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
P70661 UniProt NPD GO	NGN3_MOUSE	Neurogenin 3 (Atonal protein homolog 5) (Helix-loop-helix protein mATH-4B) (MATH4B)	0.78	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			214
Q9UBU9 UniProt NPD GO	NXF1_HUMAN	Nuclear RNA export factor 1 (Tip-associating protein) (Tip-associated protein) (mRNA export factor T ...	0.78	-	nuc	0	Nucleus; nucleoplasm. Cytoplasm. Localized predominantly in the nucleoplasm and at both the nucleopl ...		602647	1OAI	619
Q09161 UniProt NPD GO	NCBP1_HUMAN	Nuclear cap-binding protein subunit 1 (80 kDa nuclear cap-binding protein) (NCBP 80 kDa subunit) (CB ...	0.78	+	mit	0	Nucleus	nucleoplasm [TAS] nucleus [IDA]	600469	1N54	790
Q00402 UniProt NPD GO	NUM1_YEAST	Nuclear migration protein NUM1	0.78	-	nuc	0	Bud tip	bud tip [IDA] cell cortex [IDA] mitochondrion [IDA]			2748
P32505 UniProt NPD GO	NAB2_YEAST	Nuclear polyadenylated RNA-binding protein NAB2	0.78	+	nuc	0	Nucleus	cytoplasm [TAS] nucleus [IDA]			525
O08658 UniProt NPD GO	NUP88_RAT	Nuclear pore complex protein Nup88 (Nucleoporin Nup88) (88 kDa nuclear pore complex protein) (Nucleo ...	0.78	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex	nuclear pore [IDA]			742
Q7ZX96 UniProt NPD GO	NUP93_XENLA	Nuclear pore complex protein Nup93 (Nucleoporin Nup93) (93 kDa nucleoporin) (An4a)	0.78	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity). Localizes at the nuclear basket and ...				820
Q9JLI4 UniProt NPD GO	NCOA6_RAT	Nuclear receptor coactivator 6 (Amplified in breast cancer protein 3) (Cancer-amplified transcriptio ...	0.78	-	nuc	0	Nucleus				418
Q93ZH2 UniProt NPD GO	NFYA3_ARATH	Nuclear transcription factor Y subunit A-3 (AtNF-YA-3) (Transcriptional activator HAP2C)	0.78	-	nuc	0	Nucleus (Probable)				340
Q9N1A4 UniProt NPD GO	STP2_PONPY	Nuclear transition protein 2 (TP-2) (TP2) (Fragment)	0.78	+	mit	0	Nucleus (By similarity)				138
Q9D6Z1 UniProt NPD GO	NOP56_MOUSE	Nucleolar protein Nop56 (Nucleolar protein 5A)	0.78	+	nuc	0	Nucleus; nucleolus (By similarity)				580
Q9ESX4 UniProt NPD GO	NO40_MOUSE	Nucleolar protein of 40 kDa (pNO40) (Zinc finger CCHC domain-containing protein 17) (Putative S1 RNA ...	0.78	+	nuc	0	Nucleus; nucleolus	cytosolic large ribosomal subunit (sensu Eu... [IDA] nucleolus [IDA]			241
Q5RAS2 UniProt NPD GO	GLE1_PONPY	Nucleoporin GLE1 (GLE1-like protein)	0.78	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Shuttles between the nucleus and the cytoplasm. ...				698
Q9Y6R0 UniProt NPD GO	NUMBL_HUMAN	Numb-like protein (Numb-R)	0.78	-	nuc	0	Cytoplasm		604018		609
Q9WUJ8 UniProt NPD GO	ORC6_MOUSE	Origin recognition complex subunit 6	0.78	-	nuc	0	Nucleus (By similarity)				262
