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
Q6AYB3 UniProt NPD GO	ISY1_RAT	Pre-mRNA-splicing factor ISY1 homolog	0.43	-	cyt	0	Nucleus (Potential)				284
Q6C3L4 UniProt NPD GO	SLT11_YARLI	Pre-mRNA-splicing factor SLT11	0.43	-	nuc	0	Nucleus (By similarity)				356
Q6CUA3 UniProt NPD GO	SPP2_KLULA	Pre-mRNA-splicing factor SPP2	0.43	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				189
Q7SAK5 UniProt NPD GO	SYF1_NEUCR	Pre-mRNA-splicing factor syf-1	0.43	-	cyt	0	Nucleus (By similarity)				829
Q5BH69 UniProt NPD GO	SYF1_EMENI	Pre-mRNA-splicing factor syf1	0.43	-	cyt	0	Nucleus (By similarity)				851
Q99J87 UniProt NPD GO	LGP2_MOUSE	Probable ATP-dependent helicase LGP2 (EC 3.6.1.-) (Protein D11Lgp2)	0.43	-	cyt	0	Cytoplasm	cytoplasm [IDA]			678
O94468 UniProt NPD GO	MAG2_SCHPO	Probable DNA-3-methyladenine glycosylase 2 (EC 3.2.2.21) (3-methyladenine DNA glycosidase 2) (3MEA D ...	0.43	-	nuc	0					213
Q9D074 UniProt NPD GO	MGRN1_MOUSE	Probable E3 ubiquitin-protein ligase MGRN1 (EC 6.3.2.-) (Mahogunin ring finger protein 1)	0.43	-	nuc	0					532
O43194 UniProt NPD GO	GPR39_HUMAN	Probable G-protein coupled receptor 39	0.43	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602886		453
Q3UJF0 UniProt NPD GO	GPR55_MOUSE	Probable G-protein coupled receptor 55	0.43	-	end	7 *	Membrane; multi-pass membrane protein				328
Q9FHR7 UniProt NPD GO	WRK49_ARATH	Probable WRKY transcription factor 49 (WRKY DNA-binding protein 49)	0.43	-	nuc	0	Nucleus (Probable)				274
O14022 UniProt NPD GO	ATCY_SCHPO	Probable cation-transporting ATPase C29A4.19c (EC 3.6.3.-)	0.43	-	end	8	Membrane; multi-pass membrane protein				1096
O17403 UniProt NPD GO	CPSF2_CAEEL	Probable cleavage and polyadenylation specificity factor 100 kDa subunit (CPSF 100 kDa subunit)	0.43	+	cyt	0	Nucleus (Potential)				843
Q6CH28 UniProt NPD GO	ATG4_YARLI	Probable cysteine protease ATG4 (EC 3.4.22.-) (Autophagy-related protein 4)	0.43	-	cyt	0	Cytoplasm (By similarity)				545
Q9VMT6 UniProt NPD GO	C28D2_DROME	Probable cytochrome P450 28d2 (EC 1.14.-.-) (CYPXXVIIID2)	0.43	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				501
Q9W011 UniProt NPD GO	C4D20_DROME	Probable cytochrome P450 4d20 (EC 1.14.-.-) (CYPIVD20)	0.43	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				510
Q09660 UniProt NPD GO	CC44_CAEEL	Probable cytochrome P450 CYP44 (EC 1.14.-.-)	0.43	-	mit	0					489
Q9VWA2 UniProt NPD GO	DCTD_DROME	Probable deoxycytidylate deaminase (EC 3.5.4.12) (dCMP deaminase)	0.43	-	nuc	0					203
Q9XI77 UniProt NPD GO	FUT9_ARATH	Probable fucosyltransferase 9 (EC 2.4.1.-) (AtFUT9)	0.43	-	end	2 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				435
Q6CUV0 UniProt NPD GO	SPC25_KLULA	Probable kinetochore protein SPC25	0.43	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				227
Q5Y5T5 UniProt NPD GO	ZDHC8_MOUSE	Probable palmitoyltransferase ZDHHC8 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 8) (DH ...	0.43	-	mit	4 *	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein (By similarity)				762
Q9VLS1 UniProt NPD GO	KPBB_DROME	Probable phosphorylase b kinase regulatory subunit beta (Phosphorylase kinase subunit beta)	0.43	-	end	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				1093
