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
P32843 UniProt NPD GO	RNA12_YEAST	Protein RNA12	0.43	-	mit	0	Nucleus (Potential)	mitochondrial inner membrane [TAS]			850
Q3ECY6 UniProt NPD GO	SDG41_ARATH	Protein SET DOMAIN GROUP 41	0.43	-	nuc	0					558
O60224 UniProt NPD GO	SSX4_HUMAN	Protein SSX4	0.43	-	nuc	0			300326		188
Q7Z2V1 UniProt NPD GO	TNT_HUMAN	Protein TNT	0.43	-	nuc	0					217
Q9SSD1 UniProt NPD GO	TMM_ARATH	Protein TOO MANY MOUTHS precursor	0.43	+	exc	1	Membrane; multi-pass membrane protein (Probable)				496
Q8NJR4 UniProt NPD GO	URE2_KLUMA	Protein URE2	0.43	-	nuc	0					404
Q9V3C1 UniProt NPD GO	VHL_DROME	Protein Vhl	0.43	-	cyt	0		VCB complex [IDA]			178
Q9SCC7 UniProt NPD GO	CBBX_GUITH	Protein cbbX homolog, chloroplast precursor	0.43	-	cyt	0	Plastid; chloroplast				371
P40795 UniProt NPD GO	FOG_DROME	Protein folded gastrulation precursor [Contains: Protein folded gastrulation; G protein-coupled rece ...	0.43	-	exc	0		extracellular region [NAS]			730
O46244 UniProt NPD GO	HUNB_DROLI	Protein hunchback (Fragments)	0.43	-	nuc	0	Nucleus (By similarity)				198
O46248 UniProt NPD GO	HUNB_DROMM	Protein hunchback (Fragments)	0.43	-	nuc	0	Nucleus (By similarity)				158
O46256 UniProt NPD GO	HUNB_DROSL	Protein hunchback (Fragments)	0.43	-	nuc	0	Nucleus (By similarity)				196
P33886 UniProt NPD GO	WIS1_SCHPO	Protein kinase wis1 (EC 2.7.12.2) (Protein kinase sty2)	0.43	-	nuc	0					605
Q5U567 UniProt NPD GO	PELO_XENLA	Protein pelota homolog	0.43	-	cyt	0	Nucleus (Potential)				383
Q3UM45 UniProt NPD GO	PP1R7_MOUSE	Protein phosphatase 1 regulatory subunit 7 (Protein phosphatase 1 regulatory subunit 22)	0.43	-	nuc	0	Nucleus (By similarity)				361
Q01405 UniProt NPD GO	SC23A_MOUSE	Protein transport protein Sec23A (SEC23-related protein A)	0.43	-	cyt	0	Endoplasmic reticulum; smooth endoplasmic reticulum; smooth endoplasmic reticulum membrane; peripher ...	Golgi membrane [IDA] perinuclear region [IDA]			765
P15821 UniProt NPD GO	YCF2_VICFA	Protein ycf2 (Fragment)	0.43	-	nuc	0	Plastid; chloroplast; chloroplast stroma (By similarity)				121
P11309 UniProt NPD GO	PIM1_HUMAN	Proto-oncogene serine/threonine-protein kinase Pim-1 (EC 2.7.11.1)	0.43	-	nuc	0	Isoform 2: Cytoplasm. Isoform 2: Nuclear. Isoform 1: Cell membrane	cytoplasm [IDA]	164960	2C3I	404
P08922 UniProt NPD GO	ROS_HUMAN	Proto-oncogene tyrosine-protein kinase ROS precursor (EC 2.7.10.1) (c-ros-1)	0.43	-	end	1	Membrane; single-pass type I membrane protein	membrane fraction [TAS] sodium:potassium-exchanging ATPase complex [TAS]	165020		2347
Q9FIR0 UniProt NPD GO	ATL5L_ARATH	Putative RING-H2 finger protein ATL5L	0.43	-	nuc	1 *					289
Q5R962 UniProt NPD GO	CF075_PONPY	Putative RNA methylase C6orf75 homolog (EC 2.1.1.-)	0.43	-	cyt	0					463
P58840 UniProt NPD GO	ACROL_HUMAN	Putative acrosin-like protease (EC 3.4.21.-) (Fragment)	0.43	-	nuc	0					232
Q96M32 UniProt NPD GO	KAD7_HUMAN	Putative adenylate kinase 7 (EC 2.7.4.3)	0.43	-	cyt	0					723
O74794 UniProt NPD GO	CCHL_SCHPO	Putative cytochrome c heme lyase (EC 4.4.1.17) (CCHL) (Holocytochrome-c synthase)	0.43	-	nuc	0	Mitochondrion; mitochondrial inner membrane (By similarity)				377
Q9P7L6 UniProt NPD GO	METL_SCHPO	Putative methyltransferase-like protein SPBC21C3.07c (EC 2.1.1.-)	0.43	-	cyt	0					281
Q9LSJ2 UniProt NPD GO	MDR21_ARATH	Putative multidrug resistance protein 21 (P-glycoprotein 22)	0.43	+	end	7	Membrane; multi-pass membrane protein (Potential)				1262
Q9VZW8 UniProt NPD GO	OR63A_DROME	Putative odorant receptor 63a	0.43	-	cyt	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			420
Q95JX4 UniProt NPD GO	GLTL5_MACFA	Putative polypeptide N-acetylgalactosaminyltransferase-like protein 5 (EC 2.4.1.-) (Protein-UDP acet ...	0.43	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				443
Q9HE06 UniProt NPD GO	YK99_SCHPO	Putative pre-mRNA-splicing factor ATP-dependent RNA helicase C20H4.09 (EC 3.6.1.-) (DEAH-box helicas ...	0.43	-	mit	0	Nucleus (By similarity)	spliceosome complex [ISS]			647
