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
Q14990 UniProt NPD GO	ODFP_HUMAN	Outer dense fiber protein	0.63	-	nuc	0		outer dense fiber [NAS]	182878		250
Q29077 UniProt NPD GO	ODFP_PIG	Outer dense fiber protein	0.63	-	nuc	0					262
Q96SU4 UniProt NPD GO	OSBL9_HUMAN	Oxysterol-binding protein-related protein 9 (OSBP-related protein 9) (ORP-9)	0.63	-	nuc	0			606737		736
P53010 UniProt NPD GO	PAN2_YEAST	PAB-dependent poly(A)-specific ribonuclease subunit PAN2 (EC 3.1.13.4) (PAB1P-dependent poly(A)-nucl ...	0.63	-	nuc	0		cytoplasm [IDA] PAN complex [IDA]			1115
Q8CI51 UniProt NPD GO	PDLI5_MOUSE	PDZ and LIM domain protein 5 (Enigma homolog) (Enigma-like PDZ and LIM domains protein)	0.63	-	nuc	0		Z disc [IDA]		1WF7	590
P20263 UniProt NPD GO	PO5F1_MOUSE	POU domain, class 5, transcription factor 1 (Octamer-binding transcription factor 3) (Oct-3) (Oct-4) ...	0.63	+	cyt	0	Nucleus	nucleus [IC]		1OCP	352
Q62782 UniProt NPD GO	PHX2A_RAT	Paired mesoderm homeobox protein 2A (Paired-like homeobox 2A) (Aristaless homeobox protein homolog) ...	0.63	+	nuc	0	Nucleus (By similarity)				281
Q62066 UniProt NPD GO	PHX2A_MOUSE	Paired mesoderm homeobox protein 2A (Paired-like homeobox 2A) (PHOX2A homeodomain protein) (Aristale ...	0.63	+	nuc	0	Nucleus (By similarity)	nucleus [IDA]			280
Q7SFL7 UniProt NPD GO	ERFB_NEUCR	Palmitoyltransferase ERF2 (EC 2.3.1.-) (DHHC cysteine-rich domain-containing protein ERF2) (Ras prot ...	0.63	-	nuc	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				680
Q7S7C5 UniProt NPD GO	PFA3_NEUCR	Palmitoyltransferase PFA3 (EC 2.3.1.-) (Protein fatty acyltransferase 3)	0.63	-	mit	5 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				622
Q9LEK8 UniProt NPD GO	PIN1_DIGLA	Peptidyl-prolyl cis-trans isomerase 1 (EC 5.2.1.8) (Rotamase Pin1) (PPIase Pin1) (DlPar13)	0.63	-	nuc	0	Cytoplasm. Nucleus				118
P07663 UniProt NPD GO	PER_DROME	Period circadian protein (Protein clock-6) (CLK-6)	0.63	-	nuc	0	Nucleus. Cytoplasm; perinuclear region. Nuclear at specific periods of the day. First accumulates in ...	cytoplasm [TAS] nucleus [TAS]		1WA9	1224
Q6BK00 UniProt NPD GO	PEX3_DEBHA	Peroxisomal biogenesis factor 3 (Peroxin-3)	0.63	-	nuc	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein (By similarity)				420
Q92262 UniProt NPD GO	PEX3_PICPA	Peroxisomal biogenesis factor 3 (Peroxin-3) (Peroxisomal membrane protein PAS2)	0.63	-	nuc	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein				455
P22543 UniProt NPD GO	VPS34_YEAST	Phosphatidylinositol 3-kinase VPS34 (EC 2.7.1.137) (PtdIns-3-kinase VPS34) (PI3-kinase VPS34) (PI3K ...	0.63	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein. End ...	membrane fraction [IDA]			875
O60331 UniProt NPD GO	PI51C_HUMAN	Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma (EC 2.7.1.68) (Phosphatidylinositol-4-phospha ...	0.63	-	nuc	0	Cell membrane; cytoplasmic side. Cytoplasmic, associated with the plasma membrane. Detected in focal ...		606102		668
