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
P41740 UniProt NPD GO	ANPRC_RAT	Atrial natriuretic peptide clearance receptor precursor (ANP-C) (ANPRC) (NPR-C) (Atrial natriuretic ...	0.19	-	end	1	Membrane; single-pass type I membrane protein				535
Q3MQ24 UniProt NPD GO	ATG5_BOVIN	Autophagy protein 5	0.19	-	cyt	0	Cytoplasm (By similarity)				275
Q07879 UniProt NPD GO	ATG10_YEAST	Autophagy-related protein 10 (Autophagy-related E2-like-conjugating enzyme ATG10)	0.19	-	cyt	0	Cytoplasm (Probable)	cytoplasm [TAS]			167
Q9US24 UniProt NPD GO	ATG12_SCHPO	Autophagy-related protein 12 (Autophagy-related ubiquitin-like modifier atg12)	0.19	-	nuc	0	Cytoplasm (By similarity)				132
O95352 UniProt NPD GO	ATG7_HUMAN	Autophagy-related protein 7 (APG7-like) (Ubiquitin-activating enzyme E1-like protein) (hAGP7)	0.19	-	nuc	0	Cytoplasm (Probable)	cytoplasm [TAS]	608760		703
Q9D906 UniProt NPD GO	ATG7_MOUSE	Autophagy-related protein 7 (APG7-like) (Ubiquitin-activating enzyme E1-like protein) (mAGP7)	0.19	-	nuc	0	Cytoplasm (Probable)				698
Q59PZ3 UniProt NPD GO	ATG7_CANAL	Autophagy-related protein 7 (Autophagy-related E1-like-activating enzyme ATG7)	0.19	-	mit	0	Cytoplasm (By similarity)				639
P0C127 UniProt NPD GO	IAA16_ORYSA	Auxin-responsive protein IAA16 (Indoleacetic acid-induced protein 16)	0.19	-	cyt	0	Nucleus (By similarity)				228
O24409 UniProt NPD GO	IAA19_ARATH	Auxin-responsive protein IAA19 (Indoleacetic acid-induced protein 19) (MASSUGU2 protein)	0.19	-	cyt	0	Nucleus (By similarity)				197
Q09097 UniProt NPD GO	AVEF_AVESA	Avenin-F (Gamma-3 avenin) (Prolamin) (Celiac immunoreactive protein 2) (CIP-2) (Fragment)	0.19	-	nuc	0	Protein body (By similarity). Protein bodies inside vacuoles (By similarity)				43
P82252 UniProt NPD GO	BAT1_RAT	B(0,+)-type amino acid transporter 1 (B(0,+)AT) (Glycoprotein-associated amino acid transporter b0,+ ...	0.19	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				487
Q91987 UniProt NPD GO	NTRK2_CHICK	BDNF/NT-3 growth factors receptor precursor (EC 2.7.10.1) (Neurotrophic tyrosine kinase receptor typ ...	0.19	-	nuc	1	Membrane; single-pass type I membrane protein				818
Q5RBX2 UniProt NPD GO	BET1L_PONPY	BET1-like protein	0.19	-	mit	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				111
P07317 UniProt NPD GO	CRBA1_RANTE	Beta crystallin A1	0.19	-	cyt	0					198
Q9JJV1 UniProt NPD GO	CRBA2_MOUSE	Beta crystallin A2 (Beta-A2-crystallin)	0.19	-	cyt	0					196
P55165 UniProt NPD GO	CRBB3_CHICK	Beta crystallin B3 (Beta-B3-crystallin)	0.19	-	cyt	0					211
P79148 UniProt NPD GO	ADRB1_CANFA	Beta-1 adrenergic receptor (Beta-1 adrenoceptor) (Beta-1 adrenoreceptor)	0.19	+	end	7	Cell membrane; multi-pass membrane protein (By similarity). Localized at the plasma membrane. Found ...				473
Q9TST6 UniProt NPD GO	ADRB1_FELCA	Beta-1 adrenergic receptor (Beta-1 adrenoceptor) (Beta-1 adrenoreceptor)	0.19	-	end	7	Cell membrane; multi-pass membrane protein (By similarity). Localized at the plasma membrane. Found ...				474
Q9Y2C3 UniProt NPD GO	B3GT5_HUMAN	Beta-1,3-galactosyltransferase 5 (EC 2.4.1.-) (Beta-1,3-GalTase 5) (Beta3Gal-T5) (b3Gal-T5) (UDP-gal ...	0.19	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)		604066		310
Q09199 UniProt NPD GO	B4GN2_MOUSE	Beta-1,4 N-acetylgalactosaminyltransferase 2 (EC 2.4.1.-)	0.19	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				510
O70432 UniProt NPD GO	ADRB3_MERUN	Beta-3 adrenergic receptor (Beta-3 adrenoceptor) (Beta-3 adrenoreceptor) (Fragment)	0.19	-	end	3 *	Membrane; multi-pass membrane protein (By similarity)				167
P11839 UniProt NPD GO	CASB_SHEEP	Beta-casein precursor	0.19	-	exc	0	Secreted protein				222
P46165 UniProt NPD GO	BD07_BOVIN	Beta-defensin 7 (BNDB-7) (BNBD-7)	0.19	-	mit	0	Secreted protein				40
O18835 UniProt NPD GO	BGLR_CANFA	Beta-glucuronidase precursor (EC 3.2.1.31)	0.19	-	cyt	1 *	Lysosome				651
Q27713 UniProt NPD GO	DRTS_PLABA	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.19	-	cyt	0					587
