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
O60347 UniProt NPD GO	TBC12_HUMAN	TBC1 domain family member 12	0.87	+	nuc	0					769
P19447 UniProt NPD GO	ERCC3_HUMAN	TFIIH basal transcription factor complex helicase XPB subunit (EC 3.6.1.-) (Basic transcription fact ...	0.87	-	nuc	0	Nucleus	nucleus [TAS] transcription factor TFIIH complex [TAS]	601675		782
Q60HG1 UniProt NPD GO	ERCC3_MACFA	TFIIH basal transcription factor complex helicase XPB subunit (EC 3.6.1.-) (Basic transcription fact ...	0.87	-	nuc	0	Nucleus (By similarity)				782
P49135 UniProt NPD GO	ERCC3_MOUSE	TFIIH basal transcription factor complex helicase XPB subunit (EC 3.6.1.-) (Basic transcription fact ...	0.87	-	nuc	0	Nucleus	nucleus [ISS] transcription factor TFIIH complex [ISS]			783
P13782 UniProt NPD GO	REP2_ZYGRO	Trans-acting factor C (REP2)	0.87	-	nuc	0					233
Q09915 UniProt NPD GO	SPT6_SCHPO	Transcription elongation factor spt6 (Chromatin elongation factor spt6)	0.87	+	cyt	0	Nucleus (Potential)				1365
Q39204 UniProt NPD GO	RAP1_ARATH	Transcription factor AtMYC2 (R-homologous Arabidopsis protein 1) (RAP-1) (Basic helix-loop-helix pro ...	0.87	+	nuc	0	Nucleus (Probable)				623
Q75EH2 UniProt NPD GO	IWS1_ASHGO	Transcription factor IWS1	0.87	+	nuc	0	Nucleus (By similarity)				370
Q8WNV5 UniProt NPD GO	SOX30_MACFA	Transcription factor SOX-30	0.87	-	nuc	0	Nucleus (By similarity)				753
Q10655 UniProt NPD GO	ELT2_CAEEL	Transcription factor elt-2	0.87	+	nuc	0	Nucleus	nucleus [IDA]			433
P36145 UniProt NPD GO	T2EB_YEAST	Transcription initiation factor IIE subunit beta (TFIIE-beta) (Transcription factor A small subunit) ...	0.87	+	nuc	0	Nucleus (Probable)	transcription factor TFIIE complex [TAS]			328
P41896 UniProt NPD GO	T2FB_YEAST	Transcription initiation factor IIF subunit beta (EC 3.6.1.-) (ATP-dependent helicase TFG2) (TFIIF-b ...	0.87	-	nuc	0	Nucleus	transcription factor TFIIF complex [TAS]			400
P32591 UniProt NPD GO	SWI3_YEAST	Transcription regulatory protein SWI3 (SWI/SNF complex component SWI3) (Transcription factor TYE2)	0.87	-	nuc	0	Nucleus	SWI/SNF complex [TAS]		2FQ3	825
P40573 UniProt NPD GO	MET28_YEAST	Transcriptional activator of sulfur metabolism MET28 (Methionine-requiring protein 28)	0.87	-	nuc	0	Cytoplasm. Nucleus	nucleus [IDA]			187
Q8CHV6 UniProt NPD GO	TAD2L_MOUSE	Transcriptional adapter 2-like (ADA2-like protein)	0.87	+	nuc	0	Nucleus			2CUJ	443
Q6AYE3 UniProt NPD GO	TAD2L_RAT	Transcriptional adapter 2-like (ADA2-like protein)	0.87	+	nuc	0	Nucleus (By similarity)				443
P43574 UniProt NPD GO	GAT1_YEAST	Transcriptional regulatory protein GAT1	0.87	-	nuc	0	Nucleus (Potential)	cytosol [IDA] nucleus [IDA]			510
Q08705 UniProt NPD GO	CTCF_CHICK	Transcriptional repressor CTCF (CCCTC-binding factor) (CTCFL paralog) (11-zinc finger protein)	0.87	+	nuc	0	Nucleus				728
P12754 UniProt NPD GO	EI2BD_YEAST	Translation initiation factor eIF-2B subunit delta (eIF-2B GDP-GTP exchange factor subunit delta) (G ...	0.87	-	nuc	0		eukaryotic translation initiation factor 2B... [IDA] ribosome [TAS]			651
Q6UXF1 UniProt NPD GO	TM108_HUMAN	Transmembrane protein 108 precursor	0.87	-	exc	2 *	Membrane; single-pass type I membrane protein				575
P50752 UniProt NPD GO	TNNT2_MOUSE	Troponin T, cardiac muscle (TnTc) (Cardiac muscle troponin T) (cTnT)	0.87	+	nuc	0		cytoplasm [IDA] sarcomere [IDA] troponin complex [IDA]			300
P09741 UniProt NPD GO	TNNT2_RABIT	Troponin T, cardiac muscle (TnTc) (Cardiac muscle troponin T) (cTnT)	0.87	+	nuc	0					300
P02641 UniProt NPD GO	TNNT3_RABIT	Troponin T, fast skeletal muscle (TnTf) (Fast skeletal muscle troponin T) (fTnT)	0.87	-	nuc	0					278
Q8MKH6 UniProt NPD GO	TNNT1_BOVIN	Troponin T, slow skeletal muscle (TnTs) (Slow skeletal muscle troponin T) (sTnT)	0.87	-	nuc	0					262
