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
Q9C5T3 UniProt NPD GO	WRK26_ARATH	Probable WRKY transcription factor 26 (WRKY DNA-binding protein 26) (SPF1-like protein)	0.71	-	nuc	0	Nucleus (Probable)				309
P34751 UniProt NPD GO	DDC_CAEEL	Probable aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) (AADC) (DOPA decarboxylase) (DDC)	0.71	-	nuc	0					830
Q753N1 UniProt NPD GO	NDC80_ASHGO	Probable kinetochore protein NDC80	0.71	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				660
Q6BPA9 UniProt NPD GO	NUF2_DEBHA	Probable kinetochore protein NUF2	0.71	-	mit	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				488
O44411 UniProt NPD GO	NOG1_CAEEL	Probable nucleolar GTP-binding protein 1	0.71	-	nuc	0	Nucleus; nucleolus (By similarity)				681
Q5NB83 UniProt NPD GO	ABIL3_ORYSA	Probable protein ABIL3 (Abl interactor-like protein 3)	0.71	-	nuc	0					317
Q17848 UniProt NPD GO	I5P1_CAEEL	Probable type I inositol-1,4,5-trisphosphate 5-phosphatase (EC 3.1.3.56) (5PTase)	0.71	-	cyt	0					409
Q9P3U0 UniProt NPD GO	UBP2_SCHPO	Probable ubiquitin carboxyl-terminal hydrolase 2 (EC 3.1.2.15) (Ubiquitin thioesterase 2) (Ubiquitin ...	0.71	-	nuc	0					1141
Q12476 UniProt NPD GO	AIR2_YEAST	Protein AIR2 (Arginine methyltransferase-interacting RING finger protein 2)	0.71	-	nuc	0	Nucleus	nucleus [IPI] TRAMP complex [IDA]			344
Q96M53 UniProt NPD GO	CJ027_HUMAN	Protein C10orf27	0.71	-	nuc	0					351
Q5T7W7 UniProt NPD GO	CI097_HUMAN	Protein C9orf97	0.71	-	nuc	0					516
Q12150 UniProt NPD GO	CSF1_YEAST	Protein CSF1 (Cold sensitive for fermentation protein 1)	0.71	-	vac	1 *	Membrane; single-pass type II membrane protein (Potential)	mitochondrion [IDA]			2958
Q75A03 UniProt NPD GO	DIA2_ASHGO	Protein DIA2	0.71	-	nuc	0	Nucleus (Probable)				685
Q86V20 UniProt NPD GO	FA35A_HUMAN	Protein FAM35A	0.71	-	nuc	0					835
Q8IZU1 UniProt NPD GO	FAM9A_HUMAN	Protein FAM9A	0.71	-	nuc	0	Nucleus; nucleolus		300477		332
P39734 UniProt NPD GO	HPH2_YEAST	Protein HPH2 (High pH protein 2) (Functionally related to TCP1 protein 2)	0.71	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Punctate foci a ...	endoplasmic reticulum [IDA]			528
Q80U62 UniProt NPD GO	K0226_MOUSE	Protein KIAA0226	0.71	-	nuc	0					956
Q8WNU4 UniProt NPD GO	K1683_MACFA	Protein KIAA1683 homolog (Fragment)	0.71	-	mit	0					798
P38852 UniProt NPD GO	LIN1_YEAST	Protein LIN1	0.71	+	nuc	0	Nucleus. Probably associated with chromatin	chromatin [IDA] nucleus [IDA] snRNP U5 [IPI]			340
P23493 UniProt NPD GO	MBR1_YEAST	Protein MBR1	0.71	-	nuc	0					339
Q9UGL9 UniProt NPD GO	NICE1_HUMAN	Protein NICE-1	0.71	-	nuc	0					99
Q9Z304 UniProt NPD GO	MYCS_MOUSE	Protein S-myc	0.71	+	nuc	0	Nucleus (Potential)				431
Q5XPJ9 UniProt NPD GO	SCAR2_ARATH	Protein SCAR2 (AtSCAR2) (Protein WAVE4) (Protein DISTORTED3) (Protein IRREGULAR TRICHOME BRANCH1)	0.71	-	nuc	0					1399
Q63945 UniProt NPD GO	SET_RAT	Protein SET (Phosphatase 2A inhibitor I2PP2A) (I-2PP2A) (Template-activating factor I) (TAF-I) (Live ...	0.71	-	nuc	0	Cytoplasm; cytosol (By similarity). Endoplasmic reticulum (By similarity). Nucleus; nucleoplasm (By ...				289
Q8N1H7 UniProt NPD GO	S6OS1_HUMAN	Protein SIX6OS1 (Six6 opposite strand transcript 1)	0.71	-	nuc	0					587
P46679 UniProt NPD GO	STB2_YEAST	Protein STB2	0.71	-	nuc	0		nucleus [IPI] Sin3 complex [IPI]			850
P32772 UniProt NPD GO	UGX2_YEAST	Protein UGX2	0.71	+	nuc	0					223
Q06493 UniProt NPD GO	YLH47_YEAST	Protein YLH47, mitochondrial precursor (LETM1 homolog)	0.71	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein	mitochondrial inner membrane [IDA] mitochondrion [IDA]			454
