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
P70182 UniProt NPD GO	PI51A_MOUSE	Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha (EC 2.7.1.68) (Phosphatidylinositol-4-phospha ...	0.56	-	nuc	0	Cell membrane. Detected on RAC1-induced plasma membrane ruffles, and on membrane ruffles induced by ...				546
Q9Y5X4 UniProt NPD GO	NR2E3_HUMAN	Photoreceptor-specific nuclear receptor (Retina-specific nuclear receptor)	0.56	-	nuc	0	Nucleus	nucleus [TAS]	604485		410
P49764 UniProt NPD GO	PLGF_MOUSE	Placenta growth factor precursor (PlGF)	0.56	-	nuc	0	Secreted protein (By similarity)				158
P20918 UniProt NPD GO	PLMN_MOUSE	Plasminogen precursor (EC 3.4.21.7) [Contains: Plasmin heavy chain A; Activation peptide; Angiostati ...	0.56	-	nuc	0	Secreted protein	extracellular space [ISS]			812
Q53GA4 UniProt NPD GO	PHLA2_HUMAN	Pleckstrin homology-like domain family A member 2 (Imprinted in placenta and liver protein) (Tumor-s ...	0.56	-	nuc	0	Cytoplasm (By similarity)		602131		152
Q9UGN5 UniProt NPD GO	PARP2_HUMAN	Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30) (PARP-2) (NAD(+) ADP-ribosyltransferase 2) (Poly[ADP-ri ...	0.56	-	nuc	0	Nucleus		607725		583
Q99NA9 UniProt NPD GO	PCGF6_MOUSE	Polycomb group RING finger protein 6 (RING finger protein 134) (Mel18 and Bmi1-like RING finger)	0.56	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			353
Q6PCT5 UniProt NPD GO	PQBP1_RAT	Polyglutamine-binding protein 1 (Polyglutamine tract-binding protein 1) (PQBP-1)	0.56	+	nuc	0	Nucleus. Co-localized with POU3F2 (By similarity)				263
Q5A4N5 UniProt NPD GO	RAD18_CANAL	Postreplication repair ubiquitin-protein ligase E3 RAD18 (EC 6.-.-.-)	0.56	-	nuc	0	Nucleus (By similarity)				378
Q9UIX4 UniProt NPD GO	KCNG1_HUMAN	Potassium voltage-gated channel subfamily G member 1 (Voltage-gated potassium channel subunit Kv6.1) ...	0.56	-	end	4	Membrane; multi-pass membrane protein	integral to membrane [NAS]	603788		513
Q751K8 UniProt NPD GO	FIP1_ASHGO	Pre-mRNA polyadenylation factor FIP1	0.56	-	nuc	0	Nucleus (By similarity)				323
Q750V7 UniProt NPD GO	CWC15_ASHGO	Pre-mRNA-splicing factor CWC15	0.56	+	nuc	0	Nucleus (Probable)				184
Q75AG5 UniProt NPD GO	CWC26_ASHGO	Pre-mRNA-splicing factor CWC26	0.56	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				270
Q7SHY8 UniProt NPD GO	ISY1_NEUCR	Pre-mRNA-splicing factor isy-1	0.56	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				239
Q9VE50 UniProt NPD GO	GOSR1_DROME	Probable 28 kDa Golgi SNARE protein (Golgi SNAP receptor complex member 1)	0.56	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)	Golgi trans cisterna [ISS]			232
Q9UHI6 UniProt NPD GO	DDX20_HUMAN	Probable ATP-dependent RNA helicase DDX20 (EC 3.6.1.-) (DEAD box protein 20) (DEAD box protein DP 10 ...	0.56	-	nuc	0	Cytoplasm. Nucleus. Localized in subnuclear structures next to coiled bodies, called Gemini of Cajal ...	cytoplasm [TAS] cytoskeleton [TAS] nucleus [TAS]	606168		824
Q91VC3 UniProt NPD GO	DDX48_MOUSE	Probable ATP-dependent RNA helicase DDX48 (EC 3.6.1.-) (DEAD box protein 48)	0.56	-	cyt	0	Nucleus (By similarity)				410
Q9SRU7 UniProt NPD GO	TRM2_ARATH	Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase (EC 2.1.1.32) (tRNA(guanine-26,N(2)-N(2) ...	0.56	-	nuc	0					599
Q4HZQ1 UniProt NPD GO	TAH18_GIBZE	Probable NADPH reductase TAH18 (EC 1.-.-.-)	0.56	-	cyt	0					593
Q9N4C2 UniProt NPD GO	CPSF1_CAEEL	Probable cleavage and polyadenylation specificity factor 160 kDa subunit (CPSF 160 kDa subunit)	0.56	-	cyt	0	Nucleus (By similarity)	mRNA cleavage and polyadenylation specifici... [NAS]			1454
O46051 UniProt NPD GO	C4D14_DROME	Probable cytochrome P450 4d14 (EC 1.14.-.-) (CYPIVD14)	0.56	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				507
