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
P28745 UniProt NPD GO	RCC1_SCHPO	Protein pim1 (Poly(A)+ RNA transport protein 2)	0.24	-	nuc	0	Nucleus				539
P34260 UniProt NPD GO	SLP1_CAEEL	Protein slp-1	0.24	-	cyt	0					603
P52870 UniProt NPD GO	SC6B1_YEAST	Protein transport protein SBH1 (Sec61 complex subunit SBH1) (Sec61 complex subunit beta)	0.24	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein	Sec complex-associated translocon complex [TAS]			82
P82003 UniProt NPD GO	PTSP_BOMMO	Prothoracicostatic peptide precursor (Bom-PTSP)	0.24	-	exc	0	Secreted protein	extracellular space [IDA]			274
Q04929 UniProt NPD GO	CRK_CHICK	Proto-oncogene C-crk (P38)	0.24	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocated to the plasma membrane upon c ...				305
Q9Y5F2 UniProt NPD GO	PCDBB_HUMAN	Protocadherin beta 11 precursor (PCDH-beta11)	0.24	-	nuc	1 *	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606337		797
Q5DRD2 UniProt NPD GO	PCDB2_PANTR	Protocadherin beta 2 precursor (PCDH-beta2)	0.24	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				798
O60330 UniProt NPD GO	PCDGC_HUMAN	Protocadherin gamma A12 precursor (PCDH-gamma-A12) (Cadherin-21) (Fibroblast cadherin 3)	0.24	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		604968		932
Q9Y5G6 UniProt NPD GO	PCDG7_HUMAN	Protocadherin gamma A7 precursor (PCDH-gamma-A7)	0.24	-	end	1	Membrane; single-pass type I membrane protein (By similarity)		606294		932
Q9Y5G2 UniProt NPD GO	PCDGE_HUMAN	Protocadherin gamma B2 precursor (PCDH-gamma-B2)	0.24	-	nuc	1 *	Membrane; single-pass type I membrane protein (By similarity)		606300		931
Q01289 UniProt NPD GO	POR_PEA	Protochlorophyllide reductase, chloroplast precursor (EC 1.3.1.33) (PCR) (NADPH-protochlorophyllide ...	0.24	-	mit	0	Plastid; chloroplast				399
P53294 UniProt NPD GO	PUS6_YEAST	Pseudouridylate synthase 6 (EC 5.4.99.-) (Pseudouridine synthase 6) (tRNA pseudouridine 31 synthase) ...	0.24	-	mit	0	Cytoplasm. Mitochondrion	cytoplasm [IDA] mitochondrion [IDA]			404
Q750S3 UniProt NPD GO	PUS5_ASHGO	Pseudouridylate synthase PUS5 (EC 5.4.99.-) (Pseudouridine synthase 5) (Uracil hydrolyase PUS5)	0.24	-	cyt	0	Mitochondrion (By similarity)				260
Q9UIG4 UniProt NPD GO	PS1C2_HUMAN	Psoriasis susceptibility 1 candidate gene 2 protein precursor (SPR1 protein)	0.24	-	exc	0	Secreted protein (Potential)				136
P35246 UniProt NPD GO	SFTPD_BOVIN	Pulmonary surfactant-associated protein D precursor (SP-D) (PSP-D)	0.24	-	exc	0	Secreted protein; extracellular space	endocytic vesicle [ISS] extracellular region [ISS] lysosome [ISS]			369
Q8T4J9 UniProt NPD GO	CU27_MANSE	Pupal cuticle protein 27 precursor (MsCP27) (MS-PCP27)	0.24	-	nuc	0	Synthesized in the epidermis during the larval-pupal transformation and then secreted into the phara ...				180
P42852 UniProt NPD GO	CUPP_BOMMO	Pupal cuticle protein precursor	0.24	-	exc	0					253
O14286 UniProt NPD GO	YD01_SCHPO	Putative ABC transporter C15A10.01 in chromosome I	0.24	-	mit	5	Membrane; multi-pass membrane protein (Potential)	mitochondrial inner membrane [IDA]			693
P03876 UniProt NPD GO	AI2M_YEAST	Putative COX1/OXI3 intron 2 protein	0.24	-	end	3 *		mitochondrion [TAS]			854
Q9ZQ77 UniProt NPD GO	MO25L_ARATH	Putative MO25-like protein At2g03410	0.24	-	cyt	0					348
Q02895 UniProt NPD GO	YP088_YEAST	Putative aryl-alcohol dehydrogenase YPL088W (EC 1.1.1.-)	0.24	-	cyt	0					342
Q9SZR1 UniProt NPD GO	ACA10_ARATH	Putative calcium-transporting ATPase 10, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 10 ...	0.24	-	end	8	Membrane; multi-pass membrane protein				1069
Q9LU41 UniProt NPD GO	ACA9_ARATH	Putative calcium-transporting ATPase 9, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 9)	0.24	-	end	10	Membrane; multi-pass membrane protein				1073
Q09233 UniProt NPD GO	COL79_CAEEL	Putative cuticle collagen 79	0.24	-	mit	1 *					283
Q9C7P2 UniProt NPD GO	IF4E5_ARATH	Putative eukaryotic translation initiation factor 4E-5 (eIF4E type 5) (eIF-4E type 5) (mRNA cap-bind ...	0.24	-	nuc	0					240
Q9V589 UniProt NPD GO	OR45B_DROME	Putative odorant receptor 45b	0.24	-	mit	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			396
