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
P54119 UniProt NPD GO	CDC2_AJECA	Cell division control protein 2 (EC 2.7.11.22) (EC 2.7.11.23) (Cyclin-dependent protein kinase)	0.08	-	cyt	0					324
P06493 UniProt NPD GO	CDC2_HUMAN	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase) (Cyclin-d ...	0.08	-	cyt	0	Nucleus (By similarity)	nucleus [TAS]	116940	1LC9	297
O94103 UniProt NPD GO	CDC42_COLGL	Cell division control protein 42 homolog	0.08	+	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				190
P49825 UniProt NPD GO	FTSH_ODOSI	Cell division protein ftsH homolog (EC 3.4.24.-)	0.08	-	nuc	1	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				644
P30285 UniProt NPD GO	CDK4_MOUSE	Cell division protein kinase 4 (EC 2.7.11.22) (Cyclin-dependent kinase 4) (PSK-J3) (CRK3)	0.08	-	cyt	0		cyclin-dependent protein kinase holoenzyme ... [IPI] nucleus [IDA] transcription factor complex [IDA]			303
P12546 UniProt NPD GO	CERC_SCHMA	Cercarial protease precursor (EC 3.4.21.-) (Cercarial elastase)	0.08	-	mit	0	Acetabular (penetration) glands				264
O75503 UniProt NPD GO	CLN5_HUMAN	Ceroid-lipofuscinosis neuronal protein 5 (Protein CLN5)	0.08	-	mit	0	Lysosome	integral to membrane [TAS]	608102		407
Q9MBB1 UniProt NPD GO	CHSY_EQUAR	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.08	-	cyt	0					405
P22926 UniProt NPD GO	CHSF_PETHY	Chalcone synthase F (EC 2.3.1.74) (Naringenin-chalcone synthase F)	0.08	-	nuc	0					389
P30722 UniProt NPD GO	DNAK_PAVLU	Chaperone protein dnaK (Heat shock protein 70) (Heat shock 70 kDa protein) (HSP70)	0.08	-	cyt	0	Plastid; chloroplast				629
P29197 UniProt NPD GO	CH60A_ARATH	Chaperonin CPN60, mitochondrial precursor (HSP60)	0.08	-	mit	0	Mitochondrion				577
Q05045 UniProt NPD GO	CH61_CUCMA	Chaperonin CPN60-1, mitochondrial precursor (HSP60-1)	0.08	-	mit	0	Mitochondrion				575
Q05046 UniProt NPD GO	CH62_CUCMA	Chaperonin CPN60-2, mitochondrial precursor (HSP60-2)	0.08	-	mit	0	Mitochondrion				575
O00590 UniProt NPD GO	CCBP2_HUMAN	Chemokine-binding protein 2 (Chemokine-binding protein D6) (C-C chemokine receptor D6) (Chemokine re ...	0.08	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	602648		384
Q15782 UniProt NPD GO	CH3L2_HUMAN	Chitinase 3-like protein 2 precursor (YKL-39) (Chondrocyte protein 39)	0.08	-	mit	0		extracellular space [TAS]	601526		390
O35744 UniProt NPD GO	CH3L3_MOUSE	Chitinase 3-like protein 3 precursor (Secretory protein Ym1) (Eosinophil chemotactic cytokine) (ECF- ...	0.08	-	mit	0	Secreted protein	cytoplasmic membrane-bound vesicle [IDA]		1VF8	398
P51798 UniProt NPD GO	CLCN7_HUMAN	Chloride channel protein 7 (ClC-7)	0.08	-	end	11	Membrane; multi-pass membrane protein		602727		805
Q9T2L1 UniProt NPD GO	CB2C_SPIOL	Chlorophyll a-b binding protein (LHCII type I CAB) (LHCP) (Fragment)	0.08	-		0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein	thylakoid membrane (sensu Viridiplantae) [IDA]			9
Q9XF89 UniProt NPD GO	CB26_ARATH	Chlorophyll a-b binding protein CP26, chloroplast precursor (Light-harvesting complex II protein 5) ...	0.08	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				280
Q8WHY2 UniProt NPD GO	RR19_PSINU	Chloroplast 30S ribosomal protein S19	0.08	-	mit	0	Plastid; chloroplast				92
P51298 UniProt NPD GO	RR5_PORPU	Chloroplast 30S ribosomal protein S5	0.08	-	nuc	0	Plastid; chloroplast				174
Q3ZJ81 UniProt NPD GO	RR8_PSEAK	Chloroplast 30S ribosomal protein S8	0.08	-	nuc	0	Plastid; chloroplast				131
P56363 UniProt NPD GO	RK14_CHLVU	Chloroplast 50S ribosomal protein L14	0.08	-	nuc	0	Plastid; chloroplast				122
Q4G360 UniProt NPD GO	RK22_EMIHU	Chloroplast 50S ribosomal protein L22	0.08	-	nuc	0	Plastid; chloroplast				117
O62961 UniProt NPD GO	RK23_PICAB	Chloroplast 50S ribosomal protein L23	0.08	-	cyt	0	Plastid; chloroplast				91
