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
Q9GMC7 UniProt NPD GO	CP17A_BISBI	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.17	-	mit	0					509
P05185 UniProt NPD GO	CP17A_BOVIN	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.17	-	mit	0					509
Q3LFU0 UniProt NPD GO	CP1A1_BALAC	Cytochrome P450 1A1 (EC 1.14.14.1)	0.17	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				516
P12790 UniProt NPD GO	CP2B9_MOUSE	Cytochrome P450 2B9 (EC 1.14.14.1) (CYPIIB9) (Testosterone 16-alpha hydroxylase) (P450-16-alpha) (Cl ...	0.17	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				491
P05178 UniProt NPD GO	CP2C6_RAT	Cytochrome P450 2C6 (EC 1.14.14.1) (CYPIIC6) (P450 PB1) (PTF2)	0.17	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
Q6GUQ4 UniProt NPD GO	CP2E1_MACMU	Cytochrome P450 2E1 (EC 1.14.14.1) (CYPIIE1)	0.17	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				493
P79383 UniProt NPD GO	CP2E1_PIG	Cytochrome P450 2E1 (EC 1.14.14.1) (CYPIIE1) (P450-J) (P-450-J)	0.17	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				495
P20815 UniProt NPD GO	CP3A5_HUMAN	Cytochrome P450 3A5 (EC 1.14.14.1) (CYPIIIA5) (P450-PCN3) (HLp2)	0.17	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	membrane fraction [ISS] microsome [TAS]	605325		502
Q12586 UniProt NPD GO	CP52I_CANMA	Cytochrome P450 52A9 (EC 1.14.14.-) (CYPLIIA9) (Alkane-inducible P450-ALK5-A)	0.17	-	cyt	1 *					521
Q964R1 UniProt NPD GO	CP6J1_BLAGE	Cytochrome P450 6j1 (EC 1.14.-.-) (CYPVIJ1)	0.17	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				501
O65438 UniProt NPD GO	C71AR_ARATH	Cytochrome P450 71A27 (EC 1.14.-.-)	0.17	-	nuc	0					499
O04164 UniProt NPD GO	C71A6_NEPRA	Cytochrome P450 71A6 (EC 1.14.-.-) (Fragment)	0.17	-	nuc	0					511
O81970 UniProt NPD GO	C71A9_SOYBN	Cytochrome P450 71A9 (EC 1.14.-.-) (P450 CP1)	0.17	-	mit	0					499
Q9LTM0 UniProt NPD GO	C71BN_ARATH	Cytochrome P450 71B23 (EC 1.14.-.-)	0.17	-	nuc	1 *					501
P93703 UniProt NPD GO	C71C3_MAIZE	Cytochrome P450 71C3 (EC 1.14.-.-) (Benzoxazineless 5)	0.17	-	nuc	0					535
O81345 UniProt NPD GO	C79B1_SINAL	Cytochrome P450 79B1 (EC 1.14.-.-)	0.17	-	nuc	1 *					542
O02766 UniProt NPD GO	CP8B1_RABIT	Cytochrome P450 8B1 (EC 1.14.13.95) (CYPVIIIB1) (7-alpha-hydroxycholest-4-en-3-one 12-alpha-hydroxyl ...	0.17	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				499
P52650 UniProt NPD GO	CY24A_PIG	Cytochrome b-245 light chain (p22 phagocyte B-cytochrome) (Neutrophil cytochrome b 22 kDa polypeptid ...	0.17	-	cyt	2 *					191
P26291 UniProt NPD GO	UCRIA_PEA	Cytochrome b6-f complex iron-sulfur subunit, chloroplast precursor (EC 1.10.99.1) (Rieske iron-sulfu ...	0.17	-	mit	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein. The transmembran ...				230
Q6Q4H8 UniProt NPD GO	CYC_PICPA	Cytochrome c	0.17	-	nuc	0	Mitochondrion; mitochondrial matrix (By similarity)				109
P00027 UniProt NPD GO	CYC_SQUSU	Cytochrome c	0.17	-	nuc	0	Mitochondrion; mitochondrial matrix				104
P56393 UniProt NPD GO	COX7B_MOUSE	Cytochrome c oxidase polypeptide VIIb, mitochondrial precursor (EC 1.9.3.1)	0.17	-	mit	0		mitochondrion [IDA]			80
P80977 UniProt NPD GO	CX6C1_THUOB	Cytochrome c oxidase polypeptide VIc-1 (EC 1.9.3.1) (Fragments)	0.17	-	nuc	0	Mitochondrion; mitochondrial inner membrane				49
P00424 UniProt NPD GO	COX5A_YEAST	Cytochrome c oxidase polypeptide Va, mitochondrial precursor (EC 1.9.3.1)	0.17	-	mit	1	Mitochondrion; mitochondrial inner membrane	respiratory chain complex IV (sensu Eukaryota) [IPI]			153
P98025 UniProt NPD GO	COX2_CHOBI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.17	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P07255 UniProt NPD GO	COX9_YEAST	Cytochrome c oxidase subunit 7A precursor (EC 1.9.3.1) (Cytochrome c oxidase polypeptide VIIA)	0.17	-	mit	1 *	Mitochondrion; mitochondrial inner membrane	respiratory chain complex IV (sensu Eukaryota) [IPI]			58
