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
Q9NTM9 UniProt NPD GO	CUTC_HUMAN	Copper homeostasis protein cutC homolog	0.20	-	mit	0					273
Q64446 UniProt NPD GO	ATP7B_MOUSE	Copper-transporting ATPase 2 (EC 3.6.3.4) (Copper pump 2) (Wilson disease-associated protein homolog ...	0.20	-	end	7	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; multi-pass membrane protein (By ...	integral to plasma membrane [ISS] late endosome [ISS]			1462
Q64535 UniProt NPD GO	ATP7B_RAT	Copper-transporting ATPase 2 (EC 3.6.3.4) (Copper pump 2) (Wilson disease-associated protein homolog ...	0.20	-	end	7	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; multi-pass membrane protein (By ...				1451
P36552 UniProt NPD GO	HEM6_MOUSE	Coproporphyrinogen III oxidase, mitochondrial precursor (EC 1.3.3.3) (Coproporphyrinogenase) (Coprog ...	0.20	-	mit	0	Mitochondrion; mitochondrial intermembrane space				443
Q62267 UniProt NPD GO	SPR1B_MOUSE	Cornifin B (Small proline-rich protein 1B) (SPR1B) (SPR1 B)	0.20	-	nuc	0	Cytoplasm	cornified envelope [TAS]			153
Q9UQ03 UniProt NPD GO	COR2B_HUMAN	Coronin-2B (Coronin-like protein C) (ClipinC) (Protein FC96)	0.20	-	mit	0		actin cytoskeleton [NAS] membrane [NAS]	605002		475
P01376 UniProt NPD GO	DEF3_RABIT	Corticostatin-3 precursor (Corticostatin III) (CS-III) (Macrophage antibiotic peptide MCP-1) (NP-1) ...	0.20	-	exc	0	Secreted protein				95
P51661 UniProt NPD GO	DHI2_MOUSE	Corticosteroid 11-beta-dehydrogenase isozyme 2 (EC 1.1.1.-) (11-DH2) (11-beta-hydroxysteroid dehydro ...	0.20	-	mit	0	Microsome				386
Q06770 UniProt NPD GO	CBG_MOUSE	Corticosteroid-binding globulin precursor (CBG) (Transcortin) (Serpin A6)	0.20	-	vac	0	Secreted protein				397
Q60748 UniProt NPD GO	CRFR2_MOUSE	Corticotropin-releasing factor receptor 2 precursor (CRF-R 2) (CRF2) (Corticotropin-releasing hormon ...	0.20	-	end	7	Membrane; multi-pass membrane protein			1U34	431
P24387 UniProt NPD GO	CRHBP_HUMAN	Corticotropin-releasing factor-binding protein precursor (CRF-binding protein) (CRF-BP) (Corticotrop ...	0.20	-	exc	0		soluble fraction [TAS]	122559		322
Q6P8J7 UniProt NPD GO	KCRS_MOUSE	Creatine kinase, sarcomeric mitochondrial precursor (EC 2.7.3.2) (S-MtCK)	0.20	-	mit	0	Mitochondrion; mitochondrial inner membrane. Outer side (By similarity)				419
P09605 UniProt NPD GO	KCRS_RAT	Creatine kinase, sarcomeric mitochondrial precursor (EC 2.7.3.2) (S-MtCK) (Mib-CK) (Basic-type mitoc ...	0.20	-	mit	0	Mitochondrion; mitochondrial inner membrane; intermembrane side	mitochondrion [TAS] sarcomere [TAS]			419
Q28718 UniProt NPD GO	CNGA2_RABIT	Cyclic nucleotide-gated olfactory channel (Cyclic nucleotide-gated cation channel 2) (CNG channel 2) ...	0.20	-	end	4	Membrane; multi-pass membrane protein				664
Q9CPY4 UniProt NPD GO	CDKA2_MOUSE	Cyclin-dependent kinase 2-associated protein 2 (CDK2-associated protein 2) (DOC-1-related protein) ( ...	0.20	-	nuc	0					127
Q25330 UniProt NPD GO	CKS1_LEIME	Cyclin-dependent kinases regulatory subunit (P12LMMCKS1)	0.20	-	cyt	0					99
Q94504 UniProt NPD GO	CYSP7_DICDI	Cysteine proteinase 7 precursor (EC 3.4.22.-) (Proteinase 1)	0.20	-	exc	0	Lysosome				460
Q10989 UniProt NPD GO	AFP2B_SINAL	Cysteine-rich antifungal protein 2B (AFP2B) (M2B)	0.20	-	nuc	0					52
Q60477 UniProt NPD GO	CRIS2_CAVPO	Cysteine-rich secretory protein 2 precursor (CRISP-2) (Testis-specific protein TPX-1) (Autoantigen 1 ...	0.20	-	exc	0	Secreted protein (Probable)				244
P22443 UniProt NPD GO	CP19A_RAT	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.20	-	nuc	0	Membrane; peripheral membrane protein				508
O42430 UniProt NPD GO	CP1A1_LIMLI	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.20	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				521
Q9W683 UniProt NPD GO	CP1A1_LIZSA	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.20	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				521
Q92100 UniProt NPD GO	CP1A1_PLEPL	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.20	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				521
P56591 UniProt NPD GO	CP1A1_SHEEP	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1) (P450-C) (P4501A1)	0.20	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				519
P04799 UniProt NPD GO	CP1A2_RAT	Cytochrome P450 1A2 (EC 1.14.14.1) (CYPIA2) (P450-D) (P-448)	0.20	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [IDA]			513
