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
Q9NDA7 UniProt NPD GO	COW1_CONTE	Contryphan-Tx precursor	0.04	-	exc	0	Secreted protein				63
Q9P7F9 UniProt NPD GO	CTR5_SCHPO	Copper transport protein ctr5 (Copper transporter 5)	0.04	-	end	2	Membrane; multi-pass membrane protein	plasma membrane [IDA]			173
Q9S7J8 UniProt NPD GO	AHM5_ARATH	Copper-transporting ATPase RAN1 (EC 3.6.3.4) (Responsive-to-antagonist 1)	0.04	-	end	8	Membrane; multi-pass membrane protein				1001
P23775 UniProt NPD GO	CBG_RABIT	Corticosteroid-binding globulin (CBG) (Transcortin) (Serpin A6)	0.04	-	nuc	0	Secreted protein				383
P08185 UniProt NPD GO	CBG_HUMAN	Corticosteroid-binding globulin precursor (CBG) (Transcortin) (Serpin A6)	0.04	-	end	0	Secreted protein		122500		405
Q5R9E3 UniProt NPD GO	CBG_PONPY	Corticosteroid-binding globulin precursor (CBG) (Transcortin) (Serpin A6)	0.04	-	end	0	Secreted protein (By similarity)				405
P49920 UniProt NPD GO	CBG_SHEEP	Corticosteroid-binding globulin precursor (CBG) (Transcortin) (Serpin A6)	0.04	-	end	0	Secreted protein				430
Q29594 UniProt NPD GO	KCRB_PIG	Creatine kinase B-type (EC 2.7.3.2) (Creatine kinase B chain) (B-CK) (Fragment)	0.04	-	nuc	0	Cytoplasm (By similarity)				102
P83486 UniProt NPD GO	CHHB_CHEDE	Crustacean hyperglycemic hormone B (CHHB)	0.04	-	cyt	0	Secreted protein	extracellular region [NAS]			72
O97384 UniProt NPD GO	CHH2_PENMO	Crustacean hyperglycemic hormones 2 precursor (Pm-SGP-II) [Contains: CHH precursor-related peptide 2 ...	0.04	-	exc	0	Secreted protein				118
P17656 UniProt NPD GO	COL2_CAEEL	Cuticle collagen 2 precursor	0.04	-	nuc	1 *					301
P16253 UniProt NPD GO	CUC3A_HAECO	Cuticle collagen 3A3	0.04	-	nuc	1 *					295
P80674 UniProt NPD GO	CU01_BLACR	Cuticle protein 1 (Bc-NCP1)	0.04	-	nuc	0					87
P83991 UniProt NPD GO	CU106_LOCMI	Cuticle protein 10.6 (LM-10.6) (LM-ACP 10.6)	0.04	-	cyt	3 *					109
P83990 UniProt NPD GO	CU125_LOCMI	Cuticle protein 12.5 (LM-12.5) (LM-ACP 12.5)	0.04	-	cyt	3 *					129
P83354 UniProt NPD GO	CU14A_LIMPO	Cuticle protein 14 isoform a (LpCP14a)	0.04	-	cyt	0					130
P81225 UniProt NPD GO	CU21_LOCMI	Cuticle protein 21 (LM-ACP 21)	0.04	-	mit	0					169
P04375 UniProt NPD GO	CU38_LOCMI	Cuticle protein 38 (LM-38) (LM-ACP 38)	0.04	-	mit	4 *					163
P45588 UniProt NPD GO	CU76_LOCMI	Cuticle protein 76 (LM-76) (LM-ACP 76)	0.04	-	cyt	3 *					139
P81584 UniProt NPD GO	CUPC5_CANPG	Cuticle protein CP1876 (CPCP1876)	0.04	-	nuc	0					175
Q94804 UniProt NPD GO	CU23_TENMO	Cuticle protein LPCP-23 precursor (TMLPCP-23)	0.04	-	exc	1 *					231
P52956 UniProt NPD GO	CUTI1_ASPOR	Cutinase 1 precursor (EC 3.1.1.74) (Cutin hydrolase 1) (L1)	0.04	-	nuc	0	Secreted protein				213
P23402 UniProt NPD GO	RR5_CYAPA	Cyanelle 30S ribosomal protein S5	0.04	-	nuc	0	Plastid; cyanelle				169
P55273 UniProt NPD GO	CDN2D_HUMAN	Cyclin-dependent kinase 4 inhibitor D (p19-INK4d)	0.04	-	cyt	0		cytoplasm [TAS] nucleus [TAS]	600927	1BI8	166
Q17868 UniProt NPD GO	CKS1_CAEEL	Cyclin-dependent kinases regulatory subunit	0.04	-	cyt	0					94
P58434 UniProt NPD GO	CYO2_VIOOD	Cycloviolacin-O2	0.04	-	nuc	0					30
P32929 UniProt NPD GO	CGL_HUMAN	Cystathionine gamma-lyase (EC 4.4.1.1) (Gamma-cystathionase)	0.04	-	cyt	0	Cytoplasm		607657		405
