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
O88487 UniProt NPD GO	DC1I2_MOUSE	Cytoplasmic dynein 1 intermediate chain 2 (Dynein intermediate chain 2, cytosolic) (DH IC-2) (Cytopl ...	0.69	+	nuc	0					612
Q921C5 UniProt NPD GO	BICD2_MOUSE	Cytoskeleton-like bicaudal D protein homolog 2	0.69	-	nuc	0	Golgi apparatus. Cytoskeleton. In interphase cells mainly localizes to the Golgi complex and colocal ...	Golgi apparatus [IDA]			820
Q5RHX6 UniProt NPD GO	DCNL4_BRARE	DCN1-like protein 4 (Defective in cullin neddylation protein 1-like protein 4) (DCUN1 domain-contain ...	0.69	+	cyt	0					280
Q92564 UniProt NPD GO	DCNL4_HUMAN	DCN1-like protein 4 (Defective in cullin neddylation protein 1-like protein 4) (DCUN1 domain-contain ...	0.69	+	cyt	0					292
Q8L7S8 UniProt NPD GO	RH3_ARATH	DEAD-box ATP-dependent RNA helicase 3 (EC 3.6.1.-) (Protein EMBRYO DEFECTIVE 1138)	0.69	-	nuc	0					748
O88508 UniProt NPD GO	DNM3A_MOUSE	DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) (Dnmt3a) (DNA methyltransferase MmuIIIA) (DNA MT ...	0.69	-	nuc	0	Nucleus	cytoplasm [ISS] euchromatin [ISS] nuclear heterochromatin [IDA] nuclear matrix [ISS] nucleus [ISS]			908
P13468 UniProt NPD GO	K10_DROME	DNA-binding protein K10 (Female sterile protein K10)	0.69	-	nuc	0	Nucleus	nucleus [IDA]			463
O94131 UniProt NPD GO	CREA_GIBFU	DNA-binding protein creA (Carbon catabolite repressor)	0.69	-	nuc	0	Nucleus				420
O14335 UniProt NPD GO	SCR1_SCHPO	DNA-binding protein scr1	0.69	-	nuc	0	Nucleus (Probable)				565
Q9P7P1 UniProt NPD GO	RPA8_SCHPO	DNA-directed RNA polymerase I 17 kDa polypeptide (EC 2.7.7.6) (A14) (Nucleolar protein ker1)	0.69	-	nuc	0	Nucleus; nucleolus	DNA-directed RNA polymerase I complex [IDA] nucleolus [IDA]			147
P15398 UniProt NPD GO	RPA1_SCHPO	DNA-directed RNA polymerase I 190 kDa polypeptide (EC 2.7.7.6)	0.69	-	nuc	0	Nucleus				1689
P25202 UniProt NPD GO	RPC1_GIALA	DNA-directed RNA polymerase III largest subunit (EC 2.7.7.6)	0.69	-	nuc	0	Nucleus				1741
Q9TM35 UniProt NPD GO	RPOB_CYACA	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.69	-	cyt	0	Plastid; chloroplast				1081
Q6B8R8 UniProt NPD GO	RPOB_GRATL	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.69	-	cyt	0	Plastid; chloroplast				1120
Q6ENI3 UniProt NPD GO	RPOC1_ORYNI	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.69	-	cyt	0	Plastid; chloroplast				682
P12092 UniProt NPD GO	RPOC1_ORYSA	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.69	-	cyt	0	Plastid; chloroplast				682
P13433 UniProt NPD GO	RPOM_YEAST	DNA-directed RNA polymerase, mitochondrial precursor (EC 2.7.7.6)	0.69	-	nuc	0	Mitochondrion	mitochondrial nucleoid [IDA]			1351
Q8TF63 UniProt NPD GO	DCNP1_HUMAN	Dendritic cell nuclear protein 1	0.69	-	nuc	0	Nucleus. Particularly on the periphery		609710		244
Q5U464 UniProt NPD GO	DDFL1_MOUSE	Development and differentiation-enhancing factor-like 1	0.69	-	nuc	0	Cytoplasm (By similarity)				904
P38093 UniProt NPD GO	FLBA_EMENI	Developmental regulator flbA	0.69	-	nuc	0					719
O94907 UniProt NPD GO	DKK1_HUMAN	Dickkopf-related protein 1 precursor (Dkk-1) (Dickkopf-1) (hDkk-1) (SK)	0.69	-	nuc	0	Secreted protein		605189		266
Q8IXT2 UniProt NPD GO	DMRTD_HUMAN	Doublesex- and mab-3-related transcription factor C2	0.69	-	nuc	0	Nucleus (Potential)				367
Q8TD84 UniProt NPD GO	DSCL1_HUMAN	Down syndrome cell adhesion molecule-like protein 1 precursor (Down syndrome cell adhesion molecule ...	0.69	+	nuc	1	Membrane; single-pass type I membrane protein	cell surface [IDA]		1VA9	2053
O43781 UniProt NPD GO	DYRK3_HUMAN	Dual specificity tyrosine-phosphorylation-regulated kinase 3 (EC 2.7.12.1)	0.69	-	nuc	0			603497		588