P22469 UniProt NPD GO	Z600_DROME	Protein Z600	0.71	+	nuc	0		cytoplasm [IDA]			90
P91699 UniProt NPD GO	DECA_DROPS	Protein decapentaplegic precursor (Protein DPP-C)	0.71	+	nuc	0	Secreted protein. Is internalized by receptor-mediated endocytosis (By similarity)				621
Q24185 UniProt NPD GO	HOOK_DROME	Protein hook (dHK)	0.71	-	nuc	0	Cytoplasm. Endosome. Localizes to endosomes. Enriched at neuromuscular synapses, in both presynaptic ...	cytoplasm [NAS] endosome [IDA] synapse [IMP]			679
P29503 UniProt NPD GO	NEUR_DROME	Protein neuralized	0.71	+	nuc	0	Nucleus (Potential)	cytoplasm [IDA] perinuclear region [IDA] plasma membrane [IDA]			754
Q24629 UniProt NPD GO	REF2P_DROSI	Protein ref(2)P (Refractory to sigma P)	0.71	-	nuc	0	Nucleus (Potential)				599
P08044 UniProt NPD GO	SNAI_DROME	Protein snail	0.71	-	nuc	0	Nucleus	nucleus [IDA]			390
O76202 UniProt NPD GO	USP_CHOFU	Protein ultraspiracle homolog	0.71	+	nuc	0	Nucleus (By similarity)				472
P34243 UniProt NPD GO	YKB7_YEAST	Putative ATP-dependent helicase YKL017C (EC 3.6.1.-)	0.71	-	nuc	0		alpha DNA polymerase:primase complex [IPI]			683
P69781 UniProt NPD GO	GAT13_ARATH	Putative GATA transcription factor 13	0.71	-	nuc	0	Nucleus (Probable)				331
O17919 UniProt NPD GO	DKC1_CAEEL	Putative H/ACA ribonucleoprotein complex subunit 4 (EC 5.4.99.-)	0.71	-	nuc	0	Nucleus; nucleolus (By similarity)				445
O43143 UniProt NPD GO	DHX15_HUMAN	Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 (EC 3.6.1.-) (DEAH box protein 15 ...	0.71	-	nuc	0	Nucleus	minor (U12-dependent) spliceosome complex [IDA] nucleus [TAS]	603403		795
Q09092 UniProt NPD GO	SRK6_BRAOE	Putative serine/threonine-protein kinase receptor precursor (EC 2.7.11.1) (S-receptor kinase) (SRK)	0.71	+	end	2 *	Membrane; single-pass type I membrane protein				849
Q20797 UniProt NPD GO	STX3_CAEEL	Putative syntaxin-3	0.71	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)	integral to membrane [ISS]			413
Q99666 UniProt NPD GO	RGPD8_HUMAN	RANBP2-like and GRIP domain-containing protein 8 (Ran-binding protein 2-like 1) (RanBP2L1) (Sperm me ...	0.71	-	nuc	0			602752		1765
Q6ZSG1 UniProt NPD GO	RN165_HUMAN	RING finger protein 165	0.71	-	nuc	0					346
O94684 UniProt NPD GO	TFB3_SCHPO	RNA polymerase II transcription factor B subunit 3 (RNA polymerase II transcription factor B p38 sub ...	0.71	-	nuc	0	Nucleus (By similarity)	transcription factor TFIIH complex [TAS]			318
O13930 UniProt NPD GO	SEC2_SCHPO	Rab guanine nucleotide exchange factor sec2 (GDP-GTP exchange factor sec2)	0.71	-	nuc	0					527
Q13671 UniProt NPD GO	RIN1_HUMAN	Ras and Rab interactor 1 (Ras interaction/interference protein 1) (Ras inhibitor JC99)	0.71	-	nuc	0	Cytoplasm. Membrane. Some amount is membrane-associated	plasma membrane [TAS]	605965		783
Q8CJ96 UniProt NPD GO	RASF8_MOUSE	Ras association domain-containing protein 8 (Carcinoma-associated protein HOJ-1 homolog)	0.71	+	nuc	0					419
Q4TVR5 UniProt NPD GO	RIPK5_BOVIN	Receptor-interacting serine/threonine-protein kinase 5 (EC 2.7.11.1) (Dusty protein kinase) (Dusty P ...	0.71	-	cyt	0	Cytoplasm (Probable)				928
Q98936 UniProt NPD GO	PTPRG_CHICK	Receptor-type tyrosine-protein phosphatase gamma precursor (EC 3.1.3.48) (Protein-tyrosine phosphata ...	0.71	-	mit	1	Membrane; single-pass type I membrane protein (Probable)				1422
Q9PWA1 UniProt NPD GO	RGS20_CHICK	Regulator of G-protein signaling 20 (RGS20) (Gz-GAP)	0.71	-	nuc	0	Membrane; lipid-anchor (By similarity)				218

You are viewing entries 13451 to 13500 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.