Q6URB0 UniProt NPD GO	CCPR_CRYNV	Cytochrome c peroxidase, mitochondrial precursor (EC 1.11.1.5) (CCP)	0.17	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				377
Q6BV14 UniProt NPD GO	DAD2_DEBHA	DASH complex subunit DAD2 (Outer kinetochore protein DAD2)	0.17	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				149
Q9Z205 UniProt NPD GO	RFXK_MOUSE	DNA-binding protein RFXANK (Regulatory factor X subunit B) (RFX-B) (Regulatory factor X-associated a ...	0.17	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			269
Q5E981 UniProt NPD GO	ID3_BOVIN	DNA-binding protein inhibitor ID-3 (Inhibitor of DNA binding 3)	0.17	-	nuc	0	Nucleus (By similarity)				119
P70700 UniProt NPD GO	RPA2_MOUSE	DNA-directed RNA polymerase I 135 kDa polypeptide (EC 2.7.7.6) (RNA polymerase I subunit 2) (RPA135) ...	0.17	-	cyt	0	Nucleus	nucleolus [IDA]			1135
Q5REE8 UniProt NPD GO	RPA2_PONPY	DNA-directed RNA polymerase I 135 kDa polypeptide (EC 2.7.7.6) (RNA polymerase I subunit 2) (RPA135) ...	0.17	-	cyt	0	Nucleus (By similarity)				1136
O74825 UniProt NPD GO	RPB4_SCHPO	DNA-directed RNA polymerase II 16 kDa polypeptide (EC 2.7.7.6)	0.17	-	cyt	0	Nucleus	DNA-directed RNA polymerase II, holoenzyme [TAS]			135
Q09191 UniProt NPD GO	RPB5_SCHPO	DNA-directed RNA polymerases II 24 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 5)	0.17	-	cyt	0	Nucleus	DNA-directed RNA polymerase I complex [TAS] DNA-directed RNA polymerase II, holoenzyme [IDA] DNA-directed RNA polymerase III complex [TAS]			210
Q28888 UniProt NPD GO	PGS2_RABIT	Decorin precursor (Bone proteoglycan II) (PG-S2)	0.17	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
P11477 UniProt NPD GO	DEF1_MOUSE	Defensin 1 precursor (Defensin, alpha 1) (Defensin-related cryptdin peptide) (DEFCR) (Cryptdin-1)	0.17	-	exc	0	Secreted protein				93
P80571 UniProt NPD GO	DEFI_MYTGA	Defensin MGD-1 precursor (Fragment)	0.17	-	cyt	0	Secreted protein			1FJN	60
P28641 UniProt NPD GO	DHN3_PEA	Dehydrin DHN3	0.17	-	cyt	0					232
P25340 UniProt NPD GO	ERG4_YEAST	Delta(24(24(1)))-sterol reductase (EC 1.3.1.71) (Sterol delta(24(28))-reductase) (C-24(28) sterol re ...	0.17	-	end	7 *	Membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum [IDA]			473
P0C1R3 UniProt NPD GO	TXDT1_HADSP	Delta-atracotoxin-Hs20.1a (Delta-AcTx-Hs20.1a)	0.17	-	nuc	0	Secreted				42
P83257 UniProt NPD GO	TXDP2_PARLU	Delta-palutoxin IT2 (Delta-paluIT2)	0.17	-	nuc	0	Secreted protein	extracellular region [NAS]		1V91	37
Q9GLR2 UniProt NPD GO	RTD3_MACMU	Demidefensin-3 precursor	0.17	-	exc	0					76
P33316 UniProt NPD GO	DUT_HUMAN	Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (EC 3.6.1.23) (dUTPase) (d ...	0.17	-	mit	0	Isoform DUT-N: Nucleus. Isoform DUT-M: Mitochondrion	mitochondrion [TAS] nucleus [TAS]	601266	1Q5U	252
Q14126 UniProt NPD GO	DSG2_HUMAN	Desmoglein-2 precursor (HDGC)	0.17	-	end	2 *	Membrane; single-pass type I membrane protein	intercellular junction [TAS]	125671		1117
O59715 UniProt NPD GO	DSD1_SCHPO	Dihydroceramide delta(4)-desaturase (EC 1.14.-.-)	0.17	-	nuc	5	Membrane; multi-pass membrane protein (Potential)				362
Q07801 UniProt NPD GO	DYR_CRYNE	Dihydrofolate reductase (EC 1.5.1.3)	0.17	-	nuc	0					229
Q3LXA3 UniProt NPD GO	DAK_HUMAN	Dihydroxyacetone kinase (EC 2.7.1.29) (Glycerone kinase) (DHA kinase)	0.17	-	cyt	0					575
P41819 UniProt NPD GO	DIM1_YEAST	Dimethyladenosine transferase (EC 2.1.1.-) (S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltra ...	0.17	-	cyt	0		nucleolus [TAS]			318
Q04799 UniProt NPD GO	FMO5_RABIT	Dimethylaniline monooxygenase [N-oxide-forming] 5 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.17	-	end	1	Microsome				532
Q86TI2 UniProt NPD GO	DPP9_HUMAN	Dipeptidyl peptidase 9 (EC 3.4.14.5) (Dipeptidyl peptidase IX) (DP9) (Dipeptidyl peptidase-like prot ...	0.17	-	nuc	0	Cytoplasm; cytosol		608258		863

You are viewing entries 54201 to 54250 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.