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
Q9VWA1 UniProt NPD GO	CLC_DROME	Clathrin light chain (dClc)	0.43	-	nuc	0	Cytoplasmic face of coated pits and vesicles	clathrin coat of coated pit [ISS] clathrin vesicle coat [ISS] coated vesicle [TAS] synaptic vesicle [TAS]			219
P49661 UniProt NPD GO	COPD_ORYSA	Coatomer subunit delta (Delta-coat protein) (Delta-COP) (Archain)	0.43	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				518
Q9R0A8 UniProt NPD GO	CCDC5_RAT	Coiled-coil domain-containing protein 5	0.43	-	nuc	0	Cytoplasm (By similarity). Spindle (By similarity). Localizes with the spindle poles in mitotic cell ...				278
P98064 UniProt NPD GO	MASP1_MOUSE	Complement-activating component of Ra-reactive factor precursor (EC 3.4.21.-) (Ra-reactive factor se ...	0.43	-	exc	0					704
Q9BZ76 UniProt NPD GO	CNTP3_HUMAN	Contactin-associated protein-like 3 precursor (Cell recognition molecule Caspr3)	0.43	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein (Potential). Isoform 2: Secreted prote ...	integral to membrane [NAS]			1288
Q99P47 UniProt NPD GO	CNTP4_MOUSE	Contactin-associated protein-like 4 precursor (Cell recognition molecule Caspr4)	0.43	-	end	1	Membrane; single-pass type I membrane protein (Potential)	dendrite [IDA]			1310
Q9PTS1 UniProt NPD GO	CRF_CARAU	Corticoliberin precursor (Corticotropin-releasing factor) (CRF) (Corticotropin-releasing hormone)	0.43	-	exc	0	Secreted protein				162
Q5R764 UniProt NPD GO	CXAR_PONPY	Coxsackievirus and adenovirus receptor homolog precursor	0.43	-	exc	1	Cell membrane; cell-cell junction; single-pass type I membrane protein (By similarity). Localized at ...				365
P78310 UniProt NPD GO	CXAR_HUMAN	Coxsackievirus and adenovirus receptor precursor (Coxsackievirus B-adenovirus receptor) (hCAR) (CVB3 ...	0.43	-	exc	1	Isoform 1, isoform 2: Cell membrane; single-pass type I membrane protein. Isoform 3, isoform 4, isof ...	integral to plasma membrane [TAS] plasma membrane [NAS]	602621	1RSF	365
P33523 UniProt NPD GO	CRU1_BRANA	Cruciferin BnC1 precursor (11S globulin) (12S storage protein) [Contains: Cruciferin BnC1 subunit al ...	0.43	-	exc	0					490
Q8BGV9 UniProt NPD GO	ATG4D_MOUSE	Cysteine protease ATG4D (EC 3.4.22.-) (Autophagy-related protein 4 homolog D) (Autophagin-4) (Autoph ...	0.43	-	cyt	0	Cytoplasm (Probable)	cytoplasm [ISS] cytosol [ISS] microtubule associated complex [ISS]			474
O77810 UniProt NPD GO	CP1A2_CALJA	Cytochrome P450 1A2 (EC 1.14.14.1) (CYPIA2)	0.43	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				515
Q9FMA5 UniProt NPD GO	C85A1_ARATH	Cytochrome P450 85A1 (EC 1.14.-.-) (Brassinosteroid-6-oxidase 1) (BR6ox 1) (C6-oxidase 1)	0.43	-	cyt	1 *					465
O18635 UniProt NPD GO	C12A2_MUSDO	Cytochrome P450 CYP12A2 (EC 1.14.-.-) (CYPXIIA2)	0.43	-	nuc	0					537
Q95118 UniProt NPD GO	IL2RG_BOVIN	Cytokine receptor common gamma chain precursor (Gamma-C) (Interleukin-2 receptor gamma chain) (IL-2R ...	0.43	-	end	1	Membrane; single-pass type I membrane protein				379
Q8LPU5 UniProt NPD GO	CMT3_MAIZE	DNA (cytosine-5)-methyltransferase 3 (EC 2.1.1.37) (Chromomethylase 3) (DNA methyltransferase 105)	0.43	+	mit	0	Nucleus (By similarity)				915
P33611 UniProt NPD GO	DPOA2_MOUSE	DNA polymerase subunit alpha B (DNA polymerase alpha 70 kDa subunit)	0.43	-	cyt	0	Nucleus				600
Q5R587 UniProt NPD GO	RPB5_PONPY	DNA-directed RNA polymerase II 23 kDa polypeptide (EC 2.7.7.6) (RPB25) (RPB5) (RPABC1)	0.43	-	nuc	0	Nucleus (By similarity)				210
P19388 UniProt NPD GO	RPB5_HUMAN	DNA-directed RNA polymerase II 23 kDa polypeptide (EC 2.7.7.6) (RPB25) (RPB5) (RPABC1) (XAP4)	0.43	-	nuc	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS]	180664		210
P92389 UniProt NPD GO	RPOA_HETPI	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.43	-	cyt	0	Plastid; chloroplast				339
Q60F88 UniProt NPD GO	RPOA_TAKLE	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.43	-	nuc	0	Plastid; chloroplast				382
Q2L8Z9 UniProt NPD GO	RPOB_GOSHI	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.43	-	nuc	0	Plastid; chloroplast				1070
Q3C1G7 UniProt NPD GO	RPOB_NICSY	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.43	-	cyt	0	Plastid; chloroplast				1070
