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
Q8MLZ7 UniProt NPD GO	IDGF3_DROME	Chitinase-like protein Idgf3 precursor (Imaginal disk growth factor protein 3)	0.48	-	cyt	0	Secreted protein. Secreted in hemolymph. It is probably transported to target tissues via hemolymph	extracellular region [NAS]			441
P51286 UniProt NPD GO	RR10_PORPU	Chloroplast 30S ribosomal protein S10	0.48	-	nuc	0	Plastid; chloroplast				105
Q7YKX3 UniProt NPD GO	RR11_CHLRE	Chloroplast 30S ribosomal protein S11	0.48	-	mit	0	Plastid; chloroplast				130
P06364 UniProt NPD GO	RR11_MARPO	Chloroplast 30S ribosomal protein S11	0.48	-	nuc	0	Plastid; chloroplast				130
Q85FM1 UniProt NPD GO	RR14_ADICA	Chloroplast 30S ribosomal protein S14	0.48	-	nuc	0	Plastid; chloroplast				100
Q85FL8 UniProt NPD GO	RR4_ADICA	Chloroplast 30S ribosomal protein S4	0.48	-	nuc	0	Plastid; chloroplast				197
Q8S8X2 UniProt NPD GO	RR4_ATRBE	Chloroplast 30S ribosomal protein S4	0.48	-	mit	0	Plastid; chloroplast				201
P59143 UniProt NPD GO	RR4_HYPDI	Chloroplast 30S ribosomal protein S4	0.48	-	mit	0	Plastid; chloroplast				202
Q3C1H5 UniProt NPD GO	RR4_NICSY	Chloroplast 30S ribosomal protein S4	0.48	-	mit	0	Plastid; chloroplast				201
Q33C33 UniProt NPD GO	RR4_NICTO	Chloroplast 30S ribosomal protein S4	0.48	-	mit	0	Plastid; chloroplast				201
P06359 UniProt NPD GO	RR4_TOBAC	Chloroplast 30S ribosomal protein S4	0.48	-	mit	0	Plastid; chloroplast				201
P36456 UniProt NPD GO	RR4_ELEIN	Chloroplast 30S ribosomal protein S4 (Fragment)	0.48	-	mit	0	Plastid; chloroplast				196
Q9GE26 UniProt NPD GO	RR7_AMBTC	Chloroplast 30S ribosomal protein S7	0.48	-	nuc	0	Plastid; chloroplast				155
Q9GFN2 UniProt NPD GO	RR7_ASACA	Chloroplast 30S ribosomal protein S7	0.48	-	nuc	0	Plastid; chloroplast				155
Q6KGY2 UniProt NPD GO	RR7_GUNCH	Chloroplast 30S ribosomal protein S7	0.48	-	nuc	0	Plastid; chloroplast				155
Q6EM62 UniProt NPD GO	RR7_SARHE	Chloroplast 30S ribosomal protein S7	0.48	-	nuc	0	Plastid; chloroplast				155
Q6KGV8 UniProt NPD GO	RR7_SPAWA	Chloroplast 30S ribosomal protein S7	0.48	-	nuc	0	Plastid; chloroplast				155
Q27972 UniProt NPD GO	CHAD_BOVIN	Chondroadherin precursor (Cartilage leucine-rich protein) (38 kDa bone protein) [Contains: Chondroad ...	0.48	-	exc	0	Secreted protein; extracellular space; extracellular matrix				361
P19159 UniProt NPD GO	CSH2_BOVIN	Chorionic somatomammotropin hormone 2 precursor (Placental lactogen II) (BPLP-II)	0.48	-	nuc	0	Secreted protein				238
O97507 UniProt NPD GO	FA12_PIG	Coagulation factor XII precursor (EC 3.4.21.38) (Hageman factor) (HAF) [Contains: Coagulation factor ...	0.48	-	exc	0	Secreted protein				616
Q9UUF7 UniProt NPD GO	COPB_SCHPO	Coatomer subunit beta (Beta-coat protein) (Beta-COP)	0.48	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				940
Q9Y2R0 UniProt NPD GO	CCD56_HUMAN	Coiled-coil domain-containing protein 56	0.48	-	nuc	1					106
P83436 UniProt NPD GO	COG7_HUMAN	Conserved oligomeric Golgi complex component 7	0.48	-	cyt	0	Golgi apparatus		608779		770
O13881 UniProt NPD GO	CLR2_SCHPO	Cryptic loci regulator 2	0.48	-	nuc	0	Nucleus (Potential)				537
P48128 UniProt NPD GO	RK21_CYAPA	Cyanelle 50S ribosomal protein L21	0.48	-	cyt	0	Plastid; cyanelle				104
P35190 UniProt NPD GO	CLG1_YEAST	Cyclin-like protein CLG1	0.48	-	nuc	0		cyclin-dependent protein kinase holoenzyme ... [TAS]			452
Q5XH30 UniProt NPD GO	ATG4C_XENLA	Cysteine protease ATG4C (EC 3.4.22.-) (Autophagy-related protein 4 homolog C)	0.48	-	cyt	0	Cytoplasm (Probable)				450
Q06367 UniProt NPD GO	CP1A1_CAVPO	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.48	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				516
P56590 UniProt NPD GO	CP1A1_CANFA	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1) (DAH1)	0.48	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				524
