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
Q863G2 UniProt NPD GO	COX82_NYCCO	Cytochrome c oxidase polypeptide VIII-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.06	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				69
Q8SPJ9 UniProt NPD GO	CX7A1_PIG	Cytochrome c oxidase polypeptide VIIa-heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.06	-	mit	1	Mitochondrion; mitochondrial inner membrane				80
P13183 UniProt NPD GO	COX7B_BOVIN	Cytochrome c oxidase polypeptide VIIb, mitochondrial precursor (EC 1.9.3.1) (IHQ)	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane			2OCC	83
O13085 UniProt NPD GO	CX6A1_ONCMY	Cytochrome c oxidase polypeptide VIa, mitochondrial precursor (EC 1.9.3.1)	0.06	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				102
P12787 UniProt NPD GO	COX5A_MOUSE	Cytochrome c oxidase polypeptide Va, mitochondrial precursor (EC 1.9.3.1)	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA] mitochondrion [IDA]			145
P80974 UniProt NPD GO	COX5B_THUOB	Cytochrome c oxidase polypeptide Vb (EC 1.9.3.1) (Fragment)	0.06	-		0	Mitochondrion; mitochondrial inner membrane				20
P12075 UniProt NPD GO	COX5B_RAT	Cytochrome c oxidase polypeptide Vb, mitochondrial precursor (EC 1.9.3.1) (VIA*)	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane				129
Q9B840 UniProt NPD GO	COX1_OSTNU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.06	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				514
P25001 UniProt NPD GO	COX1_PISOC	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.06	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				517
P50673 UniProt NPD GO	COX2_APOSY	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.06	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O47667 UniProt NPD GO	COX2_CANAD	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.06	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P98034 UniProt NPD GO	COX2_HAPGR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.06	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P24988 UniProt NPD GO	COX2_MICPE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.06	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O03895 UniProt NPD GO	COX2_TINMA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II) (Fragment)	0.06	-	end	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				198
O46587 UniProt NPD GO	COX41_MANSP	Cytochrome c oxidase subunit 4 isoform 1 (EC 1.9.3.1) (Cytochrome c oxidase subunit IV isoform 1) (C ...	0.06	-	mit	1	Mitochondrion; mitochondrial inner membrane				99
P10888 UniProt NPD GO	COX41_RAT	Cytochrome c oxidase subunit 4 isoform 1, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxidase ...	0.06	-	nuc	1	Mitochondrion; mitochondrial inner membrane				169
Q9CPY7 UniProt NPD GO	AMPL_MOUSE	Cytosol aminopeptidase (EC 3.4.11.1) (Leucine aminopeptidase) (LAP) (Leucyl aminopeptidase) (Proline ...	0.06	-	cyt	0	Cytoplasm (By similarity)	mitochondrion [IDA]			487
Q9XSI1 UniProt NPD GO	CTLA4_CANFA	Cytotoxic T-lymphocyte protein 4 precursor (Cytotoxic T-lymphocyte-associated antigen 4) (CTLA-4) (C ...	0.06	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				223
Q8MMJ7 UniProt NPD GO	TXT1_OPIMA	Cytotoxic linear peptide IsCT precursor [Contains: Cytotoxic linear peptide IsCTf]	0.06	-	vac	0	Secreted protein			1T55	68
P01468 UniProt NPD GO	CX1_NAJPA	Cytotoxin 1 (Cardiotoxin gamma)	0.06	-	nuc	0	Secreted protein			1TGX	60
P01469 UniProt NPD GO	CX2_NAJMO	Cytotoxin 2 (Cardiotoxin XIIA) (Cytotoxin V-II-2)	0.06	-	nuc	0	Secreted protein				60
P62377 UniProt NPD GO	CXH_NAJNA	Cytotoxin-like basic protein (CLBP) (Less-cytotoxic basic polypeptide) (LCBP)	0.06	-	nuc	0	Secreted protein				62
Q61616 UniProt NPD GO	DRD1_MOUSE	D(1A) dopamine receptor	0.06	-	end	6 *	Cell membrane; multi-pass membrane protein. Endoplasmic reticulum; endoplasmic reticulum membrane; m ...	membrane fraction [IDA]			446