Q9VCZ8 UniProt NPD GO	PFD5_DROME	Probable prefoldin subunit 5	0.43	-	nuc	0					168
Q9UTQ1 UniProt NPD GO	PDX3_SCHPO	Probable pyridoxamine 5'-phosphate oxidase (EC 1.4.3.5) (PNP/PMP oxidase) (PNPOx)	0.43	-	cyt	0					231
O61749 UniProt NPD GO	SRP19_CAEEL	Probable signal recognition particle 19 kDa protein (SRP19)	0.43	-	nuc	0	Cytoplasm (By similarity)				160
Q17440 UniProt NPD GO	TRMU_CAEEL	Probable tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (EC 2.1.1.61)	0.43	-	cyt	0					375
Q8GXB7 UniProt NPD GO	TRMB_ARATH	Probable tRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33) (tRNA(m7G46)-methyltransferase)	0.43	-	cyt	1					251
Q9M2V5 UniProt NPD GO	WBC18_ARATH	Probable white-brown complex homolog protein 18	0.43	-	end	7	Membrane; multi-pass membrane protein (By similarity)				708
Q61398 UniProt NPD GO	PCOC1_MOUSE	Procollagen C-endopeptidase enhancer 1 precursor (Procollagen COOH-terminal proteinase enhancer 1) ( ...	0.43	-	nuc	0	Secreted protein				468
Q9QZA2 UniProt NPD GO	PDC6I_RAT	Programmed cell death 6-interacting protein (ALG-2-interacting protein 1) (Fragment)	0.43	-	nuc	0	Cytoplasm; cytosol (By similarity)				401
P34181 UniProt NPD GO	PRL_CORAU	Prolactin precursor (PRL)	0.43	-	exc	0	Secreted protein				210
P09585 UniProt NPD GO	PRL_CYPCA	Prolactin precursor (PRL)	0.43	-	nuc	1 *	Secreted protein				210
Q3Y4G6 UniProt NPD GO	PRL_ISOMA	Prolactin precursor (PRL)	0.43	-	exc	0	Secreted protein				228
P55151 UniProt NPD GO	PRL_MACMU	Prolactin precursor (PRL)	0.43	-	exc	0	Secreted protein				227
P09318 UniProt NPD GO	PRL2_OREMO	Prolactin-2 precursor (Prolactin II) (PRL-177)	0.43	-	exc	1 *	Secreted protein				200
Q66HE1 UniProt NPD GO	PNRC2_RAT	Proline-rich nuclear receptor coactivator 2	0.43	-	nuc	0	Nucleus (Potential)				134
P05143 UniProt NPD GO	PMP3_MOUSE	Proline-rich protein MP-3 (Fragment)	0.43	-	nuc	0					296
Q9FIV6 UniProt NPD GO	DGP10_ARATH	Protease Do-like 10, mitochondrial precursor (EC 3.4.21.-)	0.43	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				586
O09029 UniProt NPD GO	BETA3_MESAU	Protein BETA3	0.43	-	exc	0	Nucleus (Potential)				367
Q8N2C9 UniProt NPD GO	CU128_HUMAN	Protein C21orf128	0.43	-	nuc	0					162
Q99M03 UniProt NPD GO	CU006_MOUSE	Protein C21orf6 homolog	0.43	-	cyt	0					290
Q5R9U9 UniProt NPD GO	CU006_PONPY	Protein C21orf6 homolog	0.43	-	cyt	0					319
Q9H8W2 UniProt NPD GO	CF155_HUMAN	Protein C6orf155	0.43	-	nuc	0					130
Q58EM4 UniProt NPD GO	CF211_BRARE	Protein C6orf211 homolog	0.43	-	cyt	0					448
Q9BTL3 UniProt NPD GO	F103A_HUMAN	Protein FAM103A1	0.43	-	nuc	0					118
Q6ZT52 UniProt NPD GO	FA43B_HUMAN	Protein FAM43B	0.43	-	nuc	0					329
O15037 UniProt NPD GO	K0323_HUMAN	Protein KIAA0323	0.43	-	cyt	0					678
Q5RB71 UniProt NPD GO	MTO1_PONPY	Protein MTO1 homolog, mitochondrial precursor	0.43	-	nuc	0	Mitochondrion (By similarity)				692
Q4WCG2 UniProt NPD GO	OS9_ASPFU	Protein OS-9 homolog precursor	0.43	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				520
Q9P258 UniProt NPD GO	RCC2_HUMAN	Protein RCC2 (Telophase disk protein of 60 kDa) (RCC1-like protein TD-60)	0.43	-	cyt	0	Nucleus; nucleolus. Appears in the nucleus at G2, then concentrates at the inner centromere region o ...		609587		522

You are viewing entries 29901 to 29950 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.