Q9BXW6 UniProt NPD GO	OSBL1_HUMAN	Oxysterol-binding protein-related protein 1 (OSBP-related protein 1) (ORP-1)	0.78	-	nuc	0		intracellular [IC]	606730		950
Q63955 UniProt NPD GO	PO4F3_MOUSE	POU domain, class 4, transcription factor 3 (Brain-specific homeobox/POU domain protein 3C) (Brn-3C) ...	0.78	+	nuc	0	Nucleus	transcription factor complex [IC]			338
P63016 UniProt NPD GO	PAX6_RAT	Paired box protein Pax-6 (Oculorhombin)	0.78	+	nuc	0	Nucleus (By similarity)				422
Q06348 UniProt NPD GO	PRRX2_MOUSE	Paired mesoderm homeobox protein 2 (PRX-2) (Homeobox protein S8)	0.78	+	nuc	0	Nucleus (By similarity)				247
Q99811 UniProt NPD GO	PRRX2_HUMAN	Paired mesoderm homeobox protein 2 (PRX-2) (Paired-related homeobox protein 2)	0.78	+	nuc	0	Nucleus (By similarity)	nuclear chromosome [NAS]	604675		253
Q8R4K8 UniProt NPD GO	PAPPA_MOUSE	Pappalysin-1 precursor (EC 3.4.24.79) (Pregnancy-associated plasma protein-A) (PAPP-A) (Insulin-like ...	0.78	-	nuc	0	Secreted protein				1624
Q9YGL6 UniProt NPD GO	PALM_CHICK	Paralemmin	0.78	+	nuc	0	Membrane; lipid-anchor	cytoplasm [ISS] plasma membrane [ISS] synaptosome [IDA]			386
P13392 UniProt NPD GO	MYSP_DIRIM	Paramyosin (Fragment)	0.78	-	nuc	0	Thick filaments of the myofibrils				848
Q5R655 UniProt NPD GO	PTCD1_PONPY	Pentatricopeptide repeat protein 1	0.78	-	nuc	0					698
P42356 UniProt NPD GO	PI4KA_HUMAN	Phosphatidylinositol 4-kinase alpha (EC 2.7.1.67) (PI4-kinase alpha) (PtdIns-4-kinase alpha) (PI4K-a ...	0.78	-	cyt	0		Golgi-associated vesicle [TAS]	600286		2044
Q3U6Q4 UniProt NPD GO	PI3R6_MOUSE	Phosphoinositide 3-kinase regulatory subunit 6 (Phosphoinositide 3-kinase gamma adapter protein of 8 ...	0.78	-	nuc	0	Cytoplasm				756
Q9BX97 UniProt NPD GO	PLVAP_HUMAN	Plasmalemma vesicle-associated protein (Plasmalemma vesicle protein 1) (PV-1) (Fenestrated-endotheli ...	0.78	-	nuc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Membrane-associated protein of ...		607647		442
Q9HCN6 UniProt NPD GO	GPVI_HUMAN	Platelet glycoprotein VI precursor	0.78	+	exc	1	Membrane; single-pass membrane protein	integral to membrane [NAS]	605546		339
Q9XUA5 UniProt NPD GO	PME6_CAEEL	Poly(ADP-ribose) polymerase pme-6 (EC 2.4.2.30) (Poly ADP-ribose metabolism enzyme 6)	0.78	+	nuc	0	Nucleus (Probable)				737
Q8NDX5 UniProt NPD GO	PHC3_HUMAN	Polyhomeotic-like protein 3 (hPH3) (Homolog of polyhomeotic 3) (Early development regulatory protein ...	0.78	-	nuc	0	Nucleus				983
P47946 UniProt NPD GO	TRK1_SCHPO	Potassium transport protein 1	0.78	-	end	8 *	Membrane; multi-pass membrane protein				841
P40425 UniProt NPD GO	PBX2_HUMAN	Pre-B-cell leukemia transcription factor 2 (Homeobox protein PBX2) (Protein G17)	0.78	-	nuc	0	Nucleus (Probable)		176311		430
Q5XJD3 UniProt NPD GO	FIP1_BRARE	Pre-mRNA 3'-end-processing factor FIP1 (FIP1-like 1)	0.78	-	nuc	0	Nucleus (By similarity)				570