Q8N465 UniProt NPD GO	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase, mitochondrial precursor (EC 1.1.99.-)	0.06	-	mit	0	Mitochondrion (Probable)		609186		521
Q5EAD2 UniProt NPD GO	SERA_BOVIN	D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (3-PGDH)	0.06	-	cyt	0					532
Q9Z1M5 UniProt NPD GO	OXDA_CAVPO	D-amino-acid oxidase (EC 1.4.3.3) (DAMOX) (DAO) (DAAO)	0.06	-	mit	0	Peroxisome (By similarity)				347
Q6FS20 UniProt NPD GO	ALO_CANGA	D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) (ALO) (L-galactono-gamma-lactone oxidase)	0.06	-	nuc	0	Mitochondrion; mitochondrial membrane (By similarity). Membrane-embedded (By similarity)				525
Q5KEX9 UniProt NPD GO	DPB2_CRYNE	DNA polymerase epsilon subunit B (EC 2.7.7.7) (DNA polymerase II subunit B)	0.06	-	cyt	0	Nucleus (By similarity)				541
P52432 UniProt NPD GO	RPA5_MOUSE	DNA-directed RNA polymerase I 40 kDa polypeptide (EC 2.7.7.6) (RPA40)	0.06	-	cyt	0	Nucleus				346
Q1RMP0 UniProt NPD GO	RPA12_BOVIN	DNA-directed RNA polymerase I subunit 12 (EC 2.7.7.6) (Nuclear RNA polymerase I small-specific subun ...	0.06	-	cyt	0	Nucleus (Potential)				123
Q6MFY5 UniProt NPD GO	RPA12_RAT	DNA-directed RNA polymerase I subunit 12 (EC 2.7.7.6) (Nuclear RNA polymerase I small-specific subun ...	0.06	-	cyt	0	Nucleus (Potential)				123
Q9GR61 UniProt NPD GO	RPB10_CAEEL	DNA-directed RNA polymerase II 7.6 kDa polypeptide (EC 2.7.7.6) (RPB10) (RPB7.6)	0.06	-	cyt	0	Nucleus (By similarity)				67
P48337 UniProt NPD GO	RPOA_EUGGR	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.06	-	nuc	0	Plastid; chloroplast				216
P39548 UniProt NPD GO	YAJ8_YEAST	DUP240 protein YAR028C	0.06	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				234
P81462 UniProt NPD GO	DEFI_BOMPA	Defensin	0.06	-	cyt	0	Secreted protein				51
P84156 UniProt NPD GO	DEFN_ARCDE	Defensin ARD1	0.06	-	cyt	0	Secreted protein	extracellular region [TAS]		1P0A	44
P81544 UniProt NPD GO	DEFN_HELVI	Defensin heliomicin	0.06	-	cyt	0	Secreted protein			1I2V	44
O96049 UniProt NPD GO	DEFI_ORYRH	Defensin precursor	0.06	-	exc	0	Secreted protein				79
Q5RCF8 UniProt NPD GO	DHRS4_PONPY	Dehydrogenase/reductase SDR family member 4 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase/NADP- ...	0.06	-	cyt	0	Peroxisome (By similarity)				260
O04226 UniProt NPD GO	P5CS_ORYSA	Delta 1-pyrroline-5-carboxylate synthetase (P5CS) [Includes: Glutamate 5-kinase (EC 2.7.2.11) (Gamma ...	0.06	-	nuc	0					716
Q9TWM7 UniProt NPD GO	CXD6A_CONGL	Delta-conotoxin GmVIA	0.06	-	cyt	0	Secreted protein				29
Q92874 UniProt NPD GO	DNSL2_HUMAN	Deoxyribonuclease I-like 2 precursor (EC 3.1.21.-) (DNase I-like 2) (DNase I homolog protein DHP1)	0.06	-	mit	0	Secreted protein (Potential)		602622		299
P00639 UniProt NPD GO	DNAS1_BOVIN	Deoxyribonuclease-1 precursor (EC 3.1.21.1) (Deoxyribonuclease I) (DNase I)	0.06	-	end	1 *	Secretory protein, stored in zymogen granules and found in the nuclear envelope			3DNI	282
Q8SRS0 UniProt NPD GO	DUT_ENCCU	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) (dUTPase) (dUTP pyrophosphatase)	0.06	-	mit	0					144
Q9XY87 UniProt NPD GO	SIXA_MESMA	Depressant insect neurotoxin BmK ITa precursor (BmK dITAP3)	0.06	-	exc	0	Secreted protein				85
P80962 UniProt NPD GO	SIX2_BUTAR	Depressant insect toxin 2 (BaIT2)	0.06	-	cyt	0	Secreted protein				61
P68727 UniProt NPD GO	SIX2_MESMA	Depressant insect toxin BmK IT2	0.06	-	cyt	0	Secreted protein				61
O93223 UniProt NPD GO	DMS3_AGAAN	Dermaseptin AA-3-1 precursor	0.06	-	exc	0	Secreted protein				75
O93225 UniProt NPD GO	DMS5_AGAAN	Dermaseptin AA-3-4 precursor	0.06	-	exc	0	Secreted protein				72
O93453 UniProt NPD GO	DMS3_PACDA	Dermaseptin PD-3-3 precursor	0.06	-	exc	0	Secreted protein				80

You are viewing entries 71901 to 71950 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.