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
Q5AI71 UniProt NPD GO	ATG17_CANAL	Autophagy-related protein 17	0.69	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Cytoplasmic and pu ...				476
Q8X1F5 UniProt NPD GO	ATG18_PICPA	Autophagy-related protein 18 (Glucose-induced selective autophagy protein 12)	0.69	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein				543
P59054 UniProt NPD GO	AXUD1_MOUSE	Axin-1 up-regulated gene 1 protein (TGF-beta-induced apoptosis protein 3) (TAIP-3)	0.69	-	nuc	0	Nucleus (By similarity)				583
Q00436 UniProt NPD GO	YB3_XENLA	B box-binding protein (Protein YB3)	0.69	+	nuc	0	Nucleus				305
Q9YGC1 UniProt NPD GO	BLNK_CHICK	B-cell linker protein (Cytoplasmic adapter protein) (B-cell adapter SH2 domain-containing protein)	0.69	-	nuc	0	Cytoplasm (By similarity). Membrane (By similarity). BCR activation results in the translocation to ...				552
Q8WV28 UniProt NPD GO	BLNK_HUMAN	B-cell linker protein (Cytoplasmic adapter protein) (B-cell adapter containing SH2 domain protein) ( ...	0.69	-	nuc	0	Cytoplasm. Membrane. BCR activation results in the translocation to membrane fraction		604515		456
P25098 UniProt NPD GO	ARBK1_HUMAN	Beta-adrenergic receptor kinase 1 (EC 2.7.11.15) (Beta-ARK-1) (G-protein coupled receptor kinase 2)	0.69	-	cyt	0		cytoplasm [TAS] soluble fraction [TAS]	109635	1BAK	689
Q10651 UniProt NPD GO	A4_CAEEL	Beta-amyloid-like protein precursor	0.69	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				686
O88881 UniProt NPD GO	BEGIN_RAT	Brain-enriched guanylate kinase-associated protein	0.69	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	membrane fraction [IDA]			611
Q6GMN2 UniProt NPD GO	BAIP2_RAT	Brain-specific angiogenesis inhibitor 1-associated protein 2 (BAI1-associated protein 2) (BAI-associ ...	0.69	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Detected throughou ...				535
P29366 UniProt NPD GO	BEM1_YEAST	Bud emergence protein 1 (Suppressor of RHO3 protein 1)	0.69	-	nuc	0		bud neck [IDA] bud tip [IDA] incipient bud site [IDA] mating projection tip [TAS]		1IPG	551
Q9UPT6 UniProt NPD GO	JIP3_HUMAN	C-jun-amino-terminal kinase-interacting protein 3 (JNK-interacting protein 3) (JIP-3) (JNK MAP kinas ...	0.69	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]	605431		1334
Q9NZN8 UniProt NPD GO	CNOT2_HUMAN	CCR4-NOT transcription complex subunit 2 (CCR4-associated factor 2)	0.69	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)	nucleus [NAS]	604909		540
Q8C5L3 UniProt NPD GO	CNOT2_MOUSE	CCR4-NOT transcription complex subunit 2 (CCR4-associated factor 2)	0.69	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)				540
P51949 UniProt NPD GO	MAT1_MOUSE	CDK-activating kinase assembly factor MAT1 (RING finger protein MAT1) (Menage a trois) (CDK7/cyclin ...	0.69	-	nuc	0	Nucleus (By similarity)				309
Q03957 UniProt NPD GO	CTK1_YEAST	CTD kinase subunit alpha (EC 2.7.11.23) (CTD kinase 58 kDa subunit) (CTDK-I subunit alpha)	0.69	-	nuc	0	Nucleus	nucleus [IDA]			528
O54960 UniProt NPD GO	CAPON_RAT	Carboxyl-terminal PDZ ligand of neuronal nitric oxide synthase protein (C--terminal PDZ ligand of ne ...	0.69	+	nuc	0		cytoplasm [NAS]			503
O43100 UniProt NPD GO	CBF5_EMENI	Centromere/microtubule-binding protein CBF5 (Centromere-binding factor 5) (Small nucleolar RNP prote ...	0.69	+	nuc	0	Nucleus; nucleolus (By similarity)				481
Q76N32 UniProt NPD GO	CEP68_HUMAN	Centrosomal protein of 68 kDa (Cep68 protein)	0.69	-	nuc	0	Centrosome				757
Q9MUR6 UniProt NPD GO	RR14_MESVI	Chloroplast 30S ribosomal protein S14	0.69	-	nuc	0	Plastid; chloroplast				100
Q6L3A0 UniProt NPD GO	RR14_SACHY	Chloroplast 30S ribosomal protein S14	0.69	+	nuc	0	Plastid; chloroplast				103
Q85BK3 UniProt NPD GO	RR18_ANTFO	Chloroplast 30S ribosomal protein S18	0.69	-	nuc	0	Plastid; chloroplast				75