Q6GVM5 UniProt NPD GO	CY15A_PANTR	Putative testis protein CYorf15A homolog	0.43	-	nuc	0					131
P56180 UniProt NPD GO	TPTE_HUMAN	Putative tyrosine-protein phosphatase TPTE (EC 3.1.3.48) (Transmembrane phosphatase with tensin homo ...	0.43	-	end	3	Membrane; multi-pass membrane protein	integral to membrane [TAS]	604336		551
P0C035 UniProt NPD GO	ATL1M_ARATH	RING-H2 finger protein ATL1M	0.43	-	nuc	1 *					310
O64762 UniProt NPD GO	ATL2F_ARATH	RING-H2 finger protein ATL2F	0.43	-	nuc	1 *					302
Q9JJW6 UniProt NPD GO	REFP2_MOUSE	RNA and export factor-binding protein 2	0.43	-	nuc	0	Nucleus. Cytoplasm. Travels to the cytoplasm as part of the exon junction complex (EJC) bound to mRN ...				218
Q12004 UniProt NPD GO	TFB4_YEAST	RNA polymerase II transcription factor B subunit 4 (RNA polymerase II transcription factor B p34 sub ...	0.43	-	end	0	Nucleus (By similarity)	transcription factor TFIIH complex [IDA]			338
P35637 UniProt NPD GO	FUS_HUMAN	RNA-binding protein FUS (Oncogene FUS) (Oncogene TLS) (Translocated in liposarcoma protein) (POMp75) ...	0.43	-	nuc	0	Nucleus	nucleus [TAS]	137070		526
Q28009 UniProt NPD GO	FUS_BOVIN	RNA-binding protein FUS (Pigpen protein)	0.43	+	nuc	0	Nucleus. Nuclear, exhibits diffuse staining throughout (excluding nucleoli), together with a small n ...				512
P56959 UniProt NPD GO	FUS_MOUSE	RNA-binding protein FUS (Pigpen protein)	0.43	+	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			518
P51513 UniProt NPD GO	NOVA1_HUMAN	RNA-binding protein Nova-1 (Neuro-oncological ventral antigen 1) (Onconeural ventral antigen 1) (Par ...	0.43	-	nuc	0	Nucleus		602157	1DT4	510
P50397 UniProt NPD GO	GDIB_BOVIN	Rab GDP dissociation inhibitor beta (Rab GDI beta) (Guanosine diphosphate dissociation inhibitor 2) ...	0.43	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein				445
P50395 UniProt NPD GO	GDIB_HUMAN	Rab GDP dissociation inhibitor beta (Rab GDI beta) (Guanosine diphosphate dissociation inhibitor 2) ...	0.43	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	cell surface [IEP] cytoplasm [TAS]	600767		445
P69566 UniProt NPD GO	RANB9_MOUSE	Ran-binding protein 9 (RanBP9) (Ran-binding protein M) (RanBPM) (B cell antigen receptor Ig beta-ass ...	0.43	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Perinuclear in spermatids	cytoplasm [IDA]			653
Q13283 UniProt NPD GO	G3BP_HUMAN	Ras-GTPase-activating protein-binding protein 1 (EC 3.6.1.-) (ATP-dependent DNA helicase VIII) (GAP ...	0.43	-	nuc	0	Cytoplasm. Cytoplasm; cytosol. Cell membrane. Nucleus. Cytoplasmic in proliferating cells, can be re ...	nucleus [TAS]	608431		466
P97855 UniProt NPD GO	G3BP_MOUSE	Ras-GTPase-activating protein-binding protein 1 (EC 3.6.1.-) (ATP-dependent DNA helicase VIII) (GAP ...	0.43	-	nuc	0	Cytoplasm (By similarity). Cytoplasm; cytosol (By similarity). Cell membrane (By similarity). Nucleu ...				465
P13856 UniProt NPD GO	RSR1_YEAST	Ras-related protein RSR1	0.43	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	bud neck [IDA] plasma membrane [IDA]			272
O45524 UniProt NPD GO	RGS11_CAEEL	Regulator of G-protein signaling rgs-11	0.43	-	cyt	0					274
P51842 UniProt NPD GO	GUC2F_RAT	Retinal guanylyl cyclase 2 precursor (EC 4.6.1.2) (Guanylate cyclase 2F, retinal) (RETGC-2) (Rod out ...	0.43	-	end	2	Membrane; single-pass type I membrane protein				1108
O94844 UniProt NPD GO	RHBT1_HUMAN	Rho-related BTB domain-containing protein 1	0.43	-	mit	0			607351		696
P53833 UniProt NPD GO	POP3_YEAST	Ribonucleases P/MRP protein subunit POP3 (RNases MRP/P 22.6 kDa subunit) (RNA-processing protein POP ...	0.43	+	nuc	0	Nucleus (Potential)	nucleolar ribonuclease P complex [IDA] ribonuclease MRP complex [IDA]			195
Q5BGK3 UniProt NPD GO	RUVB2_EMENI	RuvB-like helicase 2 (EC 3.6.1.-)	0.43	-	cyt	0	Nucleus (By similarity)				452

You are viewing entries 29951 to 30000 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.