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
Q5PQJ7 UniProt NPD GO	TBCEL_RAT	Tubulin-specific chaperone cofactor E-like protein (Leucine-rich repeat-containing protein 35)	0.38	-	nuc	0					424
P50591 UniProt NPD GO	TNF10_HUMAN	Tumor necrosis factor ligand superfamily member 10 (TNF-related apoptosis-inducing ligand) (Protein ...	0.38	-	nuc	1 *	Membrane; single-pass type II membrane protein (Potential)	integral to plasma membrane [TAS] soluble fraction [TAS]	603598	1DU3	281
O54907 UniProt NPD GO	TNF12_MOUSE	Tumor necrosis factor ligand superfamily member 12 (TNF-related weak inducer of apoptosis) (TWEAK) [ ...	0.38	+	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	extracellular region [IDA]			249
Q5ZIW1 UniProt NPD GO	PEO1_CHICK	Twinkle protein, mitochondrial precursor (EC 3.6.1.-) (Progressive external ophthalmoplegia 1 protei ...	0.38	-	mit	0	Mitochondrion (By similarity). Colocalizes with mtDNA in mitochondrial nucleoids, a nucleoproteins c ...				669
P09760 UniProt NPD GO	FLK_RAT	Tyrosine-protein kinase FLK (EC 2.7.10.2) (Fragment)	0.38	-	mit	0					323
P43332 UniProt NPD GO	SNRPA_DROME	U1 small nuclear ribonucleoprotein A (U1 snRNP protein A) (U1-A) (Sex determination protein snf)	0.38	-	nuc	0	Nucleus	nucleus [TAS] small nuclear ribonucleoprotein complex [IDA]			216
P43123 UniProt NPD GO	UAP1_YEAST	UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23)	0.38	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IDA] nucleus [IDA]			477
Q5K915 UniProt NPD GO	HUT1_CRYNE	UDP-galactose transporter homolog 1	0.38	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				412
Q6GMI9 UniProt NPD GO	UXS1_BRARE	UDP-glucuronic acid decarboxylase 1 (EC 4.1.1.35) (UDP-glucuronate decarboxylase 1) (UXS-1)	0.38	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				418
Q9H3Y8 UniProt NPD GO	CT149_HUMAN	UPF0362 protein C20orf149	0.38	-	nuc	0					114
P54725 UniProt NPD GO	RD23A_HUMAN	UV excision repair protein RAD23 homolog A (hHR23A)	0.38	-	nuc	0	Nucleus (Probable)		600061	1TP4	363
O42666 UniProt NPD GO	BUT1_SCHPO	Uba3-binding protein but1	0.38	-	nuc	0	Nucleus	nucleus [IDA]			243
Q8BM54 UniProt NPD GO	MYLIP_MOUSE	Ubiquitin ligase MYLIP (EC 6.3.2.-) (Myosin regulatory light chain-interacting protein) (MIR)	0.38	-	nuc	0	Cytoplasm (Probable)				445
Q91Z63 UniProt NPD GO	TRI63_RAT	Ubiquitin ligase TRIM63 (EC 6.3.2.-) (Tripartite motif-containing protein 63) (Muscle-specific RING ...	0.38	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Localizes to the M- and Z-lines in skeletal musc ...	contractile fiber [IDA]			351
Q9NZ09 UniProt NPD GO	UBAP1_HUMAN	Ubiquitin-associated protein 1 (UBAP)	0.38	-	nuc	0			609787	1WGN	502
Q8WVN8 UniProt NPD GO	UB2Q2_HUMAN	Ubiquitin-conjugating enzyme E2 Q2 (EC 6.3.2.19) (Ubiquitin-protein ligase Q2) (Ubiquitin carrier pr ...	0.38	-	nuc	0	Cytoplasm			1ZUO	375
Q7YQJ9 UniProt NPD GO	UB2Q2_RABIT	Ubiquitin-conjugating enzyme E2 Q2 (EC 6.3.2.19) (Ubiquitin-protein ligase Q2) (Ubiquitin carrier pr ...	0.38	-	nuc	0	Cytoplasm (By similarity)				369
P52485 UniProt NPD GO	UBCD2_DROME	Ubiquitin-conjugating enzyme E2-24 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.38	-	nuc	0					232
Q17297 UniProt NPD GO	UN119_CAEBR	Unc-119 protein	0.38	-	nuc	0					217
Q5FVJ5 UniProt NPD GO	CP045_RAT	Uncharacterized protein C16orf45 homolog	0.38	-	nuc	0					203
Q7Z4B0 UniProt NPD GO	CR020_HUMAN	Uncharacterized protein C18orf20 precursor	0.38	-	exc	1 *					112
Q8NHU2 UniProt NPD GO	CT026_HUMAN	Uncharacterized protein C20orf26	0.38	-	mit	0					1237
Q5E9J2 UniProt NPD GO	CB024_BOVIN	Uncharacterized protein C2orf24 homolog	0.38	-	nuc	0					411