O14326 UniProt NPD GO	PUB3_SCHPO	E3 ubiquitin--protein ligase pub3 (EC 6.3.2.-)	0.69	-	nuc	0					786
Q5NVD7 UniProt NPD GO	ELMD1_PONPY	ELMO domain-containing protein 1	0.69	-	mit	0					326
P32769 UniProt NPD GO	HBS1_YEAST	Elongation factor 1 alpha-like protein	0.69	-	cyt	0		cytoplasm [IDA]			611
Q9P3S1 UniProt NPD GO	PPN1_NEUCR	Endopolyphosphatase (EC 3.6.1.10)	0.69	+	mit	0	Vacuole; vacuolar membrane; single-pass type II membrane protein				734
Q53AD2 UniProt NPD GO	ESR1_FELCA	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.69	+	nuc	0	Nucleus (By similarity)				595
Q95171 UniProt NPD GO	ESR2_CALJA	Estrogen receptor beta (ER-beta)	0.69	+	nuc	0	Nucleus	nucleus [ISS]			530
Q9V8K2 UniProt NPD GO	EXOC3_DROME	Exocyst complex component 3 (Exocyst complex component Sec6)	0.69	-	cyt	0		exocyst [NAS]			738
Q8TAG9 UniProt NPD GO	EXOC6_HUMAN	Exocyst complex component 6 (Exocyst complex component Sec15A) (Sec15-like 1)	0.69	-	cyt	0			609672		804
Q9VSJ8 UniProt NPD GO	EXOC7_DROME	Exocyst complex component 7 (Exocyst complex component Exo70)	0.69	-	nuc	0		exocyst [NAS]			693
Q53I77 UniProt NPD GO	XPO6A_XENLA	Exportin-6-A	0.69	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the nucleus and the cytoplasm				1135
P62932 UniProt NPD GO	FBX40_MOUSE	F-box only protein 40	0.69	-	nuc	0					710
Q293F6 UniProt NPD GO	SSRP1_DROPS	FACT complex subunit Ssrp1 (Facilitates chromatin transcription complex subunit Ssrp1) (Recombinatio ...	0.69	+	nuc	0	Nucleus. Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci (By ...				722
P06399 UniProt NPD GO	FIBA_RAT	Fibrinogen alpha chain precursor [Contains: Fibrinopeptide A]	0.69	-	exc	0	Secreted protein				782
P48801 UniProt NPD GO	FGF3_CHICK	Fibroblast growth factor 3 precursor (FGF-3) (HBGF-3)	0.69	+	exc	0	Secreted protein (Probable)				220
Q40168 UniProt NPD GO	AG_LYCES	Floral homeotic protein AGAMOUS (TAG1)	0.69	-	nuc	0	Nucleus				248
P41813 UniProt NPD GO	FKH2_YEAST	Fork head protein homolog 2	0.69	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			862
Q61345 UniProt NPD GO	FOXD1_MOUSE	Forkhead box protein D1 (Forkhead-related protein FKHL8) (Forkhead-related transcription factor 4) ( ...	0.69	+	nuc	0	Nucleus (Potential)				456
Q9QY14 UniProt NPD GO	FOXE3_MOUSE	Forkhead box protein E3	0.69	-	nuc	0	Nucleus				288
P55315 UniProt NPD GO	FOXGB_HUMAN	Forkhead box protein G1B (Forkhead-related protein FKHL1) (Transcription factor BF-1) (Brain factor ...	0.69	-	nuc	0	Nucleus		164874		477
Q63247 UniProt NPD GO	FOXJ1_RAT	Forkhead box protein J1 (Hepatocyte nuclear factor 3 forkhead homolog 4) (HFH-4)	0.69	-	nuc	0	Nucleus	nucleus [TAS]			421
O70291 UniProt NPD GO	GRK4_MOUSE	G protein-coupled receptor kinase 4 (EC 2.7.11.16) (G protein-coupled receptor kinase GRK4)	0.69	-	cyt	0					574
Q03569 UniProt NPD GO	GPR2_CAEEL	G-protein regulator 2	0.69	-	cyt	0	Cytoplasm; cell cortex. Spindle. Located to the spindle and cell cortex when in complex with lin-5 a ...				525
P10815 UniProt NPD GO	CG23_SCHPO	G2/mitotic-specific cyclin cdc13	0.69	-	mit	0		nucleus [IDA]			482
P23825 UniProt NPD GO	GATA3_CHICK	GATA-binding factor 3 (GATA-3) (Transcription factor NF-E1C)	0.69	-	nuc	0	Nucleus				444
P56159 UniProt NPD GO	GFRA1_HUMAN	GDNF family receptor alpha-1 precursor (GFR-alpha-1) (GDNF receptor alpha) (GDNFR-alpha) (TGF-beta-r ...	0.69	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	extrinsic to membrane [NAS]	601496		465
O60609 UniProt NPD GO	GFRA3_HUMAN	GDNF family receptor alpha-3 precursor (GFR-alpha-3)	0.69	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	extrinsic to membrane [TAS]	605710		400

You are viewing entries 14201 to 14250 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.