Q60HG7 UniProt NPD GO	CGL_MACFA	Cystathionine gamma-lyase (EC 4.4.1.1) (Gamma-cystathionase)	0.04	-	cyt	0	Cytoplasm (By similarity)				405
P80416 UniProt NPD GO	CYTA_BOVIN	Cystatin A (Stefin A) (Cystatin AS)	0.04	-	cyt	0	Cytoplasm				98
P04080 UniProt NPD GO	CYTB_HUMAN	Cystatin B (Liver thiol proteinase inhibitor) (CPI-B) (Stefin B)	0.04	-	nuc	0	Cytoplasm. Nucleus		254800	1STF	98
Q76LA0 UniProt NPD GO	CYTB_GORGO	Cystatin B (Stefin B)	0.04	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				98
P60575 UniProt NPD GO	CYTB_PANPA	Cystatin B (Stefin B)	0.04	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				98
Q8I030 UniProt NPD GO	CYTB_PANTR	Cystatin B (Stefin B)	0.04	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				98
Q29290 UniProt NPD GO	CYTB_PIG	Cystatin B (Stefin B)	0.04	-	nuc	0	Cytoplasm				98
P60576 UniProt NPD GO	CYTB_PONPY	Cystatin B (Stefin B)	0.04	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				98
P01039 UniProt NPD GO	CYTA_RAT	Cystatin alpha (Epidermal thiol proteinase inhibitor) (Stefin, epidermal) (Cystatin A)	0.04	-	cyt	0	Cytoplasm				103
Q98967 UniProt NPD GO	CYT_ONCKE	Cystatin precursor	0.04	-	nuc	1 *	Secreted protein				130
P31726 UniProt NPD GO	CYT1_MAIZE	Cystatin-1 precursor (Cystatin I) (Corn kernel cysteine proteinase inhibitor)	0.04	-	gol	1 *					135
P50462 UniProt NPD GO	CSRP3_MOUSE	Cysteine and glycine-rich protein 3 (Cysteine-rich protein 3) (CRP3) (LIM domain protein, cardiac) ( ...	0.04	-	nuc	0	Nucleus (Potential). Cytoplasm. Nuclear, associates with the actin cytoskeleton (Potential)	Z disc [IDA]			194
P32956 UniProt NPD GO	CYSP3_CARCN	Cysteine proteinase 3 (EC 3.4.22.-) (Cysteine proteinase III) (CC-III) (Fragment)	0.04	-	cyt	0					43
P14658 UniProt NPD GO	CYSP_TRYBB	Cysteine proteinase precursor (EC 3.4.22.-)	0.04	-	exc	1 *	Lysosome				450
Q9DCT8 UniProt NPD GO	CRIP2_MOUSE	Cysteine-rich protein 2 (CRP2) (Heart LIM protein)	0.04	-	nuc	0					208
P36201 UniProt NPD GO	CRIP2_RAT	Cysteine-rich protein 2 (CRP2) (Protein ESP1)	0.04	-	nuc	0					208
P84804 UniProt NPD GO	CRV23_NAJHH	Cysteine-rich venom protein 23 (CRVP-23h) (Fragment)	0.04	-		0	Secreted protein	extracellular region [IDA]			14
P79304 UniProt NPD GO	CP193_PIG	Cytochrome P450 19 type III (EC 1.14.14.1) (Aromatase) (CYPXIXA3) (Estrogen synthetase) (P-450AROM)	0.04	-	cyt	2 *	Membrane; peripheral membrane protein				501
P22779 UniProt NPD GO	CP2AX_BOVIN	Cytochrome P450 2A (EC 1.14.14.1) (OLF2) (Olfactive) (P52) (Fragment)	0.04	-		0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				18
Q9JKJ9 UniProt NPD GO	CP39A_MOUSE	Cytochrome P450 39A1 (EC 1.14.13.99) (24-hydroxycholesterol 7-alpha-hydroxylase) (Oxysterol 7-alpha- ...	0.04	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [TAS]			470
P24458 UniProt NPD GO	CP52E_CANMA	Cytochrome P450 52A5 (EC 1.14.14.-) (CYPLIIA5) (Alkane-inducible P450-ALK2-A) (CYP52A3-B)	0.04	-	nuc	1 *					523
Q9SAE1 UniProt NPD GO	C71BR_ARATH	Cytochrome P450 71B27 (EC 1.14.-.-)	0.04	-	end	3 *					503
Q6Z6K9 UniProt NPD GO	C74A4_ORYSA	Cytochrome P450 74A4 (EC 4.2.1.92) (Allene oxide synthase 4) (Hydroperoxide dehydrase 4)	0.04	-	cyt	0					510

You are viewing entries 76601 to 76650 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.