Q5U317 UniProt NPD GO	FIP1_RAT	Pre-mRNA 3'-end-processing factor FIP1 (FIP1-like 1)	0.78	+	nuc	0	Nucleus (By similarity)				536
Q6BWB8 UniProt NPD GO	CWC21_DEBHA	Pre-mRNA-splicing factor CWC21	0.78	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				179
Q9Y7Y2 UniProt NPD GO	SLU7_SCHPO	Pre-mRNA-splicing factor SLU7	0.78	-	nuc	0	Nucleus (By similarity)				379
Q52E73 UniProt NPD GO	SPP2_MAGGR	Pre-mRNA-splicing factor SPP2	0.78	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				370
Q7SGD2 UniProt NPD GO	CLF1_NEUCR	Pre-mRNA-splicing factor clf-1	0.78	+	cyt	0	Nucleus (By similarity)				695
Q4W9Z9 UniProt NPD GO	CWC26_ASPFU	Pre-mRNA-splicing factor cwc26	0.78	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				344
P09007 UniProt NPD GO	SRD1_YEAST	Pre-rRNA-processing protein SRD1 (Suppressor of rRNA-processing defect protein 1)	0.78	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			221
P56974 UniProt NPD GO	NRG2_MOUSE	Pro-neuregulin-2, membrane-bound isoform precursor (Pro-NRG2) [Contains: Neuregulin-2 (NRG-2) (Diver ...	0.78	-	nuc	1	Pro-neuregulin-2, membrane-bound isoform: Cell membrane; single-pass type I membrane protein (By sim ...				756
Q8NFN8 UniProt NPD GO	GP156_HUMAN	Probable G-protein coupled receptor 156 (GABAB-related G-protein coupled receptor) (G-protein couple ...	0.78	-	nuc	7 *	Membrane; multi-pass membrane protein				814
Q8R3C6 UniProt NPD GO	RBM19_MOUSE	Probable RNA-binding protein 19 (RNA-binding motif protein 19)	0.78	+	nuc	0	Nucleus; nucleolus (By similarity)			2CPH	952
Q9UUJ3 UniProt NPD GO	RGA9_SCHPO	Probable Rho-GTPase-activating protein 9	0.78	-	nuc	0					684
Q09462 UniProt NPD GO	UTP11_CAEEL	Probable U3 small nucleolar RNA-associated protein 11 (U3 snoRNA-associated protein 11)	0.78	-	nuc	0	Nucleus; nucleolus (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			262
Q10106 UniProt NPD GO	UTP11_SCHPO	Probable U3 small nucleolar RNA-associated protein 11 (U3 snoRNA-associated protein 11)	0.78	-	nuc	0	Nucleus; nucleolus (By similarity)				249
Q9SV15 UniProt NPD GO	WRK11_ARATH	Probable WRKY transcription factor 11 (WRKY DNA-binding protein 11)	0.78	-	nuc	0	Nucleus (Probable)				325
Q9FL92 UniProt NPD GO	WRK16_ARATH	Probable WRKY transcription factor 16 (WRKY DNA-binding protein 16)	0.78	-	cyt	0	Nucleus (Probable)				1372
Q9FGZ4 UniProt NPD GO	WRK48_ARATH	Probable WRKY transcription factor 48 (WRKY DNA-binding protein 48)	0.78	-	nuc	0	Nucleus (Potential)				399
Q93WU8 UniProt NPD GO	WRK54_ARATH	Probable WRKY transcription factor 54 (WRKY DNA-binding protein 54)	0.78	-	nuc	0	Nucleus (Probable)				346

You are viewing entries 9951 to 10000 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.