Q9SZA7 UniProt NPD GO	DRL29_ARATH	Probable disease resistance protein At4g33300	0.56	-	cyt	0					832
Q8WTX9 UniProt NPD GO	ZDHC1_HUMAN	Probable palmitoyltransferase ZDHHC1 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 1) (DH ...	0.56	-	end	4	Membrane; multi-pass membrane protein (Potential)				485
Q9VIT2 UniProt NPD GO	PMVK_DROME	Probable phosphomevalonate kinase (EC 2.7.4.2) (PMKase)	0.56	-	cyt	0					189
O22899 UniProt NPD GO	DHX15_ARATH	Probable pre-mRNA-splicing factor ATP-dependent RNA helicase (EC 3.6.1.-)	0.56	-	cyt	0	Nucleus (By similarity)				729
P07812 UniProt NPD GO	PRGR_CHICK	Progesterone receptor (PR)	0.56	+	nuc	0	Nucleus	soluble fraction [IDA]			786
Q9EQP5 UniProt NPD GO	PRELP_RAT	Prolargin precursor (Proline-arginine-rich end leucine-rich repeat protein)	0.56	-	mit	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [TAS]			377
P51453 UniProt NPD GO	RELX_CAVPO	Prorelaxin precursor [Contains: Relaxin B chain; Relaxin A chain] (Fragment)	0.56	-	nuc	0	Secreted protein				160
Q9GZY1 UniProt NPD GO	PBOV1_HUMAN	Prostate and breast cancer overexpressed gene 1 protein (Protein UROC28) (UC28)	0.56	-	nuc	0	Cytoplasm. Nucleus		605669		135
Q9BTE3 UniProt NPD GO	CJ119_HUMAN	Protein C10orf119	0.56	-	nuc	0					642
P58659 UniProt NPD GO	CU063_MOUSE	Protein C21orf63 homolog precursor	0.56	-	nuc	1					440
P58658 UniProt NPD GO	CU063_HUMAN	Protein C21orf63 precursor (SUE21)	0.56	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				441
Q96E40 UniProt NPD GO	CI009_HUMAN	Protein C9orf9	0.56	-	nuc	0					222
Q6PBQ2 UniProt NPD GO	CHMP7_BRARE	Protein CHMP7	0.56	-	cyt	0					457
Q8R1T1 UniProt NPD GO	CHMP7_MOUSE	Protein CHMP7	0.56	-	cyt	0					451
Q8BQS4 UniProt NPD GO	F102B_MOUSE	Protein FAM102B	0.56	-	nuc	0					339
Q6CQ06 UniProt NPD GO	GRC3_KLULA	Protein GRC3	0.56	-	cyt	0	Nucleus (By similarity)				631
Q92258 UniProt NPD GO	GRISA_PODAN	Protein GRISEA (MAC1 homolog)	0.56	-	nuc	0	Nucleus (By similarity)	nucleus [IC]			597
Q8C2E7 UniProt NPD GO	K0196_MOUSE	Protein KIAA0196	0.56	-	nuc	0					1159
Q00958 UniProt NPD GO	LFY_ARATH	Protein LEAFY	0.56	-	cyt	0	Nucleus (Probable)				424
P53998 UniProt NPD GO	LET1_KLULA	Protein LET1	0.56	-	nuc	0					469
P32568 UniProt NPD GO	SNQ2_YEAST	Protein SNQ2	0.56	-	end	12	Membrane; multi-pass membrane protein	mitochondrion [IDA] plasma membrane [TAS]			1501
O60225 UniProt NPD GO	SSX5_HUMAN	Protein SSX5	0.56	-	nuc	0			300327		188
P34761 UniProt NPD GO	WHI3_YEAST	Protein WHI3	0.56	-	nuc	0		cytoplasm [IDA]			661
P33206 UniProt NPD GO	FKH1_XENLA	Protein XFKH1 (XFD-1' protein)	0.56	+	nuc	0	Nucleus (Probable)				400
Q86Y01 UniProt NPD GO	DTX1_HUMAN	Protein deltex-1 (Deltex-1) (Deltex1) (hDTX1)	0.56	+	nuc	0	Cytoplasm. Predominantly. Nucleus. Partially	cytoplasm [TAS]	602582		620
O01367 UniProt NPD GO	HOW_DROME	Protein held out wings (KH-domain protein KH93F) (Putative RNA-binding protein) (Protein muscle-spec ...	0.56	-	cyt	0	Nucleus	nucleus [IDA]			405
Q99JB8 UniProt NPD GO	PACN3_MOUSE	Protein kinase C and casein kinase II substrate protein 3	0.56	-	nuc	0	Cytoplasm (By similarity). Cell membrane; cytoplasmic side (By similarity). Detected at the inner as ...	cytoplasm [IDA]			424
O13154 UniProt NPD GO	PACN2_CHICK	Protein kinase C and casein kinase substrate in neurons protein 2 (Focal adhesion protein of 52 kDa) ...	0.56	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion; peripheral membrane protein. Localization in fo ...				448
P28829 UniProt NPD GO	BYR2_SCHPO	Protein kinase byr2 (EC 2.7.11.25) (Protein kinase ste8) (MAPK kinase kinase) (MAPKKK)	0.56	-	nuc	0		cytoplasm [IDA]		1K8R	659

You are viewing entries 21551 to 21600 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.