Q75ZZ6 UniProt NPD GO	TNNT1_PIG	Troponin T, slow skeletal muscle (TnTs) (Slow skeletal muscle troponin T) (sTnT)	0.87	-	nuc	0					261
Q8L9Y3 UniProt NPD GO	ARR14_ARATH	Two-component response regulator ARR14	0.87	+	nuc	0	Nucleus				382
Q9ZWJ9 UniProt NPD GO	ARR2_ARATH	Two-component response regulator ARR2 (Receiver-like protein 5)	0.87	-	nuc	0	Nucleus				664
Q6LA42 UniProt NPD GO	APRR5_ARATH	Two-component response regulator-like APRR5 (Pseudo-response regulator 5)	0.87	-	nuc	0	Nucleus (Probable)				558
P35233 UniProt NPD GO	PTN2_RAT	Tyrosine-protein phosphatase non-receptor type 2 (EC 3.1.3.48) (Protein-tyrosine phosphatase PTP-S)	0.87	-	nuc	0	Cytoplasm				363
Q42404 UniProt NPD GO	RU17_ARATH	U1 small nuclear ribonucleoprotein 70 kDa (U1 snRNP 70 kDa) (snRNP70) (U1-70K)	0.87	-	nuc	0					427
Q922U1 UniProt NPD GO	PRPF3_MOUSE	U4/U6 small nuclear ribonucleoprotein Prp3 (Pre-mRNA-splicing factor 3)	0.87	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Colocalizes with spliceosomal snRNPs (By simi ...				683
O43395 UniProt NPD GO	PRPF3_HUMAN	U4/U6 small nuclear ribonucleoprotein Prp3 (Pre-mRNA-splicing factor 3) (U4/U6 snRNP 90 kDa protein) ...	0.87	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Colocalizes with spliceosomal snRNPs	nucleus [TAS] spliceosome complex [NAS]	601414	1X4Q	683
Q3TIX9 UniProt NPD GO	SNUT2_MOUSE	U4/U6.U5 tri-snRNP-associated protein 2 (Inactive ubiquitin-specific peptidase 39)	0.87	-	nuc	0	Nucleus (By similarity)				564
Q9UPX6 UniProt NPD GO	K1024_HUMAN	UPF0258 protein KIAA1024	0.87	-	nuc	1					916
Q01476 UniProt NPD GO	UBP2_YEAST	Ubiquitin carboxyl-terminal hydrolase 2 (EC 3.1.2.15) (Ubiquitin thioesterase 2) (Ubiquitin-specific ...	0.87	-	nuc	0		cytoplasm [IC]			1272
Q9UPU5 UniProt NPD GO	UBP24_HUMAN	Ubiquitin carboxyl-terminal hydrolase 24 (EC 3.1.2.15) (Ubiquitin thioesterase 24) (Ubiquitin-specif ...	0.87	+	nuc	0					1870
P43593 UniProt NPD GO	UBP6_YEAST	Ubiquitin carboxyl-terminal hydrolase 6 (EC 3.1.2.15) (Ubiquitin thioesterase 6) (Ubiquitin-specific ...	0.87	-	nuc	0		proteasome regulatory particle (sensu Eukar... [IPI]		1VJV	499
Q8NG27 UniProt NPD GO	PJA1_HUMAN	Ubiquitin protein ligase Praja1 (EC 6.3.2.-) (RING finger protein 70)	0.87	-	nuc	0			300420		643
Q5VTR2 UniProt NPD GO	BRE1A_HUMAN	Ubiquitin-protein ligase BRE1A (EC 6.3.2.-) (BRE1-A) (hBRE1) (RING finger protein 20)	0.87	+	nuc	0	Nucleus (Probable)		607699		975
Q4R7K7 UniProt NPD GO	BRE1B_MACFA	Ubiquitin-protein ligase BRE1B (EC 6.3.2.-) (BRE1-B) (RING finger protein 40)	0.87	+	nuc	0	Nucleus (By similarity)				1001
Q8IWV7 UniProt NPD GO	UBR1_HUMAN	Ubiquitin-protein ligase E3 component N-recognin-1 (EC 6.-.-.-) (Ubiquitin-protein ligase E3-alpha-1 ...	0.87	+	vac	0	Cytoplasm; cytosol		605981		1749
Q8NB66 UniProt NPD GO	UN13C_HUMAN	Unc-13 homolog C (Munc13-3) (Fragment)	0.87	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Localized to presy ...				1190
O75071 UniProt NPD GO	K0494_HUMAN	Uncharacterized calcium-binding protein KIAA0494	0.87	+	nuc	1					495
Q5BJE1 UniProt NPD GO	CR034_HUMAN	Uncharacterized protein C18orf34	0.87	+	nuc	0					867
Q66H35 UniProt NPD GO	CR054_RAT	Uncharacterized protein C18orf54 homolog precursor	0.87	-	nuc	0	Secreted protein (Potential)				365
Q9D722 UniProt NPD GO	CT111_MOUSE	Uncharacterized protein C20orf111 homolog	0.87	-	nuc	0					291
P48568 UniProt NPD GO	YD186_YEAST	Uncharacterized protein YDL186W	0.87	-	nuc	0					277
P38742 UniProt NPD GO	YHC3_YEAST	Uncharacterized protein YHL023C	0.87	-	nuc	0					1146
Q9C0U7 UniProt NPD GO	VPS5_SCHPO	Vacuolar protein sorting-associated protein vps5	0.87	-	nuc	0					576
O42250 UniProt NPD GO	VSX1_BRARE	Visual system homeobox 1 (Transcription factor VSX1)	0.87	+	nuc	0	Nucleus (By similarity)				344

You are viewing entries 5851 to 5900 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.