (Adhesion and aggregation mediating surface antigen)	0.96	+	nuc	0					612
Q9QZQ1 UniProt NPD GO	AFAD_MOUSE	Afadin (Protein Af-6) (Fragment)	0.96	-	nuc	0	Cell membrane; cell-cell junction; adherens junction. Not found at cell-matrix AJs	adherens junction [IDA] cytoplasm [IDA]		1WXA	885
Q8TCU4 UniProt NPD GO	ALMS1_HUMAN	Alstrom syndrome protein 1	0.96	-	nuc	0	Cytoplasm. Centrosome. Associated with centrosomes and basal body at the base of primary cilia. Duri ...	centrosome [IDA]	606844		4167
Q8K4E0 UniProt NPD GO	ALMS1_MOUSE	Alstrom syndrome protein 1 homolog	0.96	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Associated with centrosomes and basal body at ...				3251
Q58CQ5 UniProt NPD GO	ANKZ1_BOVIN	Ankyrin repeat and zinc finger domain-containing protein 1	0.96	+	nuc	0					728
Q12955 UniProt NPD GO	ANK3_HUMAN	Ankyrin-3 (ANK-3) (Ankyrin-G)	0.96	+	nuc	0			600465		4377
Q9ZT48 UniProt NPD GO	ATE1_ARATH	Arginyl-tRNA--protein transferase 1 (EC 2.3.2.8) (R-transferase 1) (Arginyltransferase 1) (Arginine- ...	0.96	-	nuc	0					632
P41696 UniProt NPD GO	AZF1_YEAST	Asparagine-rich zinc finger protein AZF1	0.96	+	nuc	0	Nucleus (Potential)	nucleus [IDA]			914
Q4WY31 UniProt NPD GO	ATG11_ASPFU	Autophagy-related protein 11	0.96	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Vacuolar and perivacuolar p ...				1264
Q9I920 UniProt NPD GO	BLM_CHICK	Bloom syndrome protein homolog (EC 3.6.1.-) (Fragment)	0.96	+	nuc	0	Nucleus (By similarity)				1142
P38398 UniProt NPD GO	BRCA1_HUMAN	Breast cancer type 1 susceptibility protein (RING finger protein 53)	0.96	+	nuc	0	Nucleus	BRCA1-BARD1 complex [IDA] gamma-tubulin ring complex [NAS] nucleus [TAS] ubiquitin ligase complex [NAS]	113705	1Y98	1863
Q6J6I8 UniProt NPD GO	BRCA1_GORGO	Breast cancer type 1 susceptibility protein homolog	0.96	-	nuc	0	Nucleus (Potential)				1863
Q6J6I9 UniProt NPD GO	BRCA1_MACMU	Breast cancer type 1 susceptibility protein homolog	0.96	-	nuc	0	Nucleus (Potential)				1863
Q5ZKG2 UniProt NPD GO	BRD7_CHICK	Bromodomain-containing protein 7	0.96	+	nuc	0	Nucleus (By similarity)				651
Q60824 UniProt NPD GO	BPAEB_MOUSE	Bullous pemphigoid antigen 1, isoforms 6/7 (BPA) (Hemidesmosomal plaque protein) (Dystonia musculoru ...	0.96	-	mit	0	Cytoplasm (By similarity)	cytoplasm [ISS] hemidesmosome [IDA]			1678
O95402 UniProt NPD GO	CRSP7_HUMAN	CRSP complex subunit 7 (Cofactor required for Sp1 transcriptional activation subunit 7) (Transcripti ...	0.96	-	nuc	0	Nucleus		605043		600
Q05682 UniProt NPD GO	CALD1_HUMAN	Caldesmon (CDM)	0.96	+	nuc	0	On thin filaments in smooth muscle and on stress fibers in fibroblasts (nonmuscle) (By similarity)	cytoskeleton [TAS]	114213		793
P32797 UniProt NPD GO	CDC13_YEAST	Cell division control protein 13	0.96	-	nuc	0		nuclear telomere cap complex [IDA]		1S40	924
Q9W679 UniProt NPD GO	P53_TETMU	Cellular tumor antigen p53 (Tumor suppressor p53)	0.96	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				367
