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
Q3BAK1 UniProt NPD GO	RR8_PHAAO	Chloroplast 30S ribosomal protein S8	0.45	-	nuc	0	Plastid; chloroplast				131
Q3C1L8 UniProt NPD GO	RK16_NICSY	Chloroplast 50S ribosomal protein L16	0.45	-	nuc	0	Plastid; chloroplast				134
P06384 UniProt NPD GO	RK16_TOBAC	Chloroplast 50S ribosomal protein L16	0.45	-	nuc	0	Plastid; chloroplast				134
Q95H50 UniProt NPD GO	RK16_WHEAT	Chloroplast 50S ribosomal protein L16	0.45	-	mit	0	Plastid; chloroplast				136
P56367 UniProt NPD GO	RK2_CHLVU	Chloroplast 50S ribosomal protein L2	0.45	+	mit	0	Plastid; chloroplast				275
Q85WY9 UniProt NPD GO	RK22_PINKO	Chloroplast 50S ribosomal protein L22	0.45	-	nuc	0	Plastid; chloroplast				142
Q7GUD1 UniProt NPD GO	RK33_PINKO	Chloroplast 50S ribosomal protein L33	0.45	-	nuc	0	Plastid; chloroplast				68
P41612 UniProt NPD GO	RK33_PINTH	Chloroplast 50S ribosomal protein L33	0.45	-	nuc	0	Plastid; chloroplast				67
P70031 UniProt NPD GO	CCKAR_XENLA	Cholecystokinin receptor (CCK-XLR)	0.45	-	end	7	Membrane; multi-pass membrane protein				453
P13222 UniProt NPD GO	CLAT_PIG	Choline O-acetyltransferase (EC 2.3.1.6) (CHOACTase) (Choline acetylase) (ChAT)	0.45	-	nuc	0					640
O70210 UniProt NPD GO	CHAD_RAT	Chondroadherin precursor (Cartilage leucine-rich protein)	0.45	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [TAS]			358
Q8VEA6 UniProt NPD GO	CRDL2_MOUSE	Chordin-like protein 2 precursor	0.45	-	nuc	0	Secreted protein (By similarity)				426
P01243 UniProt NPD GO	CSH_HUMAN	Chorionic somatomammotropin hormone precursor (Choriomammotropin) (Lactogen)	0.45	-	exc	0	Secreted protein		118820	1Z7C	217
P30385 UniProt NPD GO	1C02_GORGO	Class I histocompatibility antigen, GOGO-C0201 alpha chain precursor	0.45	-	end	1	Membrane; single-pass type I membrane protein				366
Q9W799 UniProt NPD GO	CPSF2_XENLA	Cleavage and polyadenylation specificity factor 100 kDa subunit (CPSF 100 kDa subunit)	0.45	-	cyt	0	Cytoplasm				783
Q8CC12 UniProt NPD GO	CDAN1_MOUSE	Codanin-1 (Fragment)	0.45	-	cyt	0					468
Q75CC1 UniProt NPD GO	COQ10_ASHGO	Coenzyme Q-binding protein COQ10, mitochondrial precursor	0.45	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side (By similarity ...				204
Q96BP2 UniProt NPD GO	CHCH1_HUMAN	Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 (C2360)	0.45	-	nuc	0	Nucleus		608842		118
Q8K2Q5 UniProt NPD GO	CHCH7_MOUSE	Coiled-coil-helix-coiled-coil-helix domain-containing protein 7	0.45	-	nuc	0					85
Q03380 UniProt NPD GO	COMI_DICDI	Comitin (CABP1-related protein p24) (24 kDa actin-binding protein)	0.45	-	nuc	0	Golgi apparatus; Golgi membrane; peripheral membrane protein. Intracellular membrane; peripheral mem ...				185
P79755 UniProt NPD GO	CO9_FUGRU	Complement component C9 precursor	0.45	-	exc	0	Secreted protein				586
Q95PA1 UniProt NPD GO	CPLX_LOLPE	Complexin (Synaphin)	0.45	-	nuc	0	Membrane; lipid-anchor (Potential). Cytoplasm; cytosol			1L4A	152
Q9CPW0 UniProt NPD GO	CNTP2_MOUSE	Contactin-associated protein-like 2 precursor (Cell recognition molecule Caspr2)	0.45	-	end	1	Membrane; single-pass type I membrane protein (Potential)				1332
Q8CCK0 UniProt NPD GO	H2AW_MOUSE	Core histone macro-H2A.2 (Histone macroH2A2) (mH2A2)	0.45	-	mit	0	Nucleus. Enriched in inactive X chromosome chromatin and in senescence-associated heterochromatin				371
Q8C0P5 UniProt NPD GO	COR2A_MOUSE	Coronin-2A	0.45	-	nuc	0					524
Q21624 UniProt NPD GO	CORO_CAEEL	Coronin-like protein cor-1	0.45	-	nuc	0					605
P07469 UniProt NPD GO	DEF1_RABIT	Corticostatin 1 precursor (Corticostatin I) (CS-I) (Neutrophil antibiotic peptide NP-3A) (Microbicid ...	0.45	-	exc	0	Secreted protein				93
P48136 UniProt NPD GO	RR11_CYAPA	Cyanelle 30S ribosomal protein S11	0.45	+	nuc	0	Plastid; cyanelle				130
