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
Q9ST43 UniProt NPD GO	PH1_ARATH	Pleckstrin homology domain-containing protein 1 (AtPH1)	0.15	-	cyt	0	Cytoplasm (Probable)				145
P57724 UniProt NPD GO	PCBP4_MOUSE	Poly(rC)-binding protein 4 (Alpha-CP4)	0.15	-	nuc	0	Cytoplasm (By similarity)				403
Q9P0L9 UniProt NPD GO	PK2L1_HUMAN	Polycystic kidney disease 2-like 1 protein (Polycystin-L) (Polycystin-2 homolog)	0.15	-	end	5	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]	604532		805
Q91Z22 UniProt NPD GO	PORIM_MOUSE	Porimin precursor (Transmembrane protein 123)	0.15	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				195
P19356 UniProt NPD GO	HEM3_RAT	Porphobilinogen deaminase (EC 2.5.1.61) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyrinogen ...	0.15	-	cyt	0					361
Q6XLL9 UniProt NPD GO	KAX66_OPICA	Potassium channel toxin alpha-KTx 6.6 precursor (OcKTx1)	0.15	-	exc	0	Secreted protein (By similarity)				61
P55928 UniProt NPD GO	KAX72_PANIM	Potassium channel toxin alpha-KTx 7.2 (Toxin PiTX-K-beta) (Pandinotoxin-beta) (Potassium channel-blo ...	0.15	-	nuc	0	Secreted protein			1C49	35
O22881 UniProt NPD GO	POT2_ARATH	Potassium transporter 2 (AtPOT2) (AtKUP2) (AtKT2)	0.15	-	end	12 *	Cell membrane; multi-pass membrane protein (Potential)				794
Q9WU28 UniProt NPD GO	PFD5_MOUSE	Prefoldin subunit 5 (C-myc-binding protein Mm-1) (Myc modulator 1) (EIG-1)	0.15	-	cyt	0					154
Q9TLS1 UniProt NPD GO	PREA_CYACA	Prenyl transferase (EC 2.5.1.-)	0.15	-	nuc	0	Plastid; chloroplast				323
P05222 UniProt NPD GO	CAER1_XENLA	Preprocaerulein type-1 precursor (Preprocaerulein type I) [Contains: Caerulein]	0.15	-	exc	0	Secreted protein				188
P93690 UniProt NPD GO	SECY_SPIOL	Preprotein translocase secY subunit, chloroplast precursor (CpSecY)	0.15	-	end	7	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				545
Q9H300 UniProt NPD GO	PARL_HUMAN	Presenilins-associated rhomboid-like protein, mitochondrial precursor (EC 3.4.21.105) (Mitochondrial ...	0.15	-	nuc	6	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein. Mitochondrion; mitochondri ...		607858		379
P58743 UniProt NPD GO	S26A5_HUMAN	Prestin (Solute carrier family 26 member 5)	0.15	-	end	10	Integral membrane protein; lateral wall of outer hair cells (By similarity)		604943		744
P19713 UniProt NPD GO	MCH1_ONCKE	Pro-MCH 1 precursor [Contains: Neuropeptide-glutamic acid-valine (NEV) (Neuropeptide E-V); Melanin-c ...	0.15	-	mit	0					132
P41938 UniProt NPD GO	HCDH2_CAEEL	Probable 3-hydroxyacyl-CoA dehydrogenase B0272.3 (EC 1.1.1.35)	0.15	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				309
Q9UT19 UniProt NPD GO	METE_SCHPO	Probable 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) (Methio ...	0.15	-	nuc	0					764
Q9Y7M7 UniProt NPD GO	YNT9_SCHPO	Probable ATP-dependent permease C9B6.09c	0.15	-	mit	5	Membrane; multi-pass membrane protein (Potential)				726
Q4XS21 UniProt NPD GO	RPO2J_PLACH	Probable DNA-directed RNA polymerase II subunit J (EC 2.7.7.6)	0.15	-	nuc	0	Nucleus (By similarity)				126
Q9VD25 UniProt NPD GO	RPO3F_DROME	Probable DNA-directed RNA polymerase III subunit F (EC 2.7.7.6) (DNA-directed RNA polymerase III 39 ...	0.15	-	cyt	0	Nucleus (Potential)				293
Q5T447 UniProt NPD GO	HECD3_HUMAN	Probable E3 ubiquitin-protein ligase HECTD3 (HECT domain-containing protein 3)	0.15	-	cyt	0					861
Q6QNK2 UniProt NPD GO	GP133_HUMAN	Probable G-protein coupled receptor 133 precursor (G-protein coupled receptor PGR25)	0.15	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS]			874
Q3U507 UniProt NPD GO	GP174_MOUSE	Probable G-protein coupled receptor 174	0.15	-	end	7 *	Membrane; multi-pass membrane protein				335
O16294 UniProt NPD GO	GMPR_CAEEL	Probable GMP reductase (EC 1.7.1.7) (Guanosine 5'-monophosphate oxidoreductase) (Guanosine monophosp ...	0.15	-	cyt	0					358
Q9V6L0 UniProt NPD GO	JHD3B_DROME	Probable JmjC domain-containing histone demethylation protein 3B (EC 1.14.11.-)	0.15	-	cyt	0	Nucleus (By similarity)	nucleus [ISS]			452
