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
P82158 UniProt NPD GO	ALL7_CYDPO	Cydiastatin-7	0.00	-		0	Secreted protein				7
P56567 UniProt NPD GO	CYTA_MOUSE	Cystatin A (Stefin A)	0.00	-	cyt	0	Cytoplasm (By similarity)				97
P01040 UniProt NPD GO	CYTA_HUMAN	Cystatin A (Stefin A) (Cystatin AS)	0.00	-	cyt	0	Cytoplasm	cornified envelope [IDA]	184600	1NB5	98
Q28988 UniProt NPD GO	CYTA1_PIG	Cystatin A1 (Stefin A1)	0.00	-	cyt	0	Cytoplasm				103
P19313 UniProt NPD GO	CYTS_RAT	Cystatin S precursor (LM protein)	0.00	-	vac	0					141
P19864 UniProt NPD GO	CYT3_WISFL	Cystatin WCPI-3 (Fragments)	0.00	-	cyt	0					46
P23779 UniProt NPD GO	CYTL_DROME	Cystatin-like protein	0.00	-	exc	0					126
P20347 UniProt NPD GO	CPI1_SOLTU	Cysteine protease inhibitor 1 precursor (PCPI 8.3) (P340) (P34021)	0.00	-	cyt	0	Vacuole (By similarity)				222
O24383 UniProt NPD GO	CPI10_SOLTU	Cysteine protease inhibitor 10 precursor (PCPI-10) (Pcpi10) (Fragment)	0.00	-	cyt	0	Vacuole (By similarity)				186
O24388 UniProt NPD GO	CPI3_SOLTU	Cysteine protease inhibitor 3 (PCPI-3) (Pcpi3) (Fragment)	0.00	-	cyt	0	Vacuole (By similarity)				146
O24387 UniProt NPD GO	CPI5_SOLTU	Cysteine protease inhibitor 5 (PCPI-5) (Pcpi5) (Fragment)	0.00	-	cyt	0	Vacuole (By similarity)				151
O24386 UniProt NPD GO	CPI6_SOLTU	Cysteine protease inhibitor 6 (PCPI-6) (Pcpi6) (Fragment)	0.00	-	nuc	0	Vacuole (By similarity)				140
O24384 UniProt NPD GO	CPI8_SOLTU	Cysteine protease inhibitor 8 precursor (PCPI-8) (Pcpi8) (Fragment)	0.00	-	cyt	0	Vacuole (By similarity)				221
Q00652 UniProt NPD GO	CPI9_SOLTU	Cysteine protease inhibitor 9 precursor (PKIX) (pT1)	0.00	-	cyt	0	Vacuole (By similarity)				222
Q03196 UniProt NPD GO	CYT_SOLTU	Cysteine proteinase inhibitor (Fragment)	0.00	-	cyt	0					66
P09229 UniProt NPD GO	CYT1_ORYSA	Cysteine proteinase inhibitor 1 (Oryzacystatin-1) (Oryzacystatin I)	0.00	-	cyt	0				1EQK	102
P47998 UniProt NPD GO	CYSK1_ARATH	Cysteine synthase (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserine (Thiol)-lyase) (CSase ...	0.00	-	cyt	0	Cytoplasm (By similarity)			1Z7Y	322
P38076 UniProt NPD GO	CYSK_WHEAT	Cysteine synthase (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserine (Thiol)-lyase) (CSase ...	0.00	-	cyt	0	Cytoplasm (By similarity)				325
Q9XEA6 UniProt NPD GO	CYSK1_ORYSA	Cysteine synthase (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserine (Thiol)-lyase) (CSase ...	0.00	-	cyt	0	Cytoplasm (By similarity)				321
O81155 UniProt NPD GO	CYSKP_SOLTU	Cysteine synthase, chloroplast precursor (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserin ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast stroma (By similarity). Plastid; chromoplast (By similarity)				386