Q8BWU3 UniProt NPD GO	CC040_MOUSE	Uncharacterized protein C3orf40 homolog precursor	0.38	-	nuc	0	Secreted protein (By similarity)				361
Q6ZTR5 UniProt NPD GO	CX022_HUMAN	Uncharacterized protein CXorf22	0.38	-	cyt	0					976
P38890 UniProt NPD GO	YH07_YEAST	Uncharacterized protein YHR207C	0.38	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			526
Q05789 UniProt NPD GO	YL211_YEAST	Uncharacterized protein YLR211C	0.38	-	nuc	0	Cytoplasm	cytoplasm [IDA]			226
Q3E742 UniProt NPD GO	YL412_YEAST	Uncharacterized protein YLR412C-A	0.38	+	nuc	0					68
Q12012 UniProt NPD GO	YO289_YEAST	Uncharacterized protein YOR289W	0.38	-	mit	0		cytoplasm [IDA] nucleus [IDA]			251
Q08909 UniProt NPD GO	YO385_YEAST	Uncharacterized protein YOR385W	0.38	-	nuc	0	Cytoplasm	cytoplasm [IDA]			290
P53943 UniProt NPD GO	YNG5_YEAST	Uncharacterized transporter YNL065W	0.38	-	end	10	Membrane; multi-pass membrane protein (Probable)	plasma membrane [IDA]			586
Q25566 UniProt NPD GO	PYR5_NAEGR	Uridine 5'-monophosphate synthase (UMP synthase) [Includes: Orotate phosphoribosyltransferase (EC 2. ...	0.38	-	cyt	0					494
Q924A4 UniProt NPD GO	UCN3_MOUSE	Urocortin-3 precursor (Urocortin III) (Ucn III)	0.38	-	mit	0	Secreted protein				164
P34089 UniProt NPD GO	RAG2_RABIT	V(D)J recombination-activating protein 2 (RAG-2)	0.38	-	cyt	0	Nucleus				527
P01282 UniProt NPD GO	VIP_HUMAN	VIP peptides precursor [Contains: Intestinal peptide PHV-42; Intestinal peptide PHM-27 (Peptide hist ...	0.38	-	exc	1 *	Secreted protein		192320		170
P11019 UniProt NPD GO	VATE_BOVIN	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit) ...	0.38	-	cyt	0					226
P36543 UniProt NPD GO	VATE_HUMAN	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit) ...	0.38	-	cyt	0		proton-transporting two-sector ATPase complex [TAS]	108746		226
P50944 UniProt NPD GO	AVT4_YEAST	Vacuolar amino acid transporter 4	0.38	-	end	11	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuole [IMP]			713
Q9H269 UniProt NPD GO	VPS16_HUMAN	Vacuolar protein sorting 16 (hVPS16)	0.38	-	cyt	0	Late endosome; late endosomal membrane; peripheral membrane protein. Lysosome; lysosomal membrane; p ...		608550		839
Q06508 UniProt NPD GO	VPS66_YEAST	Vacuolar protein sorting protein 66	0.38	-	mit	1 *		cytoplasm [IDA]			300
P02897 UniProt NPD GO	VSG4_TRYBR	Variant surface glycoprotein 4 precursor (VSG 4) (Metacyclic variable antigen) (Fragment)	0.38	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				476
P40166 UniProt NPD GO	YNT8_YEAST	Very hypothetical protein YNL198C	0.38	-	nuc	0					100
O81644 UniProt NPD GO	VILI2_ARATH	Villin-2	0.38	-	cyt	0					976
P27878 UniProt NPD GO	VIT1_CERCA	Vitellogenin-1 precursor (Vitellogenin I) (Yolk protein 1)	0.38	-	exc	0	Secreted protein				437
P04004 UniProt NPD GO	VTNC_HUMAN	Vitronectin precursor (Serum-spreading factor) (S-protein) (V75) [Contains: Vitronectin V65 subunit; ...	0.38	-	exc	0	Secreted protein; extracellular space	extracellular region [NAS] extracellular space [TAS]	193190	1SSU	478
Q5RFQ4 UniProt NPD GO	WDR72_PONPY	WD repeat protein 72	0.38	-	mit	0					1098
Q10272 UniProt NPD GO	CRB3_SCHPO	WD repeat-containing protein crb3	0.38	-	nuc	0					446
Q94AD9 UniProt NPD GO	ZFNL4_ARATH	Zinc finger CCCH domain-containing protein ZFN-like 4	0.38	-	nuc	0	Nucleus (By similarity)				404
Q90625 UniProt NPD GO	ZBT17_CHICK	Zinc finger and BTB domain-containing protein 17 (Zinc finger protein 151) (Zinc finger protein Z13) ...	0.38	-	nuc	0	Nucleus (By similarity)				706
O43298 UniProt NPD GO	Z297B_HUMAN	Zinc finger protein 297B (ZnF-x) (Zinc finger and BTB domain-containing protein 22B)	0.38	-	nuc	0	Nucleus (Probable)			2CSH	467

You are viewing entries 33851 to 33900 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.