P21357 UniProt NPD GO	AROF_SOLTU	Phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplast precursor (EC 2.5.1.54) (Phospho-2-keto-3 ...	0.63	-	mit	0	Plastid; chloroplast				538
P53801 UniProt NPD GO	PTTG_HUMAN	Pituitary tumor-transforming gene 1 protein-interacting protein precursor (Pituitary tumor-transform ...	0.63	-	mit	2 *	Membrane; single-pass type I membrane protein (Potential). Ref.2: Cytoplasm. Nucleus	cytoplasm [IDA] membrane [NAS] nucleus [IDA]	603784		180
Q5NVI6 UniProt NPD GO	PTTG_PONPY	Pituitary tumor-transforming gene 1 protein-interacting protein precursor (Pituitary tumor-transform ...	0.63	-	mit	2 *	Cell membrane; single-pass type I membrane protein (By similarity). Cytoplasm (By similarity). Nucle ...				180
Q2Q5Y9 UniProt NPD GO	PIWI1_SCHMD	Piwi-like protein 1 (SMEDWI-1)	0.63	-	cyt	0					808
Q9HB19 UniProt NPD GO	PKHA2_HUMAN	Pleckstrin homology domain-containing family A member 2 (Tandem PH domain-containing protein 2) (TAP ...	0.63	-	nuc	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein (By similarity). Nucleus (By s ...		607773		425
Q8R526 UniProt NPD GO	PK1L1_MOUSE	Polycystic kidney disease 1-like 1 protein (Polycystin-1L1) (Fragment)	0.63	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				531
Q13563 UniProt NPD GO	PKD2_HUMAN	Polycystin-2 (Polycystic kidney disease 2 protein homolog) (Autosomal dominant polycystic kidney dis ...	0.63	-	end	7	Membrane; multi-pass membrane protein (Potential)	actin cytoskeleton [IPI] basal body [IDA] integral to membrane [TAS] plasma membrane [TAS]	173910		968
Q9BY77 UniProt NPD GO	PDIP3_HUMAN	Polymerase delta-interacting protein 3 (46 kDa DNA polymerase delta interaction protein) (p46)	0.63	-	nuc	0	Nucleus (Probable)				421
Q8NCL4 UniProt NPD GO	GALT6_HUMAN	Polypeptide N-acetylgalactosaminyltransferase 6 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.63	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)		605148		622
Q9Z258 UniProt NPD GO	KCNT1_RAT	Potassium channel subfamily T member 1 (Sequence-like a calcium-activated potassium channel subunit) ...	0.63	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [IDA]			1237
P59994 UniProt NPD GO	KCND1_RABIT	Potassium voltage-gated channel subfamily D member 1 (Voltage-gated potassium channel subunit Kv4.1) ...	0.63	-	nuc	0	Membrane; multi-pass membrane protein				178
P56696 UniProt NPD GO	KCNQ4_HUMAN	Potassium voltage-gated channel subfamily KQT member 4 (Voltage-gated potassium channel subunit Kv7. ...	0.63	-	end	5	Cell membrane; basal cell membrane; multi-pass membrane protein. Situated at the basal membrane of c ...		603537		695
Q5KNE9 UniProt NPD GO	CLF1_CRYNE	Pre-mRNA-splicing factor CLF1	0.63	-	cyt	0	Nucleus (By similarity)				726
Q6CUS9 UniProt NPD GO	CWC23_KLULA	Pre-mRNA-splicing factor CWC23	0.63	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				270
Q06525 UniProt NPD GO	URN1_YEAST	Pre-mRNA-splicing factor URN1 (U2-U5-U6 snRNP, RES complex and NTC-interacting pre-mRNA-splicing fac ...	0.63	-	nuc	0	Nucleus	nucleus [IDA]			465
