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
O88870 UniProt NPD GO	VMD2_MOUSE	Bestrophin-1 (Vitelliform macular dystrophy protein 2 homolog)	0.50	-	end	4 *	Cell membrane; multi-pass membrane protein	basolateral plasma membrane [ISS]			551
Q30KK3 UniProt NPD GO	DB125_PANTR	Beta-defensin 125 precursor (Defensin, beta 125)	0.50	-	nuc	0	Secreted protein (Potential)				157
P25427 UniProt NPD GO	NGF_RAT	Beta-nerve growth factor precursor (Beta-NGF)	0.50	-	exc	0	Secreted protein				241
Q5R7L8 UniProt NPD GO	BL1S1_PONPY	Biogenesis of lysosome-related organelles complex-1 subunit 1 (BLOC-1 subunit 1)	0.50	-	nuc	0					125
P78537 UniProt NPD GO	BL1S1_HUMAN	Biogenesis of lysosome-related organelles complex-1 subunit 1 (BLOC-1 subunit 1) (GCN5-like protein ...	0.50	-	nuc	0			601444		125
O97967 UniProt NPD GO	BRS3_SHEEP	Bombesin receptor subtype-3 (BRS-3)	0.50	-	end	7 *	Membrane; multi-pass membrane protein				399
Q07352 UniProt NPD GO	TISB_HUMAN	Butyrate response factor 1 (TIS11B protein) (EGF-response factor 1) (ERF-1)	0.50	-	nuc	0	Nucleus		601064	1W0W	338
Q04864 UniProt NPD GO	REL_HUMAN	C-Rel proto-oncogene protein (C-Rel protein)	0.50	-	nuc	0	Nucleus (By similarity)		164910		619
P15307 UniProt NPD GO	REL_MOUSE	C-Rel proto-oncogene protein (C-Rel protein)	0.50	-	nuc	0	Nucleus	nucleus [IC]			587
P14921 UniProt NPD GO	ETS1_HUMAN	C-ets-1 protein (p54)	0.50	+	nuc	0	Nucleus		164720	2STW	441
Q8NC01 UniProt NPD GO	CLC1A_HUMAN	C-type lectin domain family 1 member A (C-type lectin-like receptor 1) (CLEC-1)	0.50	-	nuc	1 *	Membrane; single-pass type II membrane protein (Probable)		606782		280
Q8HY04 UniProt NPD GO	CD209_PAPHA	CD209 antigen (Dendritic cell-specific ICAM-3-grabbing nonintegrin 1) (DC-SIGN1)	0.50	-	nuc	0	Membrane; single-pass type II membrane protein (By similarity)				358
Q96SZ6 UniProt NPD GO	CK5P1_HUMAN	CDK5 regulatory subunit-associated protein 1 (CDK5 activator-binding protein C42)	0.50	-	mit	0			608200		601
Q6FJ48 UniProt NPD GO	CSN12_CANGA	COP9 signalosome complex subunit 12	0.50	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				449
Q9TTR7 UniProt NPD GO	COT2_BOVIN	COUP transcription factor 2 (COUP-TF2) (COUP-TF II)	0.50	-	nuc	0	Nucleus				414
O09018 UniProt NPD GO	COT2_RAT	COUP transcription factor 2 (COUP-TF2) (COUP-TF II) (Apolipoprotein AI regulatory protein 1) (ARP-1) ...	0.50	-	nuc	0	Nucleus				414
Q7Z407 UniProt NPD GO	CSMD3_HUMAN	CUB and sushi domain-containing protein 3 precursor (CUB and sushi multiple domains protein 3)	0.50	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)		608399		3670
Q9QYP2 UniProt NPD GO	CELR2_RAT	Cadherin EGF LAG seven-pass G-type receptor 2 (Multiple epidermal growth factor-like domains 3) (Fra ...	0.50	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [ISS]			2144
P97326 UniProt NPD GO	CADH6_MOUSE	Cadherin-6 precursor (Kidney-cadherin) (K-cadherin)	0.50	-	nuc	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA]			790
Q90763 UniProt NPD GO	CADH7_CHICK	Cadherin-7 precursor	0.50	+	end	1	Membrane; single-pass type I membrane protein				785
P17655 UniProt NPD GO	CAN2_HUMAN	Calpain-2 catalytic subunit precursor (EC 3.4.22.53) (Calpain-2 large subunit) (Calcium-activated ne ...	0.50	-	cyt	0	Cytoplasm. Cell membrane. Translocates to the plasma membrane upon Ca(2+) binding		114230	1KFX	699
P10562 UniProt NPD GO	CANA_CANGL	Canavalin precursor	0.50	-	exc	1 *					445
Q8N4T0 UniProt NPD GO	CBPA6_HUMAN	Carboxypeptidase A6 precursor (EC 3.4.17.1) (Carboxypeptidase B)	0.50	-	mit	0	Secreted protein (By similarity)		609562		437
Q8BGD5 UniProt NPD GO	CPT1C_MOUSE	Carnitine O-palmitoyltransferase I, brain isoform (EC 2.3.1.21) (Carnitine palmitoyltransferase 1C) ...	0.50	-	nuc	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				798
