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
Q6U8D7 UniProt NPD GO	FOXP3_MACFA	Forkhead box protein P3	0.78	-	nuc	0	Nucleus (Potential)				431
Q9WVR4 UniProt NPD GO	FXR2_MOUSE	Fragile X mental retardation syndrome-related protein 2	0.78	-	nuc	0	Cytoplasm (By similarity)				673
Q6PEM6 UniProt NPD GO	GRAM3_MOUSE	GRAM domain-containing protein 3	0.78	-	nuc	1					445
Q9JHD2 UniProt NPD GO	GCNL2_MOUSE	General control of amino acid synthesis protein 5-like 2 (EC 2.3.1.48) (Histone acetyltransferase GC ...	0.78	-	nuc	0	Nucleus	histone acetyltransferase complex [IDA]			830
Q9N1U3 UniProt NPD GO	GCR_PIG	Glucocorticoid receptor (GR) (Fragment)	0.78	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in the absence of ligand; nuclear af ...				711
Q5GJ77 UniProt NPD GO	PLSB_BOVIN	Glycerol-3-phosphate acyltransferase, mitochondrial precursor (EC 2.3.1.15) (GPAT)	0.78	-	nuc	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				825
Q8I6U8 UniProt NPD GO	GBP_PLAF7	Glycophorin-binding protein (GBP-130)	0.78	-	nuc	1 *	Erythrocyte cytoplasm of schizonts. Released into the culture supernatant at the time of schizont ru ...				824
Q9H3P7 UniProt NPD GO	GCP60_HUMAN	Golgi resident protein GCP60 (Acyl-CoA-binding domain-containing protein 3) (Golgi phosphoprotein 1) ...	0.78	+	nuc	0	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Mito ...		606809		527
Q5PPL8 UniProt NPD GO	GRHL3_XENLA	Grainyhead-like protein 3 homolog (Transcription factor CP2-like 4)	0.78	-	nuc	0	Nucleus (By similarity)				595
Q9NZ20 UniProt NPD GO	PA2G3_HUMAN	Group 3 secretory phospholipase A2 precursor (EC 3.1.1.4) (Group III secretory phospholipase A2) (Ph ...	0.78	-	exc	0	Secreted protein	extracellular space [TAS]			509
Q96PP9 UniProt NPD GO	GBP4_HUMAN	Guanylate-binding protein 4	0.78	-	cyt	0					640
Q62661 UniProt NPD GO	HBP1_RAT	HMG box-containing protein 1 (HMG box transcription factor 1) (High mobility group box transcription ...	0.78	-	nuc	0	Nucleus (By similarity)	nucleus [IC]			513
Q5A7Q2 UniProt NPD GO	ESA1_CANAL	Histone acetyltransferase ESA1 (EC 2.3.1.48)	0.78	-	nuc	0	Nucleus (By similarity)				541
P56524 UniProt NPD GO	HDAC4_HUMAN	Histone deacetylase 4 (HD4)	0.78	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the nucleus and the cytoplasm. Upon muscle cells differentiatio ...	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [NAS]	605314		1084
Q9IA18 UniProt NPD GO	EVX2_HETFR	Homeobox even-skipped homolog protein 2 (EVX-2)	0.78	+	nuc	0	Nucleus (By similarity)				424
Q24256 UniProt NPD GO	BARH2_DROME	Homeobox protein B-H2 (Homeobox protein BarH2)	0.78	+	nuc	1	Nucleus (Probable)	nucleus [NAS]			645
Q98924 UniProt NPD GO	HXA9_CHICK	Homeobox protein Hox-A9 (Fragment)	0.78	+	nuc	0	Nucleus				169
P09070 UniProt NPD GO	HXB4_XENLA	Homeobox protein Hox-B4 (Xhox-1A)	0.78	+	nuc	0	Nucleus				232
P50222 UniProt NPD GO	MEOX2_HUMAN	Homeobox protein MOX-2 (Mesenchyme homeobox 2) (Growth arrest-specific homeobox)	0.78	+	nuc	0	Nucleus (Potential)		600535		304
Q60554 UniProt NPD GO	NKX61_MESAU	Homeobox protein Nkx-6.1	0.78	+	nuc	0	Nucleus (Probable)				364
Q15475 UniProt NPD GO	SIX1_HUMAN	Homeobox protein SIX1 (Sine oculis homeobox homolog 1)	0.78	-	nuc	0	Nucleus		601205		284
O70137 UniProt NPD GO	ALX3_MOUSE	Homeobox protein aristaless-like 3 (Proline-rich transcription factor ALX3)	0.78	+	nuc	0	Nucleus (By similarity)				343