P69241 UniProt NPD GO	AFP1_RAPSA	Cysteine-rich antifungal protein 1 precursor (AFP1)	0.00	-	vac	1 *	Secreted protein				80
P30224 UniProt NPD GO	AFP1_ARATH	Cysteine-rich antifungal protein 1 precursor (AFP1) (Anther-specific protein S18 homolog) (Low-molec ...	0.00	-	cyt	1 *	Secreted protein				80
P30230 UniProt NPD GO	AFP2_RAPSA	Cysteine-rich antifungal protein 2 precursor (AFP2)	0.00	-	exc	1 *	Secreted protein				80
Q39313 UniProt NPD GO	AFP3_BRANA	Cysteine-rich antifungal protein 3 precursor (AFP3)	0.00	-	vac	1 *	Secreted protein				79
O24332 UniProt NPD GO	AFP3_RAPSA	Cysteine-rich antifungal protein 3 precursor (AFP3)	0.00	-	exc	1 *	Secreted protein				79
O24331 UniProt NPD GO	AFP4_RAPSA	Cysteine-rich antifungal protein 4 precursor (AFP4)	0.00	-	vac	1 *	Secreted protein				80
Q5G8B7 UniProt NPD GO	CYSPE_TITCO	Cysteine-rich peptide clone 2 precursor	0.00	-	mit	1 *	Secreted protein				63
Q06549 UniProt NPD GO	CDD_YEAST	Cytidine deaminase (EC 3.5.4.5) (Cytidine aminohydrolase) (CDA)	0.00	-	nuc	0		cytoplasm [IDA] nucleus [IDA]		1R5T	142
P81063 UniProt NPD GO	CYTA_THETS	Cytin chain A	0.00	-	cyt	0					43
P81064 UniProt NPD GO	CYTB_THETS	Cytin chain B	0.00	-	cyt	0					22
P80056 UniProt NPD GO	CP3A5_PAPSP	Cytochrome P450 3A5 (EC 1.14.14.1) (CYPIIIA5) (P450 FA) (6-beta-testosterone hydroxylase) (Fragment) ...	0.00	-		0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				20
Q9LTM2 UniProt NPD GO	C71BL_ARATH	Cytochrome P450 71B21 (EC 1.14.-.-)	0.00	-	end	0					499
Q37378 UniProt NPD GO	CYB_ACACA	Cytochrome b	0.00	-	end	9 *					385
Q71RU1 UniProt NPD GO	CYB_ACIJB	Cytochrome b	0.00	-	end	9 *					379
O78773 UniProt NPD GO	CYB_ADDNA	Cytochrome b	0.00	-	end	9 *					379
Q9T9A5 UniProt NPD GO	CYB_AEPME	Cytochrome b	0.00	-	end	9 *					379
Q33784 UniProt NPD GO	CYB_AILME	Cytochrome b	0.00	-	end	9 *					379
O47922 UniProt NPD GO	CYB_ALCAA	Cytochrome b	0.00	-	end	9 *					379
O78742 UniProt NPD GO	CYB_ALCBU	Cytochrome b	0.00	-	end	9 *					379
O99257 UniProt NPD GO	CYB_ALCLI	Cytochrome b	0.00	-	end	9 *					379
Q37395 UniProt NPD GO	CYB_ALLMA	Cytochrome b	0.00	-	end	10 *					382
Q9TF30 UniProt NPD GO	CYB_AMMHA	Cytochrome b	0.00	-	end	9 *					379
O78781 UniProt NPD GO	CYB_AMMLE	Cytochrome b	0.00	-	end	9 *					379
Q33645 UniProt NPD GO	CYB_ANGAN	Cytochrome b	0.00	-	end	9 *					379
O99240 UniProt NPD GO	CYB_ANGDI	Cytochrome b	0.00	-	end	9 *					379
P68533 UniProt NPD GO	CYB_ANGIN	Cytochrome b	0.00	-	end	9 *					379
P68534 UniProt NPD GO	CYB_ANGMA	Cytochrome b	0.00	-	end	9 *					379
Q33772 UniProt NPD GO	CYB_ANGMO	Cytochrome b	0.00	-	end	9 *					379
Q33842 UniProt NPD GO	CYB_ANGRE	Cytochrome b	0.00	-	end	9 *					379
P34861 UniProt NPD GO	CYB_ANGRO	Cytochrome b	0.00	-	end	9 *					379

You are viewing entries 93301 to 93350 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.