P49674 UniProt NPD GO	KC1E_HUMAN	Casein kinase I isoform epsilon (EC 2.7.11.1) (CKI-epsilon) (CKIe)	0.50	-	nuc	0	Cytoplasm (By similarity)		600863		416
P20427 UniProt NPD GO	CSK22_BOVIN	Casein kinase II subunit alpha' (EC 2.7.11.1) (CK II)	0.50	-	mit	0					350
Q91W92 UniProt NPD GO	BORG5_MOUSE	Cdc42 effector protein 1 (Binder of Rho GTPases 5)	0.50	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity)	cytoplasm [IDA]			409
Q90Z04 UniProt NPD GO	CDON_XENLA	Cell adhesion molecule-related/down-regulated by oncogenes precursor	0.50	-	nuc	1	Membrane; single-pass membrane protein (Potential)				1249
Q7ZX42 UniProt NPD GO	CDK9B_XENLA	Cell division protein kinase 9-B (EC 2.7.11.22) (EC 2.7.11.23) (Cyclin-dependent kinase 9-B)	0.50	-	cyt	0	Nucleus (By similarity)				376
Q9NPF8 UniProt NPD GO	CENA2_HUMAN	Centaurin-alpha 2	0.50	-	cyt	0	Cytoplasm. Cell membrane. Constitutively associated with the plasma membrane. Excluded from the nucl ...	cytoplasm [IDA] mitochondrial envelope [ISS] plasma membrane [IDA]	608635		381
Q9R1K9 UniProt NPD GO	CETN2_MOUSE	Centrin-2 (Caltractin isoform 1)	0.50	-	nuc	0	Centrosome (By similarity). Centrosome of interphase and mitotic cells (By similarity)	centriole [IDA]			172
Q6IP52 UniProt NPD GO	CHM2A_XENLA	Charged multivesicular body protein 2a (Chromatin-modifying protein 2a) (CHMP2a)	0.50	-	nuc	0	Cytoplasm; cytosol (By similarity)				220
Q6DFS6 UniProt NPD GO	CHM2A_XENTR	Charged multivesicular body protein 2a (Chromatin-modifying protein 2a) (CHMP2a)	0.50	-	nuc	0	Cytoplasm; cytosol (By similarity)				220
Q85FG8 UniProt NPD GO	RR15_ADICA	Chloroplast 30S ribosomal protein S15	0.50	-	nuc	0	Plastid; chloroplast				91
Q6H9L5 UniProt NPD GO	RR4_EQUBO	Chloroplast 30S ribosomal protein S4	0.50	-	nuc	0	Plastid; chloroplast				207
Q6H9L0 UniProt NPD GO	RR4_EQULA	Chloroplast 30S ribosomal protein S4	0.50	-	nuc	0	Plastid; chloroplast				207
Q6H9K5 UniProt NPD GO	RR4_EQUSC	Chloroplast 30S ribosomal protein S4	0.50	-	nuc	0	Plastid; chloroplast				207
P59142 UniProt NPD GO	RR4_HYPCP	Chloroplast 30S ribosomal protein S4	0.50	-	mit	0	Plastid; chloroplast				202
P69629 UniProt NPD GO	RR4_AGABR	Chloroplast 30S ribosomal protein S4 (Fragment)	0.50	-	mit	0	Plastid; chloroplast				196
O20234 UniProt NPD GO	RR4_IRIEN	Chloroplast 30S ribosomal protein S4 (Fragment)	0.50	-	mit	0	Plastid; chloroplast				194
O20264 UniProt NPD GO	RR4_MORST	Chloroplast 30S ribosomal protein S4 (Fragment)	0.50	-	mit	0	Plastid; chloroplast				194
O36052 UniProt NPD GO	RR4_PATSQ	Chloroplast 30S ribosomal protein S4 (Fragment)	0.50	-	mit	0	Plastid; chloroplast				196
P69651 UniProt NPD GO	RR4_SISSP	Chloroplast 30S ribosomal protein S4 (Fragment)	0.50	-	mit	0	Plastid; chloroplast				194
P69652 UniProt NPD GO	RR4_SISST	Chloroplast 30S ribosomal protein S4 (Fragment)	0.50	-	mit	0	Plastid; chloroplast				194
P69679 UniProt NPD GO	RR4_YUCFI	Chloroplast 30S ribosomal protein S4 (Fragment)	0.50	-	mit	0	Plastid; chloroplast				196
Q67ID1 UniProt NPD GO	RR7_ALLTE	Chloroplast 30S ribosomal protein S7	0.50	-	nuc	0	Plastid; chloroplast				155
P61841 UniProt NPD GO	RR7_ARATH	Chloroplast 30S ribosomal protein S7	0.50	-	nuc	0	Plastid; chloroplast				155
P61842 UniProt NPD GO	RR7_BRANA	Chloroplast 30S ribosomal protein S7	0.50	-	nuc	0	Plastid; chloroplast				155
Q6EMA2 UniProt NPD GO	RR7_CORMA	Chloroplast 30S ribosomal protein S7	0.50	-	nuc	0	Plastid; chloroplast				155
Q71T50 UniProt NPD GO	RR7_HYDCA	Chloroplast 30S ribosomal protein S7	0.50	-	nuc	0	Plastid; chloroplast				155

You are viewing entries 24851 to 24900 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.