Q9VHQ2 UniProt NPD GO	OR85D_DROME	Putative odorant receptor 85d	0.24	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			412
Q27377 UniProt NPD GO	OB10_DROME	Putative odorant-binding protein A10 precursor (Antennal protein 10) (OS-D protein)	0.24	-	exc	0	Secreted protein (Potential)				155
Q19189 UniProt NPD GO	PEX12_CAEEL	Putative peroxisome assembly protein 12 (Peroxin-12)	0.24	-	mit	1	Peroxisome; peroxisomal membrane; multi-pass membrane protein (Potential)				359
P38109 UniProt NPD GO	YBY9_YEAST	Putative serine carboxypeptidase YBR139W (EC 3.4.16.-)	0.24	-	cyt	0		vacuole (sensu Fungi) [IDA]			508
P83098 UniProt NPD GO	STLK_DROME	Putative serine/threonine-protein kinase STE20-like (EC 2.7.11.1)	0.24	-	mit	0					346
Q9Y255 UniProt NPD GO	PX19_HUMAN	Px19-like protein (25 kDa protein of relevant evolutionary and lymphoid interest) (PRELI)	0.24	-	cyt	0			605733		219
Q8BKZ9 UniProt NPD GO	ODPX_MOUSE	Pyruvate dehydrogenase protein X component, mitochondrial precursor (Dihydrolipoamide dehydrogenase- ...	0.24	-	nuc	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			501
Q9Y3C5 UniProt NPD GO	RNF11_HUMAN	RING finger protein 11 (Sid 1669)	0.24	-	nuc	0		ubiquitin ligase complex [IDA]			154
Q9SN27 UniProt NPD GO	ATL4F_ARATH	RING-H2 finger protein ATL4F	0.24	-	nuc	1 *					225
O65154 UniProt NPD GO	KIWI_ARATH	RNA polymerase II transcriptional coactivator KIWI	0.24	-	nuc	0	Nucleus (By similarity)				107
Q9V535 UniProt NPD GO	RBM8A_DROME	RNA-binding protein 8A (Protein tsunagi)	0.24	-	cyt	0	Nucleus. Cytoplasm. Part of the EJC assembled on mRNAs in the nucleus and remains part of the comple ...	cytoplasm [IDA] nucleus [IDA]		1RK8	165
Q9UNW9 UniProt NPD GO	NOVA2_HUMAN	RNA-binding protein Nova-2 (Neuro-oncological ventral antigen 2) (Astrocytic NOVA1-like RNA-binding ...	0.24	-	cyt	0	Nucleus (By similarity)		601991	1EC6	492
P60028 UniProt NPD GO	GDIA_PANTR	Rab GDP dissociation inhibitor alpha (Rab GDI alpha) (Guanosine diphosphate dissociation inhibitor 1 ...	0.24	-	nuc	0	Cytoplasm (By similarity)				447
P31150 UniProt NPD GO	GDIA_HUMAN	Rab GDP dissociation inhibitor alpha (Rab GDI alpha) (Guanosine diphosphate dissociation inhibitor 1 ...	0.24	-	nuc	0	Cytoplasm (By similarity)		309541		447
Q9XGU0 UniProt NPD GO	RAC9_ARATH	Rac-like GTP-binding protein ARAC9 (GTPase protein ROP8)	0.24	+	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				209
P34342 UniProt NPD GO	RGP2_CAEEL	Ran GTPase-activating protein 2 (Ran nuclear import/export-related protein 2) (RanGAP)	0.24	-	mit	0	Nucleus				960
Q6CXK4 UniProt NPD GO	ERFD_KLULA	Ras modification protein ERF4	0.24	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				258
P22981 UniProt NPD GO	LET60_CAEEL	Ras protein let-60 (Lethal protein 60) (Abnormal cell lineage protein 34)	0.24	-	cyt	0	Cell membrane				184
Q8K5A4 UniProt NPD GO	RR22_MOUSE	Ras-like protein RRP22 (RAS-related protein on chromosome 22 homolog)	0.24	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				203
Q9DD03 UniProt NPD GO	RAB13_MOUSE	Ras-related protein Rab-13	0.24	-	nuc	0	Cell membrane; cell-cell junction; tight junction; lipid-anchor; cytoplasmic side (By similarity). C ...	cytoplasmic membrane-bound vesicle [TAS] extrinsic to plasma membrane [TAS] Golgi apparatus [IDA] tight junction [IDA]			202
Q12829 UniProt NPD GO	RB40B_HUMAN	Ras-related protein Rab-40B (SOCS box-containing protein RAR) (Rar protein)	0.24	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				278
P05714 UniProt NPD GO	RAB4A_RAT	Ras-related protein Rab-4A	0.24	-	cyt	0	Membrane; peripheral membrane protein (By similarity). Generally associated with membranes. Cytoplas ...	cytosol [IDA] plasma membrane [IDA]			213
Q5RAV6 UniProt NPD GO	RAB6A_PONPY	Ras-related protein Rab-6A	0.24	-	cyt	0	Golgi apparatus; Golgi membrane; lipid-anchor (By similarity)				207
P20340 UniProt NPD GO	RAB6A_HUMAN	Ras-related protein Rab-6A (Rab-6)	0.24	-	cyt	0	Golgi apparatus; Golgi membrane; lipid-anchor	Golgi apparatus [IDA]	179513	2GIL	207

You are viewing entries 46751 to 46800 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.