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
Q9VQM4 UniProt NPD GO	TYDP1_DROME	Probable tyrosyl-DNA phosphodiesterase (EC 3.1.4.-) (Tyr-DNA phosphodiesterase) (Protein glaikit)	0.24	-	nuc	0	Nucleus (Probable)	nucleus [ISS]			580
Q96N76 UniProt NPD GO	HUTU_HUMAN	Probable urocanate hydratase (EC 4.2.1.49) (Urocanase) (Imidazolonepropionate hydrolase)	0.24	-	cyt	0			276880		676
P59845 UniProt NPD GO	VACHT_BRARE	Probable vesicular acetylcholine transporter (VAChT)	0.24	+	end	10 *	Membrane; multi-pass membrane protein				493
P37042 UniProt NPD GO	GON1_CHICK	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.24	-	exc	1 *	Secreted protein	extracellular region [IDA]			92
Q6NX65 UniProt NPD GO	PDC10_RAT	Programmed cell death protein 10	0.24	-	cyt	0					210
P50085 UniProt NPD GO	PHB2_YEAST	Prohibitin-2	0.24	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...	mitochondrial inner membrane [IDA] mitochondrion [IDA]			315
P16471 UniProt NPD GO	PRLR_HUMAN	Prolactin receptor precursor (PRL-R)	0.24	-	end	2 *	Membrane; single-pass type I membrane protein	cell surface [IDA]	176761	1BP3	622
P81278 UniProt NPD GO	PRRP_RAT	Prolactin-releasing peptide precursor (PrRP) (Prolactin-releasing hormone) [Contains: Prolactin-rele ...	0.24	-	exc	0	Secreted protein				83
Q60715 UniProt NPD GO	P4HA1_MOUSE	Prolyl 4-hydroxylase alpha-1 subunit precursor (EC 1.14.11.2) (4-PH alpha-1) (Procollagen-proline,2- ...	0.24	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum lumen				534
Q15185 UniProt NPD GO	TEBP_HUMAN	Prostaglandin E synthase 3 (EC 5.3.99.3) (Cytosolic prostaglandin E2 synthase) (cPGES) (Telomerase-b ...	0.24	-	nuc	0	Cytoplasm	chromosome, telomeric region [IC] telomerase holoenzyme complex [IDA]	607061	1LG0	160
Q9R0Q7 UniProt NPD GO	TEBP_MOUSE	Prostaglandin E synthase 3 (EC 5.3.99.3) (Cytosolic prostaglandin E2 synthase) (cPGES) (Telomerase-b ...	0.24	-	nuc	0	Cytoplasm (By similarity)				160
O62698 UniProt NPD GO	PGH2_BOVIN	Prostaglandin G/H synthase 2 precursor (EC 1.14.99.1) (Cyclooxygenase-2) (COX-2) (Prostaglandin-endo ...	0.24	-	exc	0	Microsome; microsomal membrane; peripheral membrane protein				604
P79208 UniProt NPD GO	PGH2_SHEEP	Prostaglandin G/H synthase 2 precursor (EC 1.14.99.1) (Cyclooxygenase-2) (COX-2) (Prostaglandin-endo ...	0.24	-	vac	0	Microsome; microsomal membrane; peripheral membrane protein	cytoplasm [ISS] nucleus [ISS]			603
P41222 UniProt NPD GO	PTGDS_HUMAN	Prostaglandin-H2 D-isomerase precursor (EC 5.3.99.2) (Lipocalin-type prostaglandin-D synthase) (Glut ...	0.24	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum. Detected on rough endoplasmic reticulum of arach ...	extracellular region [IDA] Golgi apparatus [ISS] nuclear envelope [ISS] rough endoplasmic reticulum [IDA]	176803		190
P58238 UniProt NPD GO	PSME1_MACFA	Proteasome activator complex subunit 1 (Proteasome activator 28-alpha subunit) (PA28alpha) (PA28a) ( ...	0.24	-	cyt	0					249
Q9CQT5 UniProt NPD GO	POMP_MOUSE	Proteasome maturation protein (Proteassemblin) (Protein UMP1 homolog) (mUMP1)	0.24	-	nuc	0	Cytoplasm; cytosol (By similarity). Nucleus (By similarity)				141
P32794 UniProt NPD GO	AFG2_YEAST	Protein AFG2	0.24	-	nuc	0		intracellular [IDA]			780
Q8J025 UniProt NPD GO	APCD1_HUMAN	Protein APCDD1 precursor (Adenomatosis polyposis coli down-regulated 1 protein)	0.24	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)		607479		514
Q8TBM7 UniProt NPD GO	CJ057_HUMAN	Protein C10orf57	0.24	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				123
Q8N0V1 UniProt NPD GO	CU121_HUMAN	Protein C21orf121	0.24	-	nuc	0					137
Q5SZD1 UniProt NPD GO	CF141_HUMAN	Protein C6orf141	0.24	-	nuc	0					244
Q9UI66 UniProt NPD GO	CI038_HUMAN	Protein C9orf38	0.24	-	nuc	0					118
