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
Q61164 UniProt NPD GO	CTCF_MOUSE	Transcriptional repressor CTCF (CCCTC-binding factor) (CTCFL paralog) (11-zinc finger protein)	0.88	+	nuc	0	Nucleus	nucleus [IDA]			736
Q9R1D1 UniProt NPD GO	CTCF_RAT	Transcriptional repressor CTCF (CCCTC-binding factor) (CTCFL paralog) (11-zinc finger protein)	0.88	+	nuc	0	Nucleus (By similarity)				737
P19334 UniProt NPD GO	TRP_DROME	Transient receptor potential protein	0.88	-	nuc	6	Membrane; multi-pass membrane protein (Probable). Localized on plasma membrane loops found at the ba ...	inaD signaling complex [IPI] integral to membrane [NAS] plasma membrane [IDA]			1275
Q8NDV7 UniProt NPD GO	TNR6A_HUMAN	Trinucleotide repeat-containing gene 6A protein (CAG repeat protein 26) (Glycine-tryptophan protein ...	0.88	-	nuc	0	Cytoplasm. In structures called GW bodies (GWBs)				1962
P45379 UniProt NPD GO	TNNT2_HUMAN	Troponin T, cardiac muscle (TnTc) (Cardiac muscle troponin T) (cTnT)	0.88	+	nuc	0			115195	1J1E	297
P50751 UniProt NPD GO	TNNT2_SHEEP	Troponin T, cardiac muscle (TnTc) (Cardiac muscle troponin T) (cTnT)	0.88	+	nuc	0					286
P12620 UniProt NPD GO	TNNT3_CHICK	Troponin T, fast skeletal muscle isoforms	0.88	+	nuc	0				1YV0	262
Q9JIL5 UniProt NPD GO	TULP4_MOUSE	Tubby-like protein 4 (Tubby superfamily protein)	0.88	-	nuc	0	Cytoplasm				1547
O75386 UniProt NPD GO	TULP3_HUMAN	Tubby-related protein 3 (Tubby-like protein 3)	0.88	+	nuc	0		nucleus [NAS] plasma membrane [NAS]	604730		442
Q15814 UniProt NPD GO	TBCC_HUMAN	Tubulin-specific chaperone C (Tubulin-folding cofactor C) (CFC)	0.88	-	nuc	0		cytoskeleton [TAS] microtubule [TAS]	602971		346
Q91W18 UniProt NPD GO	TDRD3_MOUSE	Tudor domain-containing protein 3	0.88	-	nuc	0					650
O14990 UniProt NPD GO	IPP4_HUMAN	Type-1 protein phosphatase inhibitor 4 (I-4) (Protein phosphatase 1, regulatory subunit 2 pseudogene ...	0.88	+	nuc	0					202
P17706 UniProt NPD GO	PTN2_HUMAN	Tyrosine-protein phosphatase non-receptor type 2 (EC 3.1.3.48) (T-cell protein-tyrosine phosphatase) ...	0.88	+	nuc	1	Cytoplasm		176887	1L8K	415
P26045 UniProt NPD GO	PTN3_HUMAN	Tyrosine-protein phosphatase non-receptor type 3 (EC 3.1.3.48) (Protein-tyrosine phosphatase H1) (PT ...	0.88	-	nuc	0	Cytoplasm		176877	2B49	913
Q92575 UniProt NPD GO	UBXD2_HUMAN	UBX domain-containing protein 2	0.88	+	nuc	0					508
O94888 UniProt NPD GO	UBXD7_HUMAN	UBX domain-containing protein 7	0.88	-	nuc	0				2DAL	489
Q5REY7 UniProt NPD GO	UBXD7_PONPY	UBX domain-containing protein 7	0.88	-	nuc	0					489
Q2HJD0 UniProt NPD GO	UBXD8_BOVIN	UBX domain-containing protein 8	0.88	+	nuc	0	Cytoplasm (By similarity)				445
Q6BDS2 UniProt NPD GO	URFB1_HUMAN	UHRF1-binding protein 1 (Ubiquitin-like containing PHD and RING finger domains 1-binding protein 1) ...	0.88	-	nuc	0					1440
Q8K3V7 UniProt NPD GO	K1024_MOUSE	UPF0258 protein KIAA1024 (DD1 protein)	0.88	-	nuc	1					917
Q01988 UniProt NPD GO	UBP11_CANFA	Ubiquitin carboxyl-terminal hydrolase 11 (EC 3.1.2.15) (Ubiquitin thioesterase 11) (Ubiquitin-specif ...	0.88	-	nuc	0					445
P38187 UniProt NPD GO	UBP13_YEAST	Ubiquitin carboxyl-terminal hydrolase 13 (EC 3.1.2.15) (Ubiquitin thioesterase 13) (Ubiquitin-specif ...	0.88	+	nuc	0					688
Q91W36 UniProt NPD GO	UBP3_MOUSE	Ubiquitin carboxyl-terminal hydrolase 3 (EC 3.1.2.15) (Ubiquitin thioesterase 3) (Ubiquitin-specific ...	0.88	-	nuc	0					520
Q70CQ3 UniProt NPD GO	UBP30_HUMAN	Ubiquitin carboxyl-terminal hydrolase 30 (EC 3.1.2.15) (Ubiquitin thioesterase 30) (Ubiquitin-specif ...	0.88	+	mit	1 *					517
Q24574 UniProt NPD GO	UBPE_DROME	Ubiquitin carboxyl-terminal hydrolase 64E (EC 3.1.2.15) (Ubiquitin thioesterase 64E) (Ubiquitin-spec ...	0.88	-	nuc	0	Nucleus (Potential)				1556