O88850 UniProt NPD GO	HIPK3_RAT	Homeodomain-interacting protein kinase 3 (EC 2.7.11.1) (Androgen receptor-interacting nuclear protei ...	0.78	-	nuc	0	Nucleus				1191
Q24645 UniProt NPD GO	ANTP_DROSU	Homeotic protein antennapedia	0.78	+	nuc	0	Nucleus (Probable)	nucleus [ISS]			394
P18488 UniProt NPD GO	EMS_DROME	Homeotic protein empty spiracles	0.78	+	nuc	0	Nucleus				497
Q41330 UniProt NPD GO	KN1_LYCES	Homeotic protein knotted-1 (TKN1)	0.78	+	nuc	0	Nucleus (Probable)				355
Q24276 UniProt NPD GO	CDC37_DROME	Hsp90 co-chaperone Cdc37 (Hsp90 chaperone protein kinase-targeting subunit) (Protein enhancer of sev ...	0.78	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			389
O35668 UniProt NPD GO	HAP1_MOUSE	Huntingtin-associated protein 1 (HAP-1)	0.78	-	nuc	0		cytoplasmic membrane-bound vesicle [IDA]			628
Q04276 UniProt NPD GO	YMX2_YEAST	Hypothetical 14.1 kDa protein in MBR3-ADH3 intergenic region	0.78	-	nuc	0					118
Q03695 UniProt NPD GO	YM58_YEAST	Hypothetical 35.0 kDa protein in PFK2-HFA1 intergenic region	0.78	-	nuc	0					313
Q02209 UniProt NPD GO	YKZ1_YEAST	Hypothetical 41.3 kDa protein in FOX2-YPT52 intergenic region	0.78	+	nuc	0		nucleus [IDA]			353
P43560 UniProt NPD GO	YFE2_YEAST	Hypothetical 76.3 kDa protein in SEC53-FET5 intergenic region	0.78	-	nuc	1					674
Q11072 UniProt NPD GO	YT44_CAEEL	Hypothetical RING finger protein B0416.4 in chromosome X	0.78	-	nuc	0					218
O13747 UniProt NPD GO	YDRD_SCHPO	Hypothetical RING finger protein C16E8.13 in chromosome I	0.78	+	nuc	0					547
Q9URV0 UniProt NPD GO	YBLC_SCHPO	Hypothetical RNA-binding protein C106.12c in chromosome II	0.78	-	nuc	0					274
Q9ZQ34 UniProt NPD GO	Y2433_ARATH	Hypothetical protein At2g24330	0.78	+	nuc	2					408
Q11125 UniProt NPD GO	YX14_CAEEL	Hypothetical protein C03F11.4	0.78	+	nuc	0					389
O74840 UniProt NPD GO	YCY3_SCHPO	Hypothetical protein C1235.03 in chromosome III	0.78	+	nuc	0					399
O13892 UniProt NPD GO	YE38_SCHPO	Hypothetical protein C20G4.08 in chromosome I	0.78	-	nuc	0					1076
Q8STH9 UniProt NPD GO	Y105_ENCCU	Hypothetical protein ECU01_0050/ECU01_1560/ECU07_0010	0.78	-	nuc	0					238
Q8STG8 UniProt NPD GO	Y2F9_ENCCU	Hypothetical protein ECU02_1590/ECU04_0060/ECU08_2120	0.78	-	nuc	0					207
P34489 UniProt NPD GO	YMM1_CAEEL	Hypothetical protein K01B6.1	0.78	-	nuc	0					732
P41843 UniProt NPD GO	YO93_CAEEL	Hypothetical protein T20B12.3 in chromosome III	0.78	-	cyt	0					504
P43032 UniProt NPD GO	INHBA_SHEEP	Inhibin beta A chain precursor (Activin beta-A chain)	0.78	-	nuc	0	Secreted protein				425
P49708 UniProt NPD GO	IFNG_CHICK	Interferon gamma precursor (IFN-gamma)	0.78	-	nuc	1 *	Secreted protein				164
O57603 UniProt NPD GO	IFNG_MELGA	Interferon gamma precursor (IFN-gamma)	0.78	+	nuc	1 *	Secreted protein (By similarity)				164
Q5S1U6 UniProt NPD GO	IFRD1_PIG	Interferon-related developmental regulator 1	0.78	-	nuc	0					450
P90901 UniProt NPD GO	IFA1_CAEEL	Intermediate filament protein ifa-1 (Intermediate filament protein A1) (IF-A1) (Cel IF A1)	0.78	-	nuc	0	Cytoplasm				575
P87245 UniProt NPD GO	KMS1_SCHPO	Karyogamy meiotic segregation protein 1	0.78	-	nuc	2	Nucleus. Associates with the spindle pole body (SPB)				607
P46872 UniProt NPD GO	KRP85_STRPU	Kinesin-II 85 kDa subunit (KRP-85/95 85 kDa subunit)	0.78	-	nuc	0					699

You are viewing entries 9851 to 9900 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.