Q95CA6 UniProt NPD GO	RR4_PSINU	Chloroplast 30S ribosomal protein S4	0.69	-	nuc	0	Plastid; chloroplast				199
Q6L397 UniProt NPD GO	RR4_SACHY	Chloroplast 30S ribosomal protein S4	0.69	-	mit	0	Plastid; chloroplast				201
Q6ENW1 UniProt NPD GO	RR4_SACOF	Chloroplast 30S ribosomal protein S4	0.69	-	mit	0	Plastid; chloroplast				201
P02355 UniProt NPD GO	RR4_MAIZE	Chloroplast 30S ribosomal protein S4 (Basic protein)	0.69	-	mit	0	Plastid; chloroplast				201
Q332U1 UniProt NPD GO	RR8_LACSA	Chloroplast 30S ribosomal protein S8	0.69	-	nuc	0	Plastid; chloroplast				134
P49556 UniProt NPD GO	RK20_ODOSI	Chloroplast 50S ribosomal protein L20	0.69	-	mit	0	Plastid; chloroplast				114
Q6ENU1 UniProt NPD GO	RK20_SACOF	Chloroplast 50S ribosomal protein L20	0.69	-	nuc	0	Plastid; chloroplast				119
Q05566 UniProt NPD GO	RK32_MAIZE	Chloroplast 50S ribosomal protein L32	0.69	-	nuc	0	Plastid; chloroplast				58
Q6B951 UniProt NPD GO	RK34_GRATL	Chloroplast 50S ribosomal protein L34	0.69	+	mit	0	Plastid; chloroplast				45
O78496 UniProt NPD GO	RK35_GUITH	Chloroplast 50S ribosomal protein L35	0.69	+	nuc	0	Plastid; chloroplast				66
P30551 UniProt NPD GO	CCKAR_RAT	Cholecystokinin type A receptor (CCK-A receptor) (CCK-AR) (Cholecystokinin-1 receptor) (CCK1-R)	0.69	-	end	7	Membrane; multi-pass membrane protein	plasma membrane [IMP]			444
Q5NVH8 UniProt NPD GO	CPSF6_PONPY	Cleavage and polyadenylation specificity factor 6	0.69	+	nuc	0	Nucleus (By similarity). In punctate subnuclear structures localized adjacent to nuclear speckles, c ...				552
Q8HZ58 UniProt NPD GO	CCHCR_PONPY	Coiled-coil alpha-helical rod protein 1 (Alpha helical coiled-coil rod protein)	0.69	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				782
Q9BUN5 UniProt NPD GO	CC28B_HUMAN	Coiled-coil domain-containing protein 28B	0.69	-	nuc	0					241
P53959 UniProt NPD GO	COG6_YEAST	Conserved oligomeric Golgi complex subunit 6 (COG complex subunit 6) (Complexed with DOR1 protein 2) ...	0.69	-	nuc	0		Golgi transport complex [IPI]			839
P06296 UniProt NPD GO	CRF_PIG	Corticoliberin precursor (Corticotropin-releasing factor) (CRF) (Corticotropin-releasing hormone)	0.69	-	nuc	0	Secreted protein				191
O13790 UniProt NPD GO	CUL1_SCHPO	Cullin-1 (Cul-1) (Cell division control 53 homolog)	0.69	-	nuc	0	Cytoplasm (By similarity)	SCF ubiquitin ligase complex [IDA]			767
Q23639 UniProt NPD GO	CUL5_CAEEL	Cullin-5	0.69	-	cyt	0					741
Q8R311 UniProt NPD GO	CTGE5_MOUSE	Cutaneous T-cell lymphoma-associated antigen 5 homolog (cTAGE-5 protein) (Meningioma-expressed antig ...	0.69	-	nuc	1 *					779
Q8T0W1 UniProt NPD GO	CVP5_PIMHY	Cysteine-rich venom protein 5 precursor	0.69	-	nuc	1 *	Secreted protein				115
Q2QLB4 UniProt NPD GO	CFTR_CALMO	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.69	-	end	11	Membrane; multi-pass membrane protein				1480
Q5U820 UniProt NPD GO	CFTR_CANFA	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.69	-	end	11	Membrane; multi-pass membrane protein				1483
Q2QL83 UniProt NPD GO	CFTR_MICMU	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.69	-	end	11	Membrane; multi-pass membrane protein				1481
Q6PQZ2 UniProt NPD GO	CFTR_PIG	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.69	-	end	11	Membrane; multi-pass membrane protein				1482
P10611 UniProt NPD GO	CP4A4_RABIT	Cytochrome P450 4A4 precursor (EC 1.14.14.1) (CYPIVA4) (Prostaglandin omega-hydroxylase) (P450-P-2)	0.69	-	cyt	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				510
Q86W10 UniProt NPD GO	CP4Z1_HUMAN	Cytochrome P450 4Z1 (EC 1.14.14.1) (CYPIVZ1)	0.69	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				505
Q9QX11 UniProt NPD GO	CYH1_MOUSE	Cytohesin-1 (CLM1)	0.69	-	cyt	0					398
P97694 UniProt NPD GO	CYH1_RAT	Cytohesin-1 (SEC7 homolog A) (msec7-1)	0.69	-	cyt	0					398

You are viewing entries 14151 to 14200 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.