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
P70582 UniProt NPD GO	NUP54_RAT	Nucleoporin p54 (54 kDa nucleoporin)	0.59	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Biased toward ...	nuclear pore [IDA]			510
O74315 UniProt NPD GO	AMO1_SCHPO	Nucleoporin-like protein amo1 (Aberrant microtubule protein 1)	0.59	-	nuc	0	Nucleus; nucleoplasm; nuclear rim	nuclear membrane [IDA] nuclear pore [IDA] spindle pole body [IDA]			475
Q794H2 UniProt NPD GO	NP1L3_MOUSE	Nucleosome assembly protein 1-like 3 (Brain-specific protein MB20)	0.59	+	nuc	0	Nucleus. Cytoplasm				544
Q5KF46 UniProt NPD GO	OXR1_CRYNE	Oxidation resistance protein 1	0.59	-	nuc	0	Mitochondrion (By similarity)				465
P31367 UniProt NPD GO	POUC_BRARE	POU domain protein C (POU[C]) (ZFPOU[C])	0.59	+	cyt	0	Nucleus				610
Q7YR49 UniProt NPD GO	PO5F1_PANTR	POU domain, class 5, transcription factor 1 (Octamer-binding transcription factor 3) (Oct-3)	0.59	+	cyt	0	Nucleus (By similarity)				360
O97552 UniProt NPD GO	PO5F1_BOVIN	POU domain, class 5, transcription factor 1 (Octamer-binding transcription factor 3) (Oct-3) (Oct-4) ...	0.59	+	cyt	0	Nucleus (By similarity)				360
Q8BZ97 UniProt NPD GO	PRDM8_MOUSE	PR domain zinc finger protein 8 (PR domain-containing protein 8)	0.59	-	nuc	0	Nucleus (By similarity)				687
Q02962 UniProt NPD GO	PAX2_HUMAN	Paired box protein Pax-2	0.59	-	nuc	0	Nucleus		167409		416
Q62915 UniProt NPD GO	CSKP_RAT	Peripheral plasma membrane protein CASK (EC 2.7.11.1) (Calcium/calmodulin-dependent serine protein k ...	0.59	-	nuc	0	Cytoplasm	plasma membrane [IDA]		1RSO	909
Q94125 UniProt NPD GO	AGE1_CAEEL	Phosphatidylinositol 3-kinase age-1 (EC 2.7.1.137) (PtdIns-3-kinase age-1) (PI3-kinase age-1) (PI3K ...	0.59	-	nuc	0		phosphoinositide 3-kinase complex [NAS]			1146
P46019 UniProt NPD GO	KPB2_HUMAN	Phosphorylase b kinase regulatory subunit alpha, liver isoform (Phosphorylase kinase alpha L subunit ...	0.59	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	phosphorylase kinase complex [TAS]	306000		1235
P58134 UniProt NPD GO	RR4_ASTLO	Plastid 30S ribosomal protein S4	0.59	+	nuc	0	Plastid				206
P46292 UniProt NPD GO	RR7_CUSEU	Plastid 30S ribosomal protein S7	0.59	-	nuc	0	Plastid				155
O64380 UniProt NPD GO	PABP3_ARATH	Polyadenylate-binding protein 3 (Poly(A)-binding protein 3) (PABP 3)	0.59	-	nuc	0					660
P08510 UniProt NPD GO	KCNAS_DROME	Potassium voltage-gated channel protein Shaker	0.59	-	end	5	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]		1HO7	655
Q9UQ05 UniProt NPD GO	KCNH4_HUMAN	Potassium voltage-gated channel subfamily H member 4 (Voltage-gated potassium channel subunit Kv12.3 ...	0.59	-	nuc	6	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	604528		1017
P97414 UniProt NPD GO	KCNQ1_MOUSE	Potassium voltage-gated channel subfamily KQT member 1 (Voltage-gated potassium channel subunit Kv7. ...	0.59	-	end	6	Membrane; multi-pass membrane protein				668
Q9MZS1 UniProt NPD GO	HCN1_RABIT	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1 (rbHCN1)	0.59	-	nuc	1	Membrane; multi-pass membrane protein				822
Q5KB05 UniProt NPD GO	CWC24_CRYNE	Pre-mRNA-splicing factor CWC24	0.59	-	mit	0	Nucleus (By similarity)				329
Q6CJI0 UniProt NPD GO	SLT11_KLULA	Pre-mRNA-splicing factor SLT11	0.59	-	nuc	0	Nucleus (By similarity)				302
Q5ADL4 UniProt NPD GO	SLU7_CANAL	Pre-mRNA-splicing factor SLU7	0.59	-	nuc	0	Nucleus (By similarity)				350
Q9SYI0 UniProt NPD GO	SECA_ARATH	Preprotein translocase secA subunit, chloroplast precursor	0.59	-	cyt	0	Plastid; chloroplast; chloroplast stroma. Minor fraction: Plastid; chloroplast; chloroplast thylakoi ...				1021
Q41062 UniProt NPD GO	SECA_PEA	Preprotein translocase secA subunit, chloroplast precursor	0.59	-	mit	0	Plastid; chloroplast; chloroplast stroma. Minor fraction: Plastid; chloroplast; chloroplast thylakoi ...				1011