Q96IN3 UniProt NPD GO	CI070_HUMAN	Protein C9orf70	0.24	-	nuc	0					58
Q03705 UniProt NPD GO	YMD6_YEAST	Protein CGI121	0.24	-	nuc	0					181
O74137 UniProt NPD GO	EPD2_CANMA	Protein EPD2 precursor (Essential for pseudohyphal development 2)	0.24	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor (Potential)				549
Q8BQH4 UniProt NPD GO	F100B_MOUSE	Protein FAM100B	0.24	-	nuc	0					164
Q8NFI4 UniProt NPD GO	F10A5_HUMAN	Protein FAM10A5	0.24	-	nuc	0	Cytoplasm (Probable)				369
Q5W0B7 UniProt NPD GO	FA23A_HUMAN	Protein FAM23A	0.24	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				351
Q6PGH1 UniProt NPD GO	G10_MOUSE	Protein G10 homolog	0.24	-	nuc	0	Nucleus (Potential)				103
O15544 UniProt NPD GO	GR6_HUMAN	Protein GR6	0.24	-	nuc	0					149
Q43213 UniProt NPD GO	H2A5_WHEAT	Protein H2A.5 (wcH2A-2)	0.24	-	mit	0	Nucleus (By similarity)				144
Q6CNH1 UniProt NPD GO	OS9_KLULA	Protein OS-9 homolog precursor	0.24	-	gol	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				457
P82623 UniProt NPD GO	SCRL4_ARATH	Protein SCRL4 precursor	0.24	-	exc	0					97
P38069 UniProt NPD GO	TTP1_YEAST	Protein TTP1 (Mannan synthesis protein MNN2)	0.24	-	cyt	1 *	Membrane; single-pass type II membrane protein (Potential)	Golgi apparatus [IDA]			597
Q9D3J8 UniProt NPD GO	U689_MOUSE	Protein UNQ689/PRO1329 homolog precursor	0.24	-	exc	0	Secreted protein (By similarity)				213
Q39090 UniProt NPD GO	UFO_ARATH	Protein UNUSUAL FLORAL ORGANS (F-box only protein 1) (AtFBX1)	0.24	-	mit	0	Nucleus (Probable)				442
P28094 UniProt NPD GO	WNT1_STRPU	Protein Wnt-1 (Fragment)	0.24	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				223
Q9UK55 UniProt NPD GO	ZPI_HUMAN	Protein Z-dependent protease inhibitor precursor (PZ-dependent protease inhibitor) (PZI) (Serpin A10 ...	0.24	-	vac	0	Secreted protein		605271		444
Q5R698 UniProt NPD GO	ANM5_PONPY	Protein arginine N-methyltransferase 5 (EC 2.1.1.-) (Shk1 kinase-binding protein 1 homolog) (SKB1 ho ...	0.24	-	cyt	0	Cytoplasm (By similarity)				636
Q922X9 UniProt NPD GO	ANM7_MOUSE	Protein arginine N-methyltransferase 7 (EC 2.1.1.-)	0.24	-	cyt	0		cytoplasm [ISS] nucleus [ISS]			692
Q24040 UniProt NPD GO	BGB_DROME	Protein big brother	0.24	-	cyt	0	Nucleus (Potential)	nucleus [IDA]			213
Q8N9W6 UniProt NPD GO	BOLL_HUMAN	Protein boule-like	0.24	-	nuc	0	Cytoplasm	cytoplasm [IDA]	606165		283
Q924M5 UniProt NPD GO	BOLL_MOUSE	Protein boule-like	0.24	-	nuc	0	Cytoplasm				281
Q80V91 UniProt NPD GO	DTX3_MOUSE	Protein deltex-3 (Deltex-3) (Deltex3) (mDTX3)	0.24	-	nuc	0	Cytoplasm (Probable)				347
P08003 UniProt NPD GO	PDIA4_MOUSE	Protein disulfide-isomerase A4 precursor (EC 5.3.4.1) (Protein ERp-72) (ERp72)	0.24	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [IDA]			638
P38659 UniProt NPD GO	PDIA4_RAT	Protein disulfide-isomerase A4 precursor (EC 5.3.4.1) (Protein ERp-72) (ERp72) (Calcium-binding prot ...	0.24	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				643
P28867 UniProt NPD GO	KPCD_MOUSE	Protein kinase C delta type (EC 2.7.11.13) (nPKC-delta)	0.24	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)			1PTR	674
P09215 UniProt NPD GO	KPCD_RAT	Protein kinase C delta type (EC 2.7.11.13) (nPKC-delta)	0.24	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein			1BDY	673
P41743 UniProt NPD GO	KPCI_HUMAN	Protein kinase C iota type (EC 2.7.11.13) (nPKC-iota) (Atypical protein kinase C-lambda/iota) (aPKC- ...	0.24	-	cyt	0	Endosome	cytosol [ISS] nucleus [ISS] polarisome [ISS]	600539	1ZRZ	587
Q01792 UniProt NPD GO	KRUP_SCICO	Protein krueppel (Fragment)	0.24	-	nuc	0	Nucleus (Probable)				74

You are viewing entries 46701 to 46750 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.