Q8WZ64 UniProt NPD GO	CEND1_HUMAN	Centaurin-delta 1 (Cnt-d1) (Arf-GAP, Rho-GAP, ankyrin repeat and pleckstrin homology domain-containi ...	0.96	-	nuc	0	Cytoplasm (By similarity)		606645	2COD	1704
Q9HC77 UniProt NPD GO	CENPJ_HUMAN	Centromere protein J (CENP-J) (Centrosomal P4.1-associated protein) (LAG-3-associated protein) (LYST ...	0.96	-	nuc	0	Centrosome. Localized within the center of microtubule asters	gamma-tubulin small complex [NAS]			1338
O43303 UniProt NPD GO	CE110_HUMAN	Centrosomal protein of 110 kDa (Cep110 protein)	0.96	-	nuc	0	Centrosome	centrosome [TAS]	609544		1012
Q7TSH4 UniProt NPD GO	CE110_MOUSE	Centrosomal protein of 110 kDa (Cep110 protein)	0.96	-	nuc	0	Centrosome (By similarity)	centrosome [ISS]			1004
Q86XR8 UniProt NPD GO	CEP57_HUMAN	Centrosomal protein of 57 kDa (Cep57 protein) (Testis-specific protein 57) (Translokin) (FGF2-intera ...	0.96	-	nuc	0	Nucleus (By similarity). Cytoplasm. Associates with microtubules and the centrosome	centrosome [IDA] Golgi apparatus [IDA] microtubule [IDA]	607951		500
P41695 UniProt NPD GO	BUB1_YEAST	Checkpoint serine/threonine-protein kinase BUB1 (EC 2.7.11.1)	0.96	-	nuc	0	Nucleus	condensed nuclear chromosome kinetochore [IDA] kinetochore [IDA] nucleus [IDA]			1021
Q6BI82 UniProt NPD GO	VID21_DEBHA	Chromatin modification-related protein VID21	0.96	-	nuc	0	Nucleus (Probable)				1193
O97159 UniProt NPD GO	CHDM_DROME	Chromodomain helicase-DNA-binding protein Mi-2 homolog (EC 3.6.1.-) (ATP-dependent helicase Mi-2) (d ...	0.96	+	nuc	0	Nucleus	nucleus [ISS] NuRD complex [TAS] polytene chromosome [IDA]			1982
Q9GLP1 UniProt NPD GO	FA5_PIG	Coagulation factor V precursor (Activated protein C cofactor) [Contains: Coagulation factor V heavy ...	0.96	+	nuc	0					2258
P40541 UniProt NPD GO	SCC3_YEAST	Cohesin subunit SCC3 (Irregular cell behavior protein 1)	0.96	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...	nuclear cohesin complex [IDA] nucleus [IDA]			1150
Q9UL16 UniProt NPD GO	CCD19_HUMAN	Coiled-coil domain-containing protein 19 (Nasopharyngeal epithelium-specific protein 1)	0.96	+	nuc	0		soluble fraction [TAS]	605152		386
Q8IVM0 UniProt NPD GO	CCD50_HUMAN	Coiled-coil domain-containing protein 50 (Protein Ymer)	0.96	+	nuc	0					306
Q7TQK5 UniProt NPD GO	CCD93_MOUSE	Coiled-coil domain-containing protein 93	0.96	-	nuc	0					629
Q5BJT7 UniProt NPD GO	CCD93_RAT	Coiled-coil domain-containing protein 93	0.96	-	nuc	0					629
Q2QLF8 UniProt NPD GO	CTTB2_CALJA	Cortactin-binding protein 2 (CortBP2)	0.96	-	nuc	0					1662
Q8WZ74 UniProt NPD GO	CTTB2_HUMAN	Cortactin-binding protein 2 (CortBP2)	0.96	-	nuc	0			609772		1663
Q2QL82 UniProt NPD GO	CTTB2_MICMU	Cortactin-binding protein 2 (CortBP2)	0.96	-	nuc	0					1647
Q2QLG9 UniProt NPD GO	CTTB2_OTOGA	Cortactin-binding protein 2 (CortBP2)	0.96	-	nuc	0					1655

You are viewing entries 1301 to 1350 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.