P01133 UniProt NPD GO	EGF_HUMAN	Pro-epidermal growth factor precursor (EGF) [Contains: Epidermal growth factor (Urogastrone)]	0.59	+	end	1	Membrane; single-pass type I membrane protein	extracellular region [IC] plasma membrane [TAS]	131530	1P9J	1207
O94379 UniProt NPD GO	RM32_SCHPO	Probable 60S ribosomal protein L32, mitochondrial precursor	0.59	-	mit	0	Mitochondrion (By similarity)	mitochondrial inner membrane [ISS]			103
Q9CWT6 UniProt NPD GO	DDX28_MOUSE	Probable ATP-dependent RNA helicase DDX28 (EC 3.6.1.-) (Mitochondrial DEAD box protein 28)	0.59	-	mit	0	Nucleus (By similarity). Mitochondrion (By similarity). Transported between these two compartments. ...				540
Q4R3Q1 UniProt NPD GO	DDX48_MACFA	Probable ATP-dependent RNA helicase DDX48 (EC 3.6.1.-) (DEAD box protein 48)	0.59	-	cyt	0	Nucleus (By similarity)				410
Q61656 UniProt NPD GO	DDX5_MOUSE	Probable ATP-dependent RNA helicase DDX5 (EC 3.6.1.-) (DEAD box protein 5) (RNA helicase p68) (DEAD ...	0.59	+	nuc	0	Nucleus (By similarity)	nucleus [IC]			614
P36009 UniProt NPD GO	DHR2_YEAST	Probable ATP-dependent RNA helicase DHR2 (EC 3.6.1.-) (DEAH box RNA helicase DHR2) (Helicase JA2)	0.59	-	mit	0	Nucleus; nucleolus	nucleolus [IDA]			735
P53756 UniProt NPD GO	YN99_YEAST	Probable ATP-dependent transporter YNR070W	0.59	-	end	9	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			1333
Q9SJA8 UniProt NPD GO	WRK17_ARATH	Probable WRKY transcription factor 17 (WRKY DNA-binding protein 17)	0.59	-	nuc	0	Nucleus (Probable)				321
Q10161 UniProt NPD GO	CLH_SCHPO	Probable clathrin heavy chain	0.59	-	cyt	0	Cytoplasmic face of coated pits and vesicles (By similarity)				1666
Q9VGB4 UniProt NPD GO	CP132_DROME	Probable cytochrome P450 313a2 (EC 1.14.-.-) (CYPCCCXIIIA2)	0.59	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				493
O77410 UniProt NPD GO	IF36_DROME	Probable eukaryotic translation initiation factor 3 subunit 6 (eIF-3 p48) (eIF3e)	0.59	-	cyt	0					435
Q9W4Q9 UniProt NPD GO	INSL7_DROME	Probable insulin-like peptide 7 precursor (Insulin-related peptide) (DILP7) [Contains: Probable insu ...	0.59	+	mit	0	Secreted protein (Potential)	extracellular region [ISS]			159
Q6FNH8 UniProt NPD GO	NUF2_CANGA	Probable kinetochore protein NUF2	0.59	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				460
Q6CGV4 UniProt NPD GO	SPC25_YARLI	Probable kinetochore protein SPC25	0.59	-	cyt	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				232
Q2UPH5 UniProt NPD GO	SPC25_ASPOR	Probable kinetochore protein spc25	0.59	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				264
Q63415 UniProt NPD GO	PCSK6_RAT	Proprotein convertase subtilisin/kexin type 6 precursor (EC 3.4.21.-) (Paired basic amino acid cleav ...	0.59	-	nuc	0					937
Q6PDI5 UniProt NPD GO	ECM29_MOUSE	Proteasome-associated protein ECM29 homolog (Ecm29)	0.59	-	nuc	0	Endoplasmic reticulum (By similarity). Endoplasmic reticulum-Golgi intermediate compartment (By simi ...				1840
Q8C263 UniProt NPD GO	CM003_MOUSE	Protein C13orf3 homolog	0.59	-	nuc	0					411
Q9GZU0 UniProt NPD GO	CF062_HUMAN	Protein C6orf62 (HBV X-transactivated gene 12 protein)	0.59	+	nuc	0					229
Q99LU8 UniProt NPD GO	CF062_MOUSE	Protein C6orf62 homolog	0.59	+	nuc	0					229
P39101 UniProt NPD GO	CAJ1_YEAST	Protein CAJ1	0.59	-	cyt	0		nucleus [TAS]			391
P11467 UniProt NPD GO	DG17_DICDI	Protein DG17	0.59	-	nuc	0					458
Q8ND56 UniProt NPD GO	FA61A_HUMAN	Protein FAM61A (Putative alpha synuclein-binding protein) (AlphaSNBP)	0.59	+	nuc	0					463
P38922 UniProt NPD GO	HRB1_YEAST	Protein HRB1 (Protein TOM34)	0.59	-	nuc	0	Nucleus (Potential)	cytoplasm [IDA] heterogeneous nuclear ribonucleoprotein com... [NAS] nucleus [IDA]			429
Q80U38 UniProt NPD GO	K0323_MOUSE	Protein KIAA0323	0.59	-	nuc	0					671
Q91YR5 UniProt NPD GO	K0859_MOUSE	Protein KIAA0859	0.59	+	mit	0					698

You are viewing entries 19751 to 19800 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.