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
P58441 UniProt NPD GO	CYO9_VIOOD	Cycloviolacin-O9	0.01	-	nuc	0					30
P82157 UniProt NPD GO	ALL6_CYDPO	Cydiastatin-6	0.01	-		0	Secreted protein				8
P31373 UniProt NPD GO	CYS3_YEAST	Cystathionine gamma-lyase (EC 4.4.1.1) (Gamma-cystathionase)	0.01	-	cyt	0	Cytoplasm	cytoplasm [IDA]		1N8P	393
P25973 UniProt NPD GO	CYT_SOYBN	Cystatin (Low molecular mass protein inhibitor of cysteine proteinases) (Fragment)	0.01	-	cyt	0					48
P01041 UniProt NPD GO	CYTB_RAT	Cystatin B (Liver thiol proteinase inhibitor) (Stefin B) (Cystatin beta)	0.01	-	cyt	0	Cytoplasm				98
Q862Z5 UniProt NPD GO	CYTB_MACFU	Cystatin B (Stefin B)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				98
P32766 UniProt NPD GO	CST8_MOUSE	Cystatin-related epididymal spermatogenic protein precursor (Cystatin-related epididymal-specific pr ...	0.01	-	exc	1 *	Secreted protein				142
Q3MHY1 UniProt NPD GO	CSRP1_BOVIN	Cysteine and glycine-rich protein 1 (Cysteine-rich protein 1) (CRP1)	0.01	-	cyt	0	Nucleus (By similarity)				192
Q5RCT4 UniProt NPD GO	CSRP1_PONPY	Cysteine and glycine-rich protein 1 (Cysteine-rich protein 1) (CRP1)	0.01	-	cyt	0	Nucleus (By similarity)				192
P21291 UniProt NPD GO	CSRP1_HUMAN	Cysteine and glycine-rich protein 1 (Cysteine-rich protein 1) (CRP1) (CRP)	0.01	-	cyt	0	Nucleus		123876		192
P97315 UniProt NPD GO	CSRP1_MOUSE	Cysteine and glycine-rich protein 1 (Cysteine-rich protein 1) (CRP1) (CRP)	0.01	-	cyt	0	Nucleus (By similarity)	actin cytoskeleton [TAS]			192
P47875 UniProt NPD GO	CSRP1_RAT	Cysteine and glycine-rich protein 1 (Cysteine-rich protein 1) (CRP1) (CRP)	0.01	-	cyt	0	Nucleus				192
Q96J86 UniProt NPD GO	CYYR1_HUMAN	Cysteine and tyrosine-rich protein 1 precursor (Proline-rich domain-containing protein)	0.01	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]			154
Q5RLY7 UniProt NPD GO	CDO_AJECA	Cysteine dioxygenase (EC 1.13.11.20) (CDO)	0.01	-	nuc	0					213
O24385 UniProt NPD GO	CPI7_SOLTU	Cysteine protease inhibitor 7 (PCPI-7) (Pcpi7) (Fragment)	0.01	-	mit	0	Vacuole (By similarity)				178
P33403 UniProt NPD GO	CYSP_TRIFO	Cysteine proteinase (EC 3.4.22.-) (Fragment)	0.01	-	nuc	0					23
Q10717 UniProt NPD GO	CYSP2_MAIZE	Cysteine proteinase 2 precursor (EC 3.4.22.-)	0.01	-	mit	0	Vacuole (Probable)				360
P36184 UniProt NPD GO	ACP1_ENTHI	Cysteine proteinase ACP1 precursor (EC 3.4.22.-)	0.01	-	end	0	Secreted protein; extracellular space				308
P20907 UniProt NPD GO	CYT2_ORYSA	Cysteine proteinase inhibitor 2 (Oryzacystatin-2) (Oryzacystatin II)	0.01	-	cyt	0					108
O81154 UniProt NPD GO	CYSK_SOLTU	Cysteine synthase (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserine (Thiol)-lyase) (CSase ...	0.01	-	mit	0	Cytoplasm (By similarity)				325
Q9XEA8 UniProt NPD GO	CYSK2_ORYSA	Cysteine synthase (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserine (Thiol)-lyase) (CSase ...	0.01	-	nuc	0	Cytoplasm (By similarity)				325
P80608 UniProt NPD GO	CYSK_MAIZE	Cysteine synthase (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserine (Thiol)-lyase) (CSase ...	0.01	-	cyt	0	Cytoplasm (By similarity)				325
O23733 UniProt NPD GO	CYSK1_BRAJU	Cysteine synthase (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserine (Thiol)-lyase) (CSase ...	0.01	-	cyt	0	Cytoplasm (By similarity)				322
