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
Q9MTQ0 UniProt NPD GO	RR16_OENHO	Chloroplast 30S ribosomal protein S16	0.09	-	mit	0	Plastid; chloroplast				88
P19170 UniProt NPD GO	RR19_EUGGR	Chloroplast 30S ribosomal protein S19	0.09	-	mit	0	Plastid; chloroplast				94
P56361 UniProt NPD GO	RR8_CHLVU	Chloroplast 30S ribosomal protein S8	0.09	-	nuc	0	Plastid; chloroplast				138
Q9TM00 UniProt NPD GO	RK1_CYACA	Chloroplast 50S ribosomal protein L1	0.09	-	nuc	0	Plastid; chloroplast				240
P49552 UniProt NPD GO	RK14_ODOSI	Chloroplast 50S ribosomal protein L14	0.09	-	cyt	0	Plastid; chloroplast				121
Q9TLU7 UniProt NPD GO	RK18_CYACA	Chloroplast 50S ribosomal protein L18	0.09	-	cyt	0	Plastid; chloroplast				105
O46905 UniProt NPD GO	RK24_GUITH	Chloroplast 50S ribosomal protein L24	0.09	-	nuc	0	Plastid; chloroplast				101
O46894 UniProt NPD GO	RK3_GUITH	Chloroplast 50S ribosomal protein L3	0.09	-	cyt	0	Plastid; chloroplast				204
P51314 UniProt NPD GO	RK3_PORPU	Chloroplast 50S ribosomal protein L3	0.09	-	cyt	0	Plastid; chloroplast				205
Q1XDH4 UniProt NPD GO	RK3_PORYE	Chloroplast 50S ribosomal protein L3	0.09	-	cyt	0	Plastid; chloroplast				205
Q8HTL1 UniProt NPD GO	RK5_CHLRE	Chloroplast 50S ribosomal protein L5	0.09	-	mit	0	Plastid; chloroplast				187
Q9MUU5 UniProt NPD GO	RK5_MESVI	Chloroplast 50S ribosomal protein L5	0.09	-	mit	0	Plastid; chloroplast				184
Q20F07 UniProt NPD GO	RK5_OLTVI	Chloroplast 50S ribosomal protein L5	0.09	-	cyt	0	Plastid; chloroplast				180
P49548 UniProt NPD GO	RK6_ODOSI	Chloroplast 50S ribosomal protein L6	0.09	-	mit	0	Plastid; chloroplast				179
P56783 UniProt NPD GO	CEMA_ARATH	Chloroplast envelope membrane protein	0.09	-	mit	3 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				229
Q6EW41 UniProt NPD GO	CEMA_NYMAL	Chloroplast envelope membrane protein	0.09	-	cyt	0	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				229
P20150 UniProt NPD GO	CEMA_PEA	Chloroplast envelope membrane protein (Heme-binding protein)	0.09	-	end	4 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein				231
P22687 UniProt NPD GO	CETP_RABIT	Cholesteryl ester transfer protein precursor (Lipid transfer protein I) (Fragment)	0.09	-	cyt	0	Secreted protein				497
Q8IWA5 UniProt NPD GO	CTL2_HUMAN	Choline transporter-like protein 2 (Solute carrier family 44 member 2)	0.09	-	end	11 *	Membrane; multi-pass membrane protein (By similarity)		606106		706
Q5R5L9 UniProt NPD GO	CTL2_PONPY	Choline transporter-like protein 2 (Solute carrier family 44 member 2)	0.09	-	end	11 *	Membrane; multi-pass membrane protein (By similarity)				711
Q810F1 UniProt NPD GO	CTL2_CAVPO	Choline transporter-like protein 2 (Solute carrier family 44 member 2) (Inner ear supporting cell an ...	0.09	-	end	10 *	Membrane; multi-pass membrane protein				705
Q6AY92 UniProt NPD GO	CTL3_RAT	Choline transporter-like protein 3 (Solute carrier family 44 member 3)	0.09	-	end	7	Membrane; multi-pass membrane protein (By similarity)				604
P07182 UniProt NPD GO	CH36_DROME	Chorion protein S36	0.09	-	nuc	0					284
P07183 UniProt NPD GO	CH38_DROME	Chorion protein S38	0.09	-	exc	0					306
P09586 UniProt NPD GO	CSH2_MOUSE	Chorionic somatomammotropin hormone 2 precursor (Placental lactogen II) (PL-II)	0.09	-	cyt	0	Secreted protein				222
