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
Q68EP9 UniProt NPD GO	ATG4C_XENTR	Cysteine protease ATG4C (EC 3.4.22.-) (Autophagy-related protein 4 homolog C)	0.30	-	cyt	0	Cytoplasm (Probable)				450
Q6Q6R3 UniProt NPD GO	CRIP3_MOUSE	Cysteine-rich protein 3 (CRP3) (Thymus LIM protein) (m17TLP)	0.30	-	nuc	0	Cytoplasm	cytoplasm [IDA]			243
Q8MJD0 UniProt NPD GO	CMAH_PANPA	Cytidine monophosphate-N-acetylneuraminic acid hydroxylase (EC 1.14.18.2) (CMP-N-acetylneuraminate m ...	0.30	-	cyt	0	Cytoplasm (By similarity)				600
Q2XVA1 UniProt NPD GO	CP17A_MACFA	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.30	-	end	0					508
Q8HYM9 UniProt NPD GO	CP17A_MACMU	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.30	-	end	0					508
P20812 UniProt NPD GO	CP2A3_RAT	Cytochrome P450 2A3 (EC 1.14.14.1) (CYPIIA3) (Coumarin 7-hydroxylase)	0.30	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				494
P11509 UniProt NPD GO	CP2A6_HUMAN	Cytochrome P450 2A6 (EC 1.14.14.1) (CYPIIA6) (Coumarin 7-hydroxylase) (P450 IIA3) (CYP2A3) (P450(I)) ...	0.30	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [TAS]	122720	1Z11	494
Q64458 UniProt NPD GO	CP2CT_MOUSE	Cytochrome P450 2C29 (EC 1.14.14.1) (CYPIIC29) (P-450 MUT-2) (Aldehyde oxygenase)	0.30	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
P20678 UniProt NPD GO	CP2H2_CHICK	Cytochrome P450 2H2 (EC 1.14.14.1) (CYPIIH2) (P450 PCHP7)	0.30	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				491
P15128 UniProt NPD GO	CP4B1_RABIT	Cytochrome P450 4B1 (EC 1.14.14.1) (CYPIVB1) (P450-isozyme 5)	0.30	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				506
Q27902 UniProt NPD GO	CP6B4_PAPGL	Cytochrome P450 6B4 (EC 1.14.14.1) (CYPVIB4) (CYP6B4V1/CYP6B4V2)	0.30	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				500
Q27698 UniProt NPD GO	CP6D1_MUSDO	Cytochrome P450 6d1 (EC 1.14.-.-) (CYPVID1) (Pyrethroid resistance cytochrome P450) (Cytochrome P450 ...	0.30	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				516
O48928 UniProt NPD GO	C77A3_SOYBN	Cytochrome P450 77A3 (EC 1.14.-.-)	0.30	-	end	1 *					513
Q940V4 UniProt NPD GO	C85A2_ARATH	Cytochrome P450 85A2 (EC 1.14.-.-) (Brassinosteroid-6-oxidase 2) (BR6ox 2) (C6-oxidase 2)	0.30	-	mit	1 *					465
O81117 UniProt NPD GO	C94A1_VICSA	Cytochrome P450 94A1 (EC 1.14.-.-) (P450-dependent fatty acid omega-hydroxylase)	0.30	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				514
Q6YFQ2 UniProt NPD GO	CX6B2_HUMAN	Cytochrome c oxidase subunit VIb isoform 2 (EC 1.9.3.1) (COX VIb-2) (Cytochrome c oxidase subunit VI ...	0.30	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)	mitochondrial crista [IDA]			88
Q96DZ5 UniProt NPD GO	CLR59_HUMAN	Cytoplasmic linker protein 170-related 59 kDa protein (CLIPR-59) (CLIP-170-related 59 kDa protein)	0.30	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi stack. Localized to Golgi stacks as well as on tubulovesicular ele ...		607382	2CP0	547
Q95137 UniProt NPD GO	DRD5_BOVIN	D(1B) dopamine receptor (D(5) dopamine receptor) (Fragment)	0.30	-	mit	2 *	Membrane; multi-pass membrane protein				174
Q5ZKU1 UniProt NPD GO	DCNL1_CHICK	DCN1-like protein 1 (Defective in cullin neddylation protein 1-like protein 1) (DCUN1 domain-contain ...	0.30	-	cyt	0					259
Q6PH85 UniProt NPD GO	DCNL2_HUMAN	DCN1-like protein 2 (Defective in cullin neddylation protein 1-like protein 2) (DCUN1 domain-contain ...	0.30	-	cyt	0					259
Q3EBD3 UniProt NPD GO	RH41_ARATH	DEAD-box ATP-dependent RNA helicase 41 (EC 3.6.1.-)	0.30	-	cyt	0					505
Q7Y1B6 UniProt NPD GO	GAI_LYCES	DELLA protein GAI (Gibberellic acid-insensitive mutant protein)	0.30	-	cyt	0	Nucleus (By similarity)				588
Q8GXW1 UniProt NPD GO	RGL2_ARATH	DELLA protein RGL2 (RGA-like protein 2) (Scarecrow-like protein 19)	0.30	-	cyt	0	Nucleus				547
P09804 UniProt NPD GO	DPO1_KLULA	DNA polymerase (EC 2.7.7.7)	0.30	-	nuc	0					995
P34778 UniProt NPD GO	RPOA_ASTLO	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.30	-	nuc	0	Plastid				220