O23735 UniProt NPD GO	CYSK2_BRAJU	Cysteine synthase (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserine (Thiol)-lyase) (CSase ...	0.01	-	cyt	0	Cytoplasm (By similarity)				324
O59701 UniProt NPD GO	CYSK1_SCHPO	Cysteine synthase 1 (EC 2.5.1.47) (O-acetylserine sulfhydrylase 1) (O-acetylserine (Thiol)-lyase 1) ...	0.01	-	mit	0					351
P32260 UniProt NPD GO	CYSKP_SPIOL	Cysteine synthase, chloroplast precursor (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserin ...	0.01	-	cyt	0	Plastid; chloroplast; chloroplast stroma. Plastid; chromoplast				383
P67966 UniProt NPD GO	CSRP1_CHICK	Cysteine-rich protein 1 (CRP1) (CRP)	0.01	-	nuc	0	Cytoplasm. Cytoskeleton. Associates with the actin cytoskeleton			1CTL	191
P67967 UniProt NPD GO	CSRP1_COTJA	Cysteine-rich protein 1 (CRP1) (CRP)	0.01	-	nuc	0	Cytoplasm (By similarity). Associates with the actin cytoskeleton (By similarity)				191
Q5R7Y1 UniProt NPD GO	CRIP2_PONPY	Cysteine-rich protein 2	0.01	-	nuc	0					208
P52943 UniProt NPD GO	CRIP2_HUMAN	Cysteine-rich protein 2 (CRP2) (Protein ESP1)	0.01	-	nuc	0			601183	2CU8	208
P80055 UniProt NPD GO	CP2A7_PAPSP	Cytochrome P450 2A7 (EC 1.14.14.1) (CYPIIA7) (P450 FI) (Coumarin 7-hydroxylase) (Fragment)	0.01	-		1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				20
Q9LTM1 UniProt NPD GO	C71BM_ARATH	Cytochrome P450 71B22 (EC 1.14.-.-)	0.01	-	end	0					500
Q96242 UniProt NPD GO	CP74A_ARATH	Cytochrome P450 74A, chloroplast precursor (EC 4.2.1.92) (Allene oxide synthase) (Hydroperoxide dehy ...	0.01	-	mit	0	Plastid; chloroplast; chloroplast membrane (Potential)				518
Q7XYS3 UniProt NPD GO	C74A2_ORYSA	Cytochrome P450 74A2 (EC 4.2.1.92) (Allene oxide synthase 2) (Hydroperoxide dehydrase 2)	0.01	-	cyt	0					478
Q40778 UniProt NPD GO	C74A2_PARAR	Cytochrome P450 74A2 (EC 4.2.1.92) (Allene oxide synthase) (Rubber particle protein) (RPP)	0.01	-	mit	0	Rubber particle				473
O49858 UniProt NPD GO	C82A3_SOYBN	Cytochrome P450 82A3 (EC 1.14.-.-) (P450 CP6)	0.01	-	nuc	1 *					527
O49859 UniProt NPD GO	C82A4_SOYBN	Cytochrome P450 82A4 (EC 1.14.-.-) (P450 CP9)	0.01	-	nuc	1 *					525
P34033 UniProt NPD GO	CP2BX_CAVPO	Cytochrome P450IIB (EC 1.14.14.1) (Fragment)	0.01	-		1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				20
Q9G3M2 UniProt NPD GO	CYB_ACIPE	Cytochrome b	0.01	-	end	8 *					380
P11669 UniProt NPD GO	CYB_ACITR	Cytochrome b	0.01	-	end	8 *					380
P48517 UniProt NPD GO	CYB_AKOAE	Cytochrome b	0.01	-	end	9 *					379
P21714 UniProt NPD GO	CYB_AKOBO	Cytochrome b	0.01	-	end	9 *					379
Q5QFW5 UniProt NPD GO	CYB_AKOBU	Cytochrome b	0.01	-	end	9 *					379
P48518 UniProt NPD GO	CYB_AKOCU	Cytochrome b	0.01	-	end	9 *					379
Q5QFW4 UniProt NPD GO	CYB_AKOFU	Cytochrome b	0.01	-	end	9 *					379
P21716 UniProt NPD GO	CYB_AKOJU	Cytochrome b	0.01	-	end	9 *					379
P21717 UniProt NPD GO	CYB_AKOKO	Cytochrome b	0.01	-	end	9 *					379
P21723 UniProt NPD GO	CYB_AKOMI	Cytochrome b	0.01	-	end	9 *					379
P48519 UniProt NPD GO	CYB_AKOMO	Cytochrome b	0.01	-	end	9 *					379
P21718 UniProt NPD GO	CYB_AKOOR	Cytochrome b	0.01	-	end	9 *					379

You are viewing entries 87251 to 87300 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.