Q68S14 UniProt NPD GO	RPOB_PANGI	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.43	-	cyt	0	Plastid; chloroplast				1071
Q589C0 UniProt NPD GO	RPOB_SILLA	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.43	-	cyt	0	Plastid; chloroplast				1070
P06271 UniProt NPD GO	RPOB_TOBAC	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.43	-	cyt	0	Plastid; chloroplast				1070
Q4G3A6 UniProt NPD GO	RPOC1_EMIHU	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.43	-	nuc	0	Plastid; chloroplast				609
Q9P4B9 UniProt NPD GO	RPB5_KLUMA	DNA-directed RNA polymerases II 24 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 5)	0.43	-	cyt	0	Nucleus				215
Q682D3 UniProt NPD GO	XRCC2_ARATH	DNA-repair protein XRCC2 homolog (X-ray repair cross-complementing protein 2 homolog) (AtXRCC2)	0.43	-	cyt	0	Nucleus (By similarity)				372
Q8CIZ5 UniProt NPD GO	DMBT1_RAT	Deleted in malignant brain tumors 1 protein precursor (Ebnerin) (Pancrin)	0.43	-	end	1	Secreted protein. Membrane. Localized to the lumenal aspect of crypt cells in the small intestine. I ...				1418
Q25338 UniProt NPD GO	LITD_LATMA	Delta-latroinsectotoxin precursor (Delta-LIT)	0.43	-	nuc	0	Secreted protein				1214
O42929 UniProt NPD GO	DENR_SCHPO	Density-regulated protein homolog	0.43	+	nuc	0					190
P22238 UniProt NPD GO	DHA_CRAPL	Desiccation-related protein clone PCC27-04	0.43	-	nuc	0					117
P48675 UniProt NPD GO	DESM_RAT	Desmin	0.43	-	nuc	0	Cytoplasm				468
Q02487 UniProt NPD GO	DSC2_HUMAN	Desmocollin-2 precursor (Desmosomal glycoprotein II and III) (Desmocollin-3)	0.43	-	end	2 *	Membrane; single-pass type I membrane protein		125645		901
O35902 UniProt NPD GO	DSG3_MOUSE	Desmoglein-3 precursor (130 kDa pemphigus vulgaris antigen homolog)	0.43	-	end	0	Membrane; single-pass type I membrane protein (By similarity)	desmosome [TAS] integral to plasma membrane [TAS] spot adherens junction [TAS]			993
P83757 UniProt NPD GO	CACT_DROYA	Developmental protein cactus	0.43	-	nuc	0	Cytoplasm	cytoplasm [ISS]			489
Q91WG7 UniProt NPD GO	DGKG_MOUSE	Diacylglycerol kinase gamma (EC 2.7.1.107) (Diglyceride kinase gamma) (DGK-gamma) (DAG kinase gamma) ...	0.43	-	cyt	0					788
O08532 UniProt NPD GO	CAC2D_MOUSE	Dihydropyridine-sensitive L-type calcium channel subunits alpha-2/delta precursor [Contains: L-type ...	0.43	-	cyt	0	Membrane; multi-pass membrane protein				1103
Q7SC98 UniProt NPD GO	DPH1_NEUCR	Diphthamide biosynthesis protein 1	0.43	-	cyt	0	Cytoplasm (By similarity)				459
Q5ZKZ4 UniProt NPD GO	DJC16_CHICK	DnaJ homolog subfamily C member 16 precursor	0.43	-	end	0	Membrane; single-pass type IV membrane protein (Potential)				777
P92029 UniProt NPD GO	DNJ60_DROME	DnaJ-like protein 60	0.43	-	nuc	1					217
Q9Y5R5 UniProt NPD GO	DMRT2_HUMAN	Doublesex- and mab-3-related transcription factor 2 (Doublesex-like 2 protein) (DSXL-2)	0.43	-	nuc	1	Nucleus (Potential)		604935		226
Q9PW71 UniProt NPD GO	DUS4_CHICK	Dual specificity protein phosphatase 4 (EC 3.1.3.48) (EC 3.1.3.16) (Mitogen-activated protein kinase ...	0.43	-	nuc	0	Nucleus (By similarity)				375
Q63572 UniProt NPD GO	TESK1_RAT	Dual specificity testis-specific protein kinase 1 (EC 2.7.12.1) (Testicular protein kinase 1)	0.43	-	nuc	0					628
Q8VZ40 UniProt NPD GO	PUB14_ARATH	E3 ubiquitin ligase PUB14 (EC 6.3.2.-) (Prototypical U-box domain protein 14)	0.43	-	mit	0				1T1H	632
Q99K41 UniProt NPD GO	EMIL1_MOUSE	EMILIN-1 precursor (Elastin microfibril interface-located protein 1) (Elastin microfibril interfacer ...	0.43	-	nuc	0	Secreted protein; extracellular space; extracellular matrix. Found mainly at the interface between a ...	extracellular matrix (sensu Metazoa) [IDA]			1017
Q9NT22 UniProt NPD GO	EMIL3_HUMAN	EMILIN-3 precursor (EMILIN-5) (Elastin microfibril interface-located protein 5) (Elastin microfibril ...	0.43	-	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		608929		766
O74401 UniProt NPD GO	ERO11_SCHPO	ERO1-like protein 1 precursor (EC 1.8.4.-) (Endoplasmic oxidoreductin-1-like protein A)	0.43	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side				467
P28324 UniProt NPD GO	ELK4_HUMAN	ETS domain-containing protein Elk-4 (Serum response factor accessory protein 1) (SAP-1)	0.43	+	nuc	0	Nucleus		600246	1K6O	431

You are viewing entries 29551 to 29600 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.