Q10193 UniProt NPD GO	SRP1_SCHPO	Pre-mRNA-splicing factor srp1	0.63	+	mit	0	Nucleus (Potential)	nucleus [IDA]			275
P07522 UniProt NPD GO	EGF_RAT	Pro-epidermal growth factor precursor (EGF) [Contains: Epidermal growth factor]	0.63	+	end	1	Membrane; single-pass type I membrane protein				1133
O16368 UniProt NPD GO	PRS4_CAEEL	Probable 26S protease regulatory subunit 4	0.63	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				443
Q9LQR8 UniProt NPD GO	PSD32_ARATH	Probable 26S proteasome non-ATPase regulatory subunit 3b (26S proteasome subunit S3-b)	0.63	-	nuc	0					487
Q4FZF3 UniProt NPD GO	DDX49_MOUSE	Probable ATP-dependent RNA helicase DDX49 (EC 3.6.1.-) (DEAD box protein 49)	0.63	-	cyt	0					480
Q18904 UniProt NPD GO	YYO1_CAEEL	Probable G-protein coupled receptor C56G3.1	0.63	-	end	6	Membrane; multi-pass membrane protein (Potential)				490
Q9VK89 UniProt NPD GO	TRM1_DROME	Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase (EC 2.1.1.32) (tRNA(guanine-26,N(2)-N(2) ...	0.63	-	nuc	0					578
Q93WV5 UniProt NPD GO	WRK69_ARATH	Probable WRKY transcription factor 69 (WRKY DNA-binding protein 69)	0.63	-	nuc	0	Nucleus (Probable)				271
Q9LD37 UniProt NPD GO	CNG20_ARATH	Probable cyclic nucleotide-gated ion channel 20, chloroplast precursor (Cyclic nucleotide-binding tr ...	0.63	+	end	6	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Potential)				764
Q9VJ71 UniProt NPD GO	CP310_DROME	Probable cytochrome P450 310a1 (EC 1.14.-.-) (CYPCCCXA1)	0.63	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				492
O14217 UniProt NPD GO	TOM70_SCHPO	Probable mitochondrial import receptor subunit tom40 (Translocase of outer membrane 40 kDa subunit)	0.63	+	nuc	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				625
Q09349 UniProt NPD GO	UBE4_CAEEL	Probable ubiquitin conjugation factor E4	0.63	-	cyt	0					980
Q28590 UniProt NPD GO	PRGR_SHEEP	Progesterone receptor (PR) (Fragment)	0.63	+	nuc	0	Nucleus				377
Q04594 UniProt NPD GO	PRLR_CHICK	Prolactin receptor precursor (PRL-R) (CPRLP)	0.63	+	exc	2 *	Membrane; single-pass type I membrane protein				831
P15309 UniProt NPD GO	PPAP_HUMAN	Prostatic acid phosphatase precursor (EC 3.1.3.2)	0.63	-	exc	1 *			171790	2HPA	386
Q5R6J0 UniProt NPD GO	ECM29_PONPY	Proteasome-associated protein ECM29 homolog (Ecm29) (Fragment)	0.63	-	nuc	0	Endoplasmic reticulum (By similarity). Endoplasmic reticulum-Golgi intermediate compartment (By simi ...				1810
P22136 UniProt NPD GO	ATP13_YEAST	Protein ATP13, mitochondrial precursor	0.63	-	mit	0	Mitochondrion	mitochondrion [IDA]			580
Q8R0X2 UniProt NPD GO	CJ046_MOUSE	Protein C10orf46 homolog	0.63	-	nuc	0					377
O15165 UniProt NPD GO	CR001_HUMAN	Protein C18orf1	0.63	-	nuc	1	Cell membrane; single-pass membrane protein (Potential)	integral to membrane [NAS]	606571		306

You are viewing entries 17551 to 17600 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.