P12789 UniProt NPD GO	CP2B5_RABIT	Cytochrome P450 2B5 (EC 1.14.14.1) (CYPIIB5) (P450 type B2) (P450 form HP1)	0.20	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				491
P20813 UniProt NPD GO	CP2B6_HUMAN	Cytochrome P450 2B6 (EC 1.14.14.1) (CYPIIB6) (P450 IIB1)	0.20	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	endoplasmic reticulum [NAS] microsome [NAS]	123930		491
P24470 UniProt NPD GO	CP2CN_RAT	Cytochrome P450 2C23 (EC 1.14.14.1) (CYPIIC23) (Arachidonic acid epoxygenase)	0.20	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [IDA]			494
P11712 UniProt NPD GO	CP2C9_HUMAN	Cytochrome P450 2C9 (EC 1.14.13.80) ((R)-limonene 6-monooxygenase) (EC 1.14.13.48) ((S)-limonene 6-m ...	0.20	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	endoplasmic reticulum [NAS] microsome [TAS]	601130	1R9O	490
P24456 UniProt NPD GO	CP2DA_MOUSE	Cytochrome P450 2D10 (EC 1.14.14.1) (CYPIID10) (P450-16-alpha) (P450CB) (Testosterone 16-alpha hydro ...	0.20	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				504
O18963 UniProt NPD GO	CP2E1_BOVIN	Cytochrome P450 2E1 (EC 1.14.14.1) (CYPIIE1)	0.20	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				495
Q9Y758 UniProt NPD GO	CP52M_DEBHA	Cytochrome P450 52A13 (EC 1.14.14.-) (Alkane hydroxylase 2) (Alkane-inducible p450alk 2) (DH-ALK2)	0.20	-	end	1 *					519
P30607 UniProt NPD GO	CP52B_CANTR	Cytochrome P450 52A2 (EC 1.14.14.-) (CYPLIIA2) (Alkane-inducible P450-ALK2)	0.20	-	end	1 *					522
P58048 UniProt NPD GO	C71B8_ARATH	Cytochrome P450 71B8 (EC 1.14.-.-)	0.20	-	vac	0					506
Q50LE0 UniProt NPD GO	C85A3_LYCES	Cytochrome P450 85A3 (EC 1.14.-.-) (C6-oxidase)	0.20	-	mit	1 *					467
O81973 UniProt NPD GO	C93A3_SOYBN	Cytochrome P450 93A3 (EC 1.14.-.-) (P450 CP5)	0.20	-	end	1 *					510
P93149 UniProt NPD GO	C93B1_GLYEC	Cytochrome P450 93B1 (EC 1.14.13.87) (Licodione synthase) ((2S)-flavanone 2-hydroxylase) (Flavone sy ...	0.20	-	mit	1 *					523
P06182 UniProt NPD GO	CCHL_YEAST	Cytochrome c heme lyase (EC 4.4.1.17) (CCHL) (Holocytochrome-c synthase)	0.20	-	nuc	0	Mitochondrion; mitochondrial inner membrane	mitochondrial intermembrane space [IDA]			269
Q6CS47 UniProt NPD GO	COX19_KLULA	Cytochrome c oxidase assembly protein COX19	0.20	-	nuc	0	Cytoplasm (By similarity). Mitochondrion; mitochondrial intermembrane space (By similarity)				99
O74988 UniProt NPD GO	COX5_SCHPO	Cytochrome c oxidase polypeptide V, mitochondrial precursor (EC 1.9.3.1)	0.20	-	mit	1	Mitochondrion; mitochondrial inner membrane (By similarity)				174
P48771 UniProt NPD GO	CX7A2_MOUSE	Cytochrome c oxidase polypeptide VIIa-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.20	-	mit	1	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA] mitochondrion [IDA]			83
Q7YRK3 UniProt NPD GO	COX6C_PONPY	Cytochrome c oxidase polypeptide VIc precursor (EC 1.9.3.1)	0.20	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				75
Q4R374 UniProt NPD GO	CX6B1_MACFA	Cytochrome c oxidase subunit VIb isoform 1 (EC 1.9.3.1) (COX VIb-1)	0.20	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				86
Q53CG4 UniProt NPD GO	CX6B1_MACMU	Cytochrome c oxidase subunit VIb isoform 1 (EC 1.9.3.1) (COX VIb-1)	0.20	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				86
Q9JM58 UniProt NPD GO	CRLF1_MOUSE	Cytokine receptor-like factor 1 precursor (Cytokine-like factor 1) (CLF-1) (Cytokine receptor-like m ...	0.20	-	mit	0	Secreted protein (By similarity)				425
Q6CG88 UniProt NPD GO	ALO_YARLI	D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) (ALO) (L-galactono-gamma-lactone oxidase)	0.20	-	mit	0	Mitochondrion; mitochondrial membrane (By similarity). Membrane-embedded (By similarity)				526
Q9C8Y3 UniProt NPD GO	RGL1_ARATH	DELLA protein RGL1 (RGA-like protein 1) (RGA-like protein)	0.20	-	cyt	0	Nucleus	nucleus [TAS]			511
P18466 UniProt NPD GO	HA19_CANFA	DLA class I histocompatibility antigen, A9/A9 alpha chain precursor	0.20	-	end	1	Membrane; single-pass type I membrane protein				362
Q39199 UniProt NPD GO	RECAC_ARATH	DNA repair protein recA homolog 1, chloroplast precursor (Recombinase A homolog 1)	0.20	-	mit	0	Plastid; chloroplast; chloroplast stroma				439
P24274 UniProt NPD GO	DRP90_SOYBN	DNA-binding protein DRP90	0.20	-	cyt	0					90

You are viewing entries 50501 to 50550 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.