O19885 UniProt NPD GO	RK27_CYACA	Chloroplast 50S ribosomal protein L27	0.08	-	nuc	0	Plastid; chloroplast				100
Q7YJW1 UniProt NPD GO	CEMA_CALFE	Chloroplast envelope membrane protein	0.08	-	end	2 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				229
Q8TDN8 UniProt NPD GO	COAS3_HUMAN	Chromosome 1 amplified sequence 3 (COAS-3)	0.08	-	gol	0			608609		59
P83545 UniProt NPD GO	CHY1_PAGMA	Chrysophsin-1	0.08	-	cyt	0	Secreted protein				25
Q8WUH1 UniProt NPD GO	CHUR_HUMAN	Churchill protein	0.08	-	cyt	0			608577		112
Q5R6Q5 UniProt NPD GO	CHUR_PONPY	Churchill protein	0.08	-	cyt	0					112
Q08406 UniProt NPD GO	CNTFR_RAT	Ciliary neurotrophic factor receptor alpha precursor (CNTFR alpha)	0.08	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				372
P50746 UniProt NPD GO	CADH_EUCBO	Cinnamyl alcohol dehydrogenase (EC 1.1.1.195) (CAD)	0.08	-	cyt	0					355
P83372 UniProt NPD GO	CISY_FRAAN	Citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.08	-	mit	0	Mitochondrion; mitochondrial matrix				469
P23068 UniProt NPD GO	HB2L_CHICK	Class II histocompatibility antigen, B-L beta chain (Fragment)	0.08	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				231
O95500 UniProt NPD GO	CLD14_HUMAN	Claudin-14	0.08	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]	605608		239
Q7TQI0 UniProt NPD GO	CLP24_MOUSE	Claudin-like protein 24	0.08	-	end	4 *	Cell membrane; cell-cell junction; adherens junction; multi-pass membrane protein (By similarity). C ...				226
Q5M962 UniProt NPD GO	CLP24_RAT	Claudin-like protein 24	0.08	-	end	4 *	Cell membrane; cell-cell junction; adherens junction; multi-pass membrane protein (By similarity). C ...				226
P00740 UniProt NPD GO	FA9_HUMAN	Coagulation factor IX precursor (EC 3.4.21.22) (Christmas factor) (Plasma thromboplastin component) ...	0.08	-	mit	0	Secreted protein	extracellular region [NAS]	306900	1RFN	461
Q6SA95 UniProt NPD GO	FA9_FELCA	Coagulation factor IX precursor (EC 3.4.21.22) (Christmas factor) [Contains: Coagulation factor IXa ...	0.08	-	mit	0	Secreted protein (By similarity)				466
Q95ND7 UniProt NPD GO	FA9_PANTR	Coagulation factor IX precursor (EC 3.4.21.22) (Christmas factor) [Contains: Coagulation factor IXa ...	0.08	-	mit	0	Secreted protein (By similarity)				461
P16294 UniProt NPD GO	FA9_MOUSE	Coagulation factor IX precursor (EC 3.4.21.22) (Christmas factor) [Contains: Coagulation factor IXa ...	0.08	-	end	0	Secreted protein				459
Q696W1 UniProt NPD GO	LC2_VIPLE	Coagulation factor X-activating enzyme light chain 2 precursor (VLFXA light chain 2)	0.08	-	exc	0	Secreted protein				158
P25318 UniProt NPD GO	CO8A2_MOUSE	Collagen alpha-2(VIII) chain precursor (Endothelial collagen)	0.08	-	mit	0					699
Q28679 UniProt NPD GO	CO8G_RABIT	Complement component C8 gamma chain precursor	0.08	-	end	0	Secreted protein				202
P29279 UniProt NPD GO	CTGF_HUMAN	Connective tissue growth factor precursor (Hypertrophic chondrocyte-specific protein 24)	0.08	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity). Secreted protein (By si ...	extracellular matrix (sensu Metazoa) [TAS] plasma membrane [TAS]	121009		349
P58625 UniProt NPD GO	CX2A_CONBE	Conotoxin BeTXIIa	0.08	-	nuc	0	Secreted protein				30
P84707 UniProt NPD GO	CX14C_CONFF	Conotoxin flf14c	0.08	-	nuc	0	Secreted protein				27
Q07409 UniProt NPD GO	CNTN3_MOUSE	Contactin-3 precursor (Brain-derived immunoglobulin superfamily protein 1) (BIG-1) (Plasmacytoma-ass ...	0.08	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				1028
P38865 UniProt NPD GO	CTR2_YEAST	Copper transport protein CTR2 (Copper transporter 2)	0.08	-	end	2	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuolar membrane (sensu Fungi) [IDA]			189

You are viewing entries 67751 to 67800 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.