Q6B8X4 UniProt NPD GO	RPOA_GRATL	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.30	-	cyt	0	Plastid; chloroplast				314
O98462 UniProt NPD GO	RPOA_SPIMX	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.30	-	cyt	0	Plastid; chloroplast				344
Q9N5K2 UniProt NPD GO	RPB5_CAEEL	DNA-directed RNA polymerases II 24 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 5)	0.30	-	cyt	0	Nucleus (By similarity)				211
Q682V0 UniProt NPD GO	XRCC4_ARATH	DNA-repair protein XRCC4	0.30	-	nuc	0	Nucleus (Probable)				264
Q9U3C8 UniProt NPD GO	DCN1_CAEEL	Defective in cullin neddylation protein 1	0.30	-	mit	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			295
P93835 UniProt NPD GO	DRE1B_ARATH	Dehydration-responsive element-binding protein 1B (DREB1B protein) (C-repeat-binding factor 1) (C-re ...	0.30	-	nuc	0	Nucleus (Probable)				213
Q9D7J6 UniProt NPD GO	DNSL1_MOUSE	Deoxyribonuclease I-like 1 precursor (EC 3.1.21.-) (DNase I-like 1)	0.30	-	mit	0	Endoplasmic reticulum (By similarity)				314
Q61495 UniProt NPD GO	DSG1A_MOUSE	Desmoglein-1 alpha precursor (Dsg1-alpha) (Desmoglein-1) (Desmosomal glycoprotein I) (DG1) (DGI)	0.30	-	end	0	Membrane; single-pass type I membrane protein (By similarity)	desmosome [IDA] plasma membrane [IDA]			1057
O75907 UniProt NPD GO	DGAT1_HUMAN	Diacylglycerol O-acyltransferase 1 (EC 2.3.1.20) (Diglyceride acyltransferase) (ACAT-related gene pr ...	0.30	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)		604900		488
O88673 UniProt NPD GO	DGKA_MOUSE	Diacylglycerol kinase alpha (EC 2.7.1.107) (Diglyceride kinase alpha) (DGK-alpha) (DAG kinase alpha) ...	0.30	-	cyt	0		cytosol [IDA] plasma membrane [IDA]			730
O62583 UniProt NPD GO	DYR_ENCCU	Dihydrofolate reductase (EC 1.5.1.3)	0.30	-	mit	0					205
Q6FKY3 UniProt NPD GO	DIM1_CANGA	Dimethyladenosine transferase (EC 2.1.1.-) (S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltra ...	0.30	-	cyt	0					317
Q5U2X4 UniProt NPD GO	DPEP3_RAT	Dipeptidase 3 precursor (EC 3.4.13.19)	0.30	-	mit	0	Membrane; lipid-anchor; GPI-anchor (By similarity)				488
O59713 UniProt NPD GO	DPH1_SCHPO	Diphthamide biosynthesis protein 1	0.30	-	nuc	0	Cytoplasm (By similarity)				436
P67800 UniProt NPD GO	DIUH_MUSDO	Diuretic hormone (DH) (Diuretic peptide) (DP)	0.30	-	nuc	0	Secreted protein				44
P67801 UniProt NPD GO	DIUH_STOCA	Diuretic hormone (DH) (Diuretic peptide) (DP)	0.30	-	nuc	0	Secreted protein				44
P21819 UniProt NPD GO	DIUH1_MANSE	Diuretic hormone 1 precursor (DH-1) (Diuretic peptide 1) (DP-1) (Mas-DH)	0.30	-	exc	0	Secreted protein				138
Q8WW22 UniProt NPD GO	DNJA4_HUMAN	DnaJ homolog subfamily A member 4	0.30	-	cyt	0	Membrane; lipid-anchor (Potential)				397
Q99KV1 UniProt NPD GO	DNJBB_MOUSE	DnaJ homolog subfamily B member 11 precursor	0.30	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	cytoplasm [IDA] nucleus [IDA]			358
Q9UBS4 UniProt NPD GO	DNJBB_HUMAN	DnaJ homolog subfamily B member 11 precursor (ER-associated dnaJ protein 3) (ErJ3) (ER-associated Hs ...	0.30	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [TAS]			358
O35723 UniProt NPD GO	DNJB3_MOUSE	DnaJ homolog subfamily B member 3 (DnaJ protein homolog 3) (Heat shock J3 protein) (HSJ-3) (MSJ-1)	0.30	-	cyt	0					242
Q8NHS0 UniProt NPD GO	DNJB8_HUMAN	DnaJ homolog subfamily B member 8	0.30	-	cyt	0					232
Q9QYI6 UniProt NPD GO	DNJB9_MOUSE	DnaJ homolog subfamily B member 9 (mDJ7)	0.30	-	mit	1 *	Cytoplasm (By similarity). Nucleus (By similarity). Stress induces its translocation to the nucleus ...				222
Q8TCJ2 UniProt NPD GO	STT3B_HUMAN	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B (EC 2.4.1.119) (Oligosa ...	0.30	+	end	10	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein		608605		826
Q24563 UniProt NPD GO	DOPR2_DROME	Dopamine receptor 2	0.30	-	end	7	Membrane; multi-pass membrane protein				539

You are viewing entries 40251 to 40300 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.