O77809 UniProt NPD GO	CP1A2_MACFA	Cytochrome P450 1A2 (EC 1.14.14.1) (CYPIA2)	0.48	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				515
Q16678 UniProt NPD GO	CP1B1_HUMAN	Cytochrome P450 1B1 (EC 1.14.14.1) (CYPIB1)	0.48	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		604229		543
Q9VUF8 UniProt NPD GO	CP314_DROME	Cytochrome P450 314a1, mitochondrial precursor (EC 1.14.99.22) (CYPCCCXIVA1) (Ecdysone 20-monooxygen ...	0.48	-	end	0	Mitochondrion	mitochondrion [IDA]			540
P08516 UniProt NPD GO	CP4AA_RAT	Cytochrome P450 4A10 (EC 1.14.15.3) (CYPIVA10) (Lauric acid omega-hydroxylase) (P450-LA-omega 1) (P4 ...	0.48	+	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				509
P78329 UniProt NPD GO	CP4F2_HUMAN	Cytochrome P450 4F2 (EC 1.14.13.30) (CYPIVF2) (Leukotriene-B(4) omega-hydroxylase) (Leukotriene-B(4) ...	0.48	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		604426		520
O18596 UniProt NPD GO	C4D10_DROMT	Cytochrome P450 4d10 (EC 1.14.-.-) (CYPIVD10)	0.48	+	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				513
O64989 UniProt NPD GO	C90B1_ARATH	Cytochrome P450 90B1 (EC 1.14.-.-) (Steroid 22-alpha-hydroxylase) (Dwarf4) (Dwarf protein 4)	0.48	-	end	1 *	Membrane; single-pass membrane protein (Potential)				513
P34902 UniProt NPD GO	IL2RG_MOUSE	Cytokine receptor common gamma chain precursor (Gamma-C) (Interleukin-2 receptor gamma chain) (IL-2R ...	0.48	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			369
O73810 UniProt NPD GO	DRD2_MELGA	D(2) dopamine receptor (Dopamine D2 receptor)	0.48	-	end	7 *	Membrane; multi-pass membrane protein				436
Q03954 UniProt NPD GO	SPC19_YEAST	DASH complex subunit SPC19 (Outer kinetochore protein SPC19) (19 kDa spindle pole component protein) ...	0.48	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore	DASH complex [IDA] spindle microtubule [IDA] spindle pole body [IDA]			165
Q9HDZ6 UniProt NPD GO	DAM1_SCHPO	DASH complex subunit dam1 (Outer kinetochore protein dam1)	0.48	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore. Kinetochore association occurs onl ...	DASH complex [IDA] spindle pole body [IDA]			155
Q94BZ7 UniProt NPD GO	GYRBM_ARATH	DNA gyrase subunit B, mitochondrial precursor (EC 5.99.1.3)	0.48	-	mit	0	Mitochondrion	mitochondrion [IDA]			732
P49642 UniProt NPD GO	PRI1_HUMAN	DNA primase small subunit (EC 2.7.7.-) (DNA primase 49 kDa subunit) (p49)	0.48	-	cyt	0			176635		420
Q9V461 UniProt NPD GO	MCM6_DROME	DNA replication licensing factor Mcm6 (Minichromosome maintenance 6 protein) (DmMCM6)	0.48	-	cyt	0	Nucleus. Associated with chromatin during cell cycles	nucleus [IDA]			817
P50525 UniProt NPD GO	APN1_SCHPO	DNA-(apurinic or apyrimidinic site) lyase 1 (EC 4.2.99.18) (AP endonuclease 1) (Apurinic-apyrimidini ...	0.48	-	mit	0	Nucleus (By similarity)	mitochondrion [TAS]			342
P38420 UniProt NPD GO	RPB2_ARATH	DNA-directed RNA polymerase II 135 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 2)	0.48	-	cyt	0	Nucleus				1188
P92209 UniProt NPD GO	RPOA_AGRCR	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.48	-	cyt	0	Plastid; chloroplast				339
P92225 UniProt NPD GO	RPOA_CRIDE	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.48	-	cyt	0	Plastid; chloroplast				339
Q8MAI9 UniProt NPD GO	RPOA_ELYCL	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.48	-	cyt	0	Plastid; chloroplast				339
P93956 UniProt NPD GO	RPOA_FESSE	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.48	-	cyt	0	Plastid; chloroplast				339
Q7H6J2 UniProt NPD GO	RPOA_HORBU	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.48	-	cyt	0	Plastid; chloroplast				339

You are viewing entries 26151 to 26200 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.