Q12640 UniProt NPD GO	AROC_NEUCR	Chorismate synthase (EC 4.2.3.5) (5-enolpyruvylshikimate-3-phosphate phospholyase)	0.09	-	cyt	0					432
Q08955 UniProt NPD GO	CSM4_YEAST	Chromosome segregation in meiosis protein 4	0.09	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein	endoplasmic reticulum membrane [IDA]			156
P10832 UniProt NPD GO	ISC2_BOMMO	Chymotrypsin inhibitor SCI-II	0.09	-	nuc	0					62
P30359 UniProt NPD GO	CADH4_TOBAC	Cinnamyl alcohol dehydrogenase (EC 1.1.1.195) (CAD)	0.09	-	cyt	0					357
Q93XP7 UniProt NPD GO	CZOG1_MAIZE	Cis-zeatin O-glucosyltransferase 1 (EC 2.4.1.215) (cisZOG1)	0.09	-	mit	0					467
Q8RXA5 UniProt NPD GO	CZOG2_MAIZE	Cis-zeatin O-glucosyltransferase 2 (EC 2.4.1.215) (cisZOG2)	0.09	-	mit	0					463
P03997 UniProt NPD GO	COAG_CARRO	Coagulogen [Contains: Coagulin chain A; Peptide C; Coagulin chain B]	0.09	-	mit	0	Secreted protein				175
P54706 UniProt NPD GO	COFI_DICDI	Cofilin	0.09	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				137
P11149 UniProt NPD GO	COL_SQUAC	Colipase (Fragment)	0.09	-	nuc	0	Secreted protein				39
P18856 UniProt NPD GO	CAF1_EPHMU	Collagen EMF1-alpha precursor (Fibrillar collagen) (Fragment)	0.09	-	cyt	0	Secreted protein; extracellular space; extracellular matrix				547
Q00780 UniProt NPD GO	CO8A1_MOUSE	Collagen alpha-1(VIII) chain precursor	0.09	-	cyt	0				1O91	743
Q91145 UniProt NPD GO	COCA1_NOTVI	Collagen alpha-1(XII) chain (Fragment)	0.09	-	cyt	0					929
P98086 UniProt NPD GO	C1QA_MOUSE	Complement C1q subcomponent subunit A precursor	0.09	-	mit	0	Secreted protein				245
P31722 UniProt NPD GO	C1QC_RAT	Complement C1q subcomponent subunit C precursor	0.09	-	exc	0	Secreted protein				245
P58923 UniProt NPD GO	CX7A_CONTU	Conotoxin TVIIA	0.09	-	nuc	0	Secreted protein			1EYO	30
Q5K0D7 UniProt NPD GO	CXO3_CONST	Conotoxin-3 precursor	0.09	-	exc	1 *	Secreted protein (By similarity)				72
Q9VF71 UniProt NPD GO	CUTC_DROME	Copper homeostasis protein cutC homolog	0.09	-	cyt	0					263
O62772 UniProt NPD GO	CRFR1_SHEEP	Corticotropin-releasing factor receptor 1 precursor (CRF-R) (CRF1) (Corticotropin-releasing hormone ...	0.09	-	end	7	Membrane; multi-pass membrane protein				415
P05122 UniProt NPD GO	KCRB_CHICK	Creatine kinase B-type (EC 2.7.3.2) (Creatine kinase B chain) (B-CK)	0.09	-	nuc	0	Cytoplasm			1QH4	381
P52753 UniProt NPD GO	CRYP_CRYPA	Cryparin precursor	0.09	-	nuc	0	Cell wall. Cell wall of aerial hyphae and sporulation structures. Secreted protein. Abundantly secre ...				118
P21837 UniProt NPD GO	CRYS_DICDI	Crystal protein precursor	0.09	-	mit	0	Membrane. Membrane-enclosed crystals (esterosome)				550
P83356 UniProt NPD GO	CU16B_LIMPO	Cuticle protein 16 isoform b (LpCP16b) (Fragment)	0.09	-	cyt	0					70
P29138 UniProt NPD GO	CUDP_METAN	Cuticle-degrading protease precursor (EC 3.4.21.-) (PR1) (Chymoelastase)	0.09	-	exc	0	Secreted protein				388
P48140 UniProt NPD GO	RR20_CYAPA	Cyanelle 30S ribosomal protein S20	0.09	-	nuc	0	Plastid; cyanelle				95
P42771 UniProt NPD GO	CD2A1_HUMAN	Cyclin-dependent kinase inhibitor 2A, isoforms 1/2/3 (Cyclin-dependent kinase 4 inhibitor A) (CDK4I) ...	0.09	-	cyt	0			151623	2A5E	156

You are viewing entries 65901 to 65950 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.