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
Q5ZMS4 UniProt NPD GO	NCOA7_CHICK	Nuclear receptor coactivator 7	0.89	+	nuc	0	Nucleus (By similarity)				907
Q9LNP6 UniProt NPD GO	NFYA8_ARATH	Nuclear transcription factor Y subunit A-8 (AtNF-YA-8)	0.89	-	nuc	0	Nucleus (Probable)				328
Q9EPJ0 UniProt NPD GO	NUCKS_RAT	Nuclear ubiquitous casein and cyclin-dependent kinases substrate	0.89	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			243
Q80XU3 UniProt NPD GO	NUCKS_MOUSE	Nuclear ubiquitous casein and cyclin-dependent kinases substrate (JC7)	0.89	+	nuc	0	Nucleus (By similarity)	nucleus [IDA]			234
Q9H1E3 UniProt NPD GO	NUCKS_HUMAN	Nuclear ubiquitous casein and cyclin-dependent kinases substrate (P1)	0.89	-	nuc	0	Nucleus				243
Q9NBX5 UniProt NPD GO	GAGXE_DROME	Nucleic-acid-binding protein from transposon X-element	0.89	+	nuc	0		viral nucleocapsid [NAS]			501
Q99P77 UniProt NPD GO	NOG1_RAT	Nucleolar GTP-binding protein 1 (Chronic renal failure gene protein)	0.89	+	nuc	0	Nucleus; nucleolus (By similarity)	nucleus [IDA]			636
Q9BZE4 UniProt NPD GO	NOG1_HUMAN	Nucleolar GTP-binding protein 1 (Chronic renal failure gene protein) (GTP-binding protein NGB)	0.89	+	nuc	0	Nucleus; nucleolus				633
Q8LNU5 UniProt NPD GO	NOC2L_ORYSA	Nucleolar complex protein 2 homolog (Protein NOC2 homolog)	0.89	+	nuc	0	Nucleus (By similarity)				757
Q3SYU1 UniProt NPD GO	NOC2L_BOVIN	Nucleolar complex protein 2 homolog (Protein NOC2 homolog) (NOC2-like)	0.89	-	cyt	0	Nucleus; nucleolus (By similarity)				746
Q91Y26 UniProt NPD GO	NOC3L_CRIGR	Nucleolar complex protein 3 homolog (NOC3 protein homolog) (NOC3-like protein) (Nucleolar complex-as ...	0.89	+	nuc	0	Nucleus; nucleolus (By similarity)				800
O75665 UniProt NPD GO	OFD1_HUMAN	Oral-facial-digital syndrome 1 protein (Protein 71-7A)	0.89	-	nuc	0	Cytoplasm. Centrosome		311200		1012
Q13133 UniProt NPD GO	NR1H3_HUMAN	Oxysterols receptor LXR-alpha (Liver X receptor alpha) (Nuclear orphan receptor LXR-alpha)	0.89	-	nuc	0	Nucleus (Potential)	nucleus [TAS]	602423	1UHL	447
Q6ZMN7 UniProt NPD GO	PZRN4_HUMAN	PDZ domain-containing RING finger protein 4 (Ligand of Numb-protein X 4) (SEMACAP3-like protein)	0.89	+	nuc	0			609730		1036
Q9D8M7 UniProt NPD GO	PHF10_MOUSE	PHD finger protein 10	0.89	-	nuc	0	Nucleus (Probable)				410
Q63ZP1 UniProt NPD GO	PHF10_XENLA	PHD finger protein 10	0.89	-	nuc	0	Nucleus (Probable)				417
P31360 UniProt NPD GO	PO3F2_MOUSE	POU domain, class 3, transcription factor 2 (Nervous system-specific octamer-binding transcription f ...	0.89	+	nuc	0	Nucleus	nucleus [IDA]			445
P56222 UniProt NPD GO	PO3F2_RAT	POU domain, class 3, transcription factor 2 (Nervous system-specific octamer-binding transcription f ...	0.89	+	nuc	0	Nucleus				445
P24610 UniProt NPD GO	PAX3_MOUSE	Paired box protein Pax-3	0.89	+	nuc	0	Nucleus	transcription factor complex [TAS]			479
O75781 UniProt NPD GO	PALM_HUMAN	Paralemmin	0.89	+	nuc	0	Membrane; peripheral membrane protein (By similarity)	cytoplasmic membrane-bound vesicle [TAS] integral to plasma membrane [TAS] plasma membrane [NAS]	608134		387
Q9Z0P4 UniProt NPD GO	PALM_MOUSE	Paralemmin	0.89	+	nuc	0	Membrane; lipid-anchor	cytoplasm [IDA] plasma membrane [IDA]			383
P35417 UniProt NPD GO	MYSP_ECHGR	Paramyosin	0.89	-	nuc	0	Thick filaments of the myofibrils				863
O96064 UniProt NPD GO	MYSP_MYTGA	Paramyosin	0.89	-	nuc	0	Thick filaments of the myofibrils				864
P35418 UniProt NPD GO	MYSP_TAESO	Paramyosin (Antigen B) (AgB)	0.89	-	nuc	0	Thick filaments of the myofibrils. Can also be secreted				863
P35416 UniProt NPD GO	MYSP2_DROME	Paramyosin, short form (Miniparamyosin)	0.89	-	nuc	0	Thick filaments of the myofibrils				640
Q9GLC7 UniProt NPD GO	PTHR_RABIT	Parathyroid hormone-related protein precursor (PTH-rP) (PTHrP) [Contains: Osteostatin]	0.89	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Secreted protein (By similarity)				177