O95155 UniProt NPD GO	UBE4B_HUMAN	Ubiquitin conjugation factor E4 B (Ubiquitin fusion degradation protein 2) (Homozygously deleted in ...	0.88	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS] ubiquitin ligase complex [TAS]			1302
Q9NB71 UniProt NPD GO	HIW_DROME	Ubiquitin ligase protein highwire (EC 6.3.2.-) (Protein pam/highwire/rpm-1)	0.88	+	nuc	0	Nucleus (By similarity)	cytoplasmic membrane-bound vesicle [IDA] plasma membrane [IDA]			5233
Q9UPW8 UniProt NPD GO	UN13A_HUMAN	Unc-13 homolog A (Munc13-1)	0.88	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Localized to the active zone of presynap ...		609894		1703
Q8BGQ6 UniProt NPD GO	K0494_MOUSE	Uncharacterized calcium-binding protein KIAA0494	0.88	+	nuc	1					484
Q68FW6 UniProt NPD GO	CN050_RAT	Uncharacterized protein C14orf50 homolog	0.88	-	nuc	0					411
P38335 UniProt NPD GO	YB9C_YEAST	Uncharacterized protein YBR255W	0.88	-	end	1		cytoplasm [IDA]			694
P53251 UniProt NPD GO	YG2I_YEAST	Uncharacterized protein YGR081C	0.88	+	nuc	0		nucleolus [IDA] nucleus [IDA]			210
P39523 UniProt NPD GO	YM11_YEAST	Uncharacterized protein YMR124W	0.88	-	nuc	0		cytoplasm [IDA]			943
Q08229 UniProt NPD GO	YO070_YEAST	Uncharacterized protein YOL070C	0.88	-	nuc	0	Bud neck. Cytoplasm. Assembles at the inner surface of the cell membrane	bud neck [IDA] cytoplasm [IDA]			501
Q5E9F6 UniProt NPD GO	VPS72_BOVIN	Vacuolar protein sorting protein 72 homolog (Transcription factor-like 1)	0.88	-	nuc	0	Nucleus (By similarity)				364
P53950 UniProt NPD GO	VAC7_YEAST	Vacuolar segregation protein 7	0.88	-	nuc	1	Vacuole; vacuolar membrane; single-pass type II membrane protein	cytoplasm [IDA] integral to membrane [IDA] vacuole (sensu Fungi) [IDA]			1165
P48582 UniProt NPD GO	BRO1_YEAST	Vacuolar sorting protein BRO1 (BRO domain-containing protein 1) (BCK1-like resistance to osmotic sho ...	0.88	-	nuc	0	Cytoplasm. Endosome	cytoplasm [TAS] endosome [IDA] membrane fraction [IDA]		1ZB1	844
Q91062 UniProt NPD GO	VIT_ICHUN	Vitellogenin precursor (VTG) [Contains: Lipovitellin LV-1N; Lipovitellin LV-1C; Lipovitellin LV-2]	0.88	-	nuc	0				1LSH	1823
Q8IZQ1 UniProt NPD GO	WDFY3_HUMAN	WD repeat and FYVE domain-containing protein 3 (Autophagy-linked FYVE protein) (Alfy)	0.88	-	cyt	0	Membrane; peripheral membrane protein; cytoplasmic side. Co-localizes with autophagic structures in ...				3526
Q80T85 UniProt NPD GO	WDR22_MOUSE	WD repeat protein 22	0.88	-	nuc	0					946
Q6GQQ9 UniProt NPD GO	CEZ1_HUMAN	Zinc finger A20 domain-containing protein 1 (EC 3.-.-.-) (Cellular zinc finger anti-NF-kappa B prote ...	0.88	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			843
Q8TE49 UniProt NPD GO	CEZ2_HUMAN	Zinc finger A20 domain-containing protein ? (EC 3.-.-.-) (Zinc finger protein Cezanne 2) (OTU domain ...	0.88	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				926
Q8IXZ2 UniProt NPD GO	ZC3H3_HUMAN	Zinc finger CCCH domain-containing protein 3	0.88	-	nuc	0					948
Q9C0B0 UniProt NPD GO	ZC3H5_HUMAN	Zinc finger CCCH domain-containing protein 5	0.88	-	nuc	0					810
Q9UBW7 UniProt NPD GO	ZN198_HUMAN	Zinc finger protein 198 (Zinc finger MYM-type protein 2) (Fused in myeloproliferative disorders prot ...	0.88	-	nuc	0	Nucleus (Potential)		602221		1377
Q96JM2 UniProt NPD GO	ZN462_HUMAN	Zinc finger protein 462	0.88	-	nuc	0	Nucleus (Potential)			1X6F	1412
Q92618 UniProt NPD GO	ZN516_HUMAN	Zinc finger protein 516	0.88	-	nuc	0	Nucleus (Probable)				1163
Q8BHZ4 UniProt NPD GO	ZN592_MOUSE	Zinc finger protein 592 (Zfp-592)	0.88	-	nuc	0	Nucleus (Probable)				1262
Q96AP4 UniProt NPD GO	CF113_HUMAN	Zinc finger protein C6orf113	0.88	-	nuc	0					578
P81183 UniProt NPD GO	HELI_MOUSE	Zinc finger protein Helios	0.88	-	nuc	0	Nucleus				526

You are viewing entries 5401 to 5450 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.