P54230 UniProt NPD GO	BCTN1_SHEEP	Cyclic dodecapeptide precursor (Bactenecin-1) (Bac1) (Cathelicidin-1)	0.45	-	nuc	0	Secreted protein				155
Q24278 UniProt NPD GO	CNG_DROME	Cyclic nucleotide-gated cation channel (CNG channel)	0.45	+	end	4	Membrane; multi-pass membrane protein (Potential)	intracellular cyclic nucleotide activated c... [NAS]			665
Q9JJZ9 UniProt NPD GO	CNGB3_MOUSE	Cyclic nucleotide-gated cation channel beta 3 (CNG channel beta 3) (Cyclic nucleotide-gated channel ...	0.45	-	nuc	4	Membrane; multi-pass membrane protein	photoreceptor outer segment [IDA] plasma membrane [IC]			694
O75909 UniProt NPD GO	CCNK_HUMAN	Cyclin-K	0.45	-	nuc	0			603544		357
Q16667 UniProt NPD GO	CDKN3_HUMAN	Cyclin-dependent kinase inhibitor 3 (EC 3.1.3.48) (EC 3.1.3.16) (CDK2-associated dual-specificity ph ...	0.45	-	nuc	0			114550	1FQ1	212
P20486 UniProt NPD GO	CKS1_YEAST	Cyclin-dependent kinases regulatory subunit (Cell division control protein CKS1)	0.45	-	nuc	0		cytoplasm [IDA] nucleus [IDA]		1QB3	150
Q68FJ9 UniProt NPD GO	ATG4D_XENLA	Cysteine protease ATG4D (EC 3.4.22.-) (Autophagy-related protein 4 homolog D)	0.45	-	nuc	0	Cytoplasm (Probable)				469
Q64408 UniProt NPD GO	C11B1_CAVPO	Cytochrome P450 11B1, mitochondrial precursor (EC 1.14.15.4) (CYPXIB1) (P450C11) (Steroid 11-beta-hy ...	0.45	-	mit	0	Mitochondrion				500
Q64391 UniProt NPD GO	CP1A2_CAVPO	Cytochrome P450 1A2 (EC 1.14.14.1) (CYPIA2)	0.45	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				515
P79739 UniProt NPD GO	CP26A_BRARE	Cytochrome P450 26A1 (EC 1.14.-.-) (Retinoic acid-metabolizing cytochrome) (P450RAI) (Retinoic acid ...	0.45	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				492
Q9NGX9 UniProt NPD GO	CP302_DROME	Cytochrome P450 302a1, mitochondrial precursor (EC 1.14.99.-) (Disembodied protein)	0.45	-	mit	0	Mitochondrion	mitochondrion [IDA]			489
Q964T1 UniProt NPD GO	CP4CU_BLAGE	Cytochrome P450 4c21 (EC 1.14.14.1) (CYPIVC21)	0.45	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				501
O46420 UniProt NPD GO	CP51A_PIG	Cytochrome P450 51A1 (EC 1.14.13.70) (CYPLI) (P450LI) (Sterol 14-alpha demethylase) (Lanosterol 14-a ...	0.45	-	end	1 *	Microsome (Potential)				503
Q16850 UniProt NPD GO	CP51A_HUMAN	Cytochrome P450 51A1 (EC 1.14.13.70) (CYPLI) (P450LI) (Sterol 14-alpha demethylase) (Lanosterol 14-a ...	0.45	-	mit	1 *	Microsome (Potential)		601637		503
P30609 UniProt NPD GO	CP52G_CANTR	Cytochrome P450 52A7 (EC 1.14.14.-) (CYPLIIA7) (Alkane-inducible P450-ALK4)	0.45	+	cyt	1 *					507
P93147 UniProt NPD GO	C81E1_GLYEC	Cytochrome P450 81E1 (EC 1.14.13.89) (Isoflavone 2'-hydroxylase) (P450 91A4) (CYP GE-3)	0.45	-	end	1 *					499
Q94BV4 UniProt NPD GO	RH6_ARATH	DEAD-box ATP-dependent RNA helicase 6 (EC 3.6.1.-)	0.45	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				528
O13807 UniProt NPD GO	DDB1_SCHPO	DNA damage-binding protein 1 (Damage-specific DNA-binding protein 1)	0.45	-	end	0	Nucleus (By similarity)	Cul4B-RING ubiquitin ligase complex [IPI] nucleolus [IDA] nucleus [IDA]			1072
P25847 UniProt NPD GO	MSH2_YEAST	DNA mismatch repair protein MSH2	0.45	-	mit	0	Nucleus (Probable)	nuclear chromosome [IDA]			964
Q6CJD7 UniProt NPD GO	DPB4_KLULA	DNA polymerase epsilon subunit D (EC 2.7.7.7) (DNA polymerase II subunit D)	0.45	-	nuc	0	Nucleus (By similarity)				216
Q9CWP8 UniProt NPD GO	DPOD4_MOUSE	DNA polymerase subunit delta 4 (DNA polymerase subunit delta p12)	0.45	-	nuc	0	Nucleus (By similarity)				107
Q8GXF0 UniProt NPD GO	RA51C_ARATH	DNA repair protein RAD51 homolog 3 (DNA repair-recombination protein RAD51C) (AtRAD51C)	0.45	-	nuc	0	Nucleus (Probable)				363

You are viewing entries 28201 to 28250 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.