Q4WE62 UniProt NPD GO	CWC27_ASPFU	Peptidyl-prolyl isomerase cwc27 (EC 5.2.1.8)	0.89	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				559
O60164 UniProt NPD GO	PESC_SCHPO	Pescadillo homolog	0.89	+	nuc	0	Nucleus; nucleolus				607
P23727 UniProt NPD GO	P85A_BOVIN	Phosphatidylinositol 3-kinase regulatory subunit alpha (PI3-kinase p85-subunit alpha) (PtdIns-3-kina ...	0.89	-	nuc	0		phosphoinositide 3-kinase complex, class IA [ISS]		2PNI	724
P27986 UniProt NPD GO	P85A_HUMAN	Phosphatidylinositol 3-kinase regulatory subunit alpha (PI3-kinase p85-subunit alpha) (PtdIns-3-kina ...	0.89	-	nuc	0		phosphoinositide 3-kinase complex, class IA [ISS]	171833	2IUI	724
Q63787 UniProt NPD GO	P85A_RAT	Phosphatidylinositol 3-kinase regulatory subunit alpha (PI3-kinase p85-subunit alpha) (PtdIns-3-kina ...	0.89	-	nuc	0		phosphoinositide 3-kinase complex, class IA [ISS]		1FU6	724
P39104 UniProt NPD GO	PIK1_YEAST	Phosphatidylinositol 4-kinase PIK1 (EC 2.7.1.67) (PI4-kinase) (PtdIns-4-kinase)	0.89	-	nuc	0	Nucleus	Golgi apparatus [IDA] nucleus [IDA]			1066
O00750 UniProt NPD GO	P3C2B_HUMAN	Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing beta polypeptide (EC 2.7.1.154) (Phos ...	0.89	-	nuc	0	Microsome. Cell membrane. Cytoplasm; cytosol. Found mostly in the microsome, but also in the plasma ...	cytosol [NAS] microsome [NAS] plasma membrane [NAS]	602838		1634
Q9W751 UniProt NPD GO	PITX1_XENLA	Pituitary homeobox 1 (X-PITX-1) (xPitx1)	0.89	+	nuc	0	Nucleus				305
P56673 UniProt NPD GO	PITX1_CHICK	Pituitary homeobox 1 (cPTX1)	0.89	+	nuc	0	Nucleus				311
Q9R0W1 UniProt NPD GO	PITX2_RAT	Pituitary homeobox 2 (rPtx2)	0.89	+	nuc	0	Nucleus				324
Q9PWR3 UniProt NPD GO	PITX2_XENLA	Pituitary homeobox 2 (xPtx2)	0.89	+	nuc	0	Nucleus				326
Q08478 UniProt NPD GO	PIT1_ONCMY	Pituitary-specific positive transcription factor 1 (Pit-1) (Growth hormone factor 1) (GHF-1)	0.89	+	nuc	0	Nucleus				358
P13698 UniProt NPD GO	PDGFA_XENLA	Platelet-derived growth factor A chain precursor (PDGF A-chain) (Platelet-derived growth factor alph ...	0.89	-	exc	0					226
P25500 UniProt NPD GO	PAPOA_BOVIN	Poly(A) polymerase alpha (EC 2.7.7.19) (PAP) (Polynucleotide adenylyltransferase alpha)	0.89	+	nuc	0	Nucleus			1Q79	738
O65312 UniProt NPD GO	MEDEA_ARATH	Polycomb group protein MEDEA (Maternal embryogenesis control protein) (Protein FERTILIZATION-INDEPEN ...	0.89	-	nuc	0	Nucleus. Excluded from the nucleolus				689
Q6CHI1 UniProt NPD GO	RAD18_YARLI	Postreplication repair ubiquitin-protein ligase E3 RAD18 (EC 6.-.-.-)	0.89	-	nuc	0	Nucleus (By similarity)				344
Q4IP34 UniProt NPD GO	PRP5_GIBZE	Pre-mRNA-processing ATP-dependent RNA helicase PRP5 (EC 3.6.1.-)	0.89	+	nuc	0	Nucleus (By similarity)				1227
Q12381 UniProt NPD GO	PRP1_SCHPO	Pre-mRNA-splicing factor prp1	0.89	-	nuc	0	Nucleus (Probable)				906
Q5BC69 UniProt NPD GO	SYF2_EMENI	Pre-mRNA-splicing factor syf2	0.89	-	nuc	0	Nucleus (By similarity)				297
Q01329 UniProt NPD GO	PTA1_YEAST	Pre-tRNA-processing protein PTA1	0.89	-	mit	0	Nucleus	mRNA cleavage and polyadenylation specifici... [IPI]			785
O19911 UniProt NPD GO	SECA_CYACA	Preprotein translocase secA subunit	0.89	-	nuc	0	Plastid; chloroplast				895
Q80Y44 UniProt NPD GO	DDX10_MOUSE	Probable ATP-dependent RNA helicase DDX10 (EC 3.6.1.-) (DEAD box protein 10)	0.89	-	nuc	0					875
Q04217 UniProt NPD GO	DHR1_YEAST	Probable ATP-dependent RNA helicase DHR1 (EC 3.6.1.-) (DEAH box RNA helicase DHR1) (Extracellular ma ...	0.89	+	nuc	0	Nucleus; nucleolus	mitochondrion [IDA] nucleolus [IDA] small nucleolar ribonucleoprotein complex [IPI]			1267
Q9VD51 UniProt NPD GO	PIT_DROME	Probable ATP-dependent RNA helicase pitchoune (EC 3.6.1.-)	0.89	-	nuc	0	Nucleus; nucleolus				680

You are viewing entries 4751 to 4800 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.)

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