Q09840 UniProt NPD GO	AMY1_SCHPO	Probable alpha-amylase C23D3.14c precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.15	-	exc	1 *					581
Q10454 UniProt NPD GO	KARG1_CAEEL	Probable arginine kinase F46H5.3 (EC 2.7.3.3) (AK)	0.15	-	mit	0					396
O74781 UniProt NPD GO	SYRC_SCHPO	Probable arginyl-tRNA synthetase, cytoplasmic (EC 6.1.1.19) (Arginine--tRNA ligase) (ArgRS)	0.15	-	cyt	0	Cytoplasm (Potential)				618
P78753 UniProt NPD GO	ASNS_SCHPO	Probable asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine ...	0.15	-	cyt	0					556
O75185 UniProt NPD GO	AT2C2_HUMAN	Probable calcium-transporting ATPase KIAA0703 (EC 3.6.3.8)	0.15	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				963
Q9CTG6 UniProt NPD GO	AT132_MOUSE	Probable cation-transporting ATPase 13A2 (EC 3.6.3.-)	0.15	-	end	9	Membrane; multi-pass membrane protein (By similarity)				1169
Q9W092 UniProt NPD GO	CHIT2_DROME	Probable chitinase 2 precursor (EC 3.2.1.14)	0.15	-	exc	0					484
O64748 UniProt NPD GO	COPE_ARATH	Probable coatomer subunit epsilon (Epsilon-coat protein) (Epsilon-COP)	0.15	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				293
Q18726 UniProt NPD GO	CIA30_CAEEL	Probable complex I intermediate-associated protein 30, mitochondrial precursor	0.15	-	mit	0	Mitochondrion (Probable)				340
Q9V419 UniProt NPD GO	C28A5_DROME	Probable cytochrome P450 28a5 (EC 1.14.-.-) (CYPXXVIIIA5)	0.15	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				505
Q9W3V8 UniProt NPD GO	ALG8_DROME	Probable dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase (EC 2.4.1.-) (Dolichyl ...	0.15	-	end	13 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				511
Q17017 UniProt NPD GO	FABP_ANOGA	Probable fatty acid-binding protein	0.15	-	nuc	0					112
Q90218 UniProt NPD GO	GLRK_ANAPL	Probable glutamate receptor precursor (Kainate-binding protein)	0.15	-	end	4	Membrane; multi-pass membrane protein				487
Q9FZ22 UniProt NPD GO	GPAT2_ARATH	Probable glycerol-3-phosphate acyltransferase 2 (EC 2.3.1.15) (AtGPAT2)	0.15	-	end	1 *	Membrane; multi-pass membrane protein (Potential). Not mitochondrial				530
Q5XF03 UniProt NPD GO	GPAT8_ARATH	Probable glycerol-3-phosphate acyltransferase 8 (EC 2.3.1.15)	0.15	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				500
Q4WI46 UniProt NPD GO	CRF2_ASPFU	Probable glycosidase crf2 precursor (EC 3.2.-.-) (Crh-like protein 2)	0.15	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				443
Q75L11 UniProt NPD GO	H2A6_ORYSA	Probable histone H2A.6	0.15	-	nuc	0	Nucleus (By similarity)				156
P53096 UniProt NPD GO	HOS2_YEAST	Probable histone deacetylase HOS2	0.15	-	nuc	0	Nucleus	histone deacetylase complex [IPI]			452
P0C0M2 UniProt NPD GO	GH32_ORYSA	Probable indole-3-acetic acid-amido synthetase GH3.2 (EC 6.3.2.-) (Auxin-responsive GH3-like protein ...	0.15	-	cyt	0					614
Q18060 UniProt NPD GO	ILG1_CAEEL	Probable insulin-like peptide gamma-type 1 precursor (Ceinsulin-3) [Contains: B-chain-like peptide; ...	0.15	-	exc	1 *	Secreted protein (Potential)				91
Q9UTH5 UniProt NPD GO	PLB6_SCHPO	Probable lysophospholipase C1786.02 precursor (EC 3.1.1.5) (Phospholipase B)	0.15	-	exc	0	Secreted protein (Probable)				644
Q6CKB6 UniProt NPD GO	ARX1_KLULA	Probable metalloprotease ARX1 (EC 3.-.-.-) (Associated with ribosomal export complex protein 1)	0.15	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				571
Q9QYA2 UniProt NPD GO	TOM40_MOUSE	Probable mitochondrial import receptor subunit TOM40 homolog (Translocase of outer membrane 40 kDa s ...	0.15	-	mit	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)	mitochondrion [IDA]			359
Q9LK94 UniProt NPD GO	MDAR2_ARATH	Probable monodehydroascorbate reductase, cytoplasmic isoform 2 (EC 1.6.5.4) (MDAR 2)	0.15	-	nuc	1 *	Cytoplasm (Potential)	peroxisomal membrane [IDA]			488
P84031 UniProt NPD GO	TX20_PHORI	Probable neurotoxin PRTx20C1	0.15	-	nuc	0	Secreted protein				58

You are viewing entries 57401 to 57450 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.