Q6QNY1 UniProt NPD GO	BL1S2_HUMAN	Biogenesis of lysosome-related organelles complex-1 subunit 2 (BLOC subunit 2) (Centrosome-associate ...	0.19	-	nuc	0	Centrosome. Localizes to the centrosomes in a microtubule-dependent manner		609768		142
O54798 UniProt NPD GO	BRS3_MOUSE	Bombesin receptor subtype-3 (BRS-3)	0.19	-	end	7 *	Membrane; multi-pass membrane protein				399
P33720 UniProt NPD GO	BXA3_SAMCY	Bombyxin A-3 homolog precursor [Contains: Bombyxin A-3 homolog B chain; Bombyxin A-3 homolog A chain ...	0.19	-	mit	0	Secreted protein				98
P16346 UniProt NPD GO	IBBWT_MEDSA	Bowman-Birk type wound-induced trypsin inhibitor	0.19	-	nuc	0					58
Q25113 UniProt NPD GO	BRAC_HEMPU	Brachyury protein homolog (T protein) (HpTa)	0.19	-	nuc	0	Nucleus (Potential)				434
O70183 UniProt NPD GO	BDNF_CAVPO	Brain-derived neurotrophic factor precursor (BDNF)	0.19	-	nuc	0	Secreted protein				255
Q8WUG5 UniProt NPD GO	BOCT_HUMAN	Brain-type organic cation transporter (Solute carrier family 22 member 17)	0.19	-	end	11	Membrane; multi-pass membrane protein (Potential)				538
P07245 UniProt NPD GO	C1TC_YEAST	C-1-tetrahydrofolate synthase, cytoplasmic (C1-THF synthase) [Includes: Methylenetetrahydrofolate de ...	0.19	-	cyt	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			946
Q15800 UniProt NPD GO	ERG25_HUMAN	C-4 methylsterol oxidase (EC 1.14.13.72) (Methylsterol monooxygenase)	0.19	-	nuc	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum [TAS] integral to membrane [TAS] plasma membrane [TAS]	607545		293
Q5R574 UniProt NPD GO	ERG25_PONPY	C-4 methylsterol oxidase (EC 1.14.13.72) (Methylsterol monooxygenase)	0.19	-	nuc	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				293
P56493 UniProt NPD GO	CCR5_CERAE	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.19	-	end	6 *	Membrane; multi-pass membrane protein				352
P56491 UniProt NPD GO	CXCR4_PAPAN	C-X-C chemokine receptor type 4 (CXC-R4) (CXCR-4) (SDF-1 receptor) (Stromal cell-derived factor 1 re ...	0.19	-	end	7 *	Membrane; multi-pass membrane protein				352
O62747 UniProt NPD GO	CXCR4_CERTO	C-X-C chemokine receptor type 4 (CXC-R4) (CXCR-4) (SDF-1 receptor) (Stromal cell-derived factor 1 re ...	0.19	-	end	7 *	Membrane; multi-pass membrane protein				352
Q28474 UniProt NPD GO	CXCR4_MACFA	C-X-C chemokine receptor type 4 (CXC-R4) (CXCR-4) (SDF-1 receptor) (Stromal cell-derived factor 1 re ...	0.19	-	end	7 *	Membrane; multi-pass membrane protein				352
P79394 UniProt NPD GO	CXCR4_MACMU	C-X-C chemokine receptor type 4 (CXC-R4) (CXCR-4) (SDF-1 receptor) (Stromal cell-derived factor 1 re ...	0.19	-	end	7 *	Membrane; multi-pass membrane protein				352
Q8VCP9 UniProt NPD GO	CLC14_MOUSE	C-type lectin domain family 14 member A precursor	0.19	-	end	1	Membrane; single-pass type I membrane protein (Potential)				459
Q8WTT0 UniProt NPD GO	CLC4C_HUMAN	C-type lectin domain family 4 member C (C-type lectin superfamily member 7) (Blood dendritic cell an ...	0.19	-	nuc	1 *	Membrane; single-pass type II membrane protein (Probable)		606677		213
Q8AYR6 UniProt NPD GO	ANFC1_ORYLA	C-type natriuretic peptide 1 precursor	0.19	-	mit	0	Secreted protein				131
Q8RWC9 UniProt NPD GO	CIPK1_ARATH	CBL-interacting serine/threonine-protein kinase 1 (EC 2.7.11.1) (SOS2-like protein kinase PKS13) (SN ...	0.19	-	nuc	0					444
Q9UFF9 UniProt NPD GO	CNOT8_HUMAN	CCR4-NOT transcription complex subunit 8 (CCR4-associated factor 8) (CAF1-like protein) (CALIFp) (CA ...	0.19	-	cyt	0	Cytoplasm. Nucleus	nucleus [NAS]	603731		292
P61130 UniProt NPD GO	SIA4C_PANTR	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.-) (Beta-galactosi ...	0.19	-	end	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				328
Q6KB59 UniProt NPD GO	SIA4A_PANTR	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.4) (Beta-galactosi ...	0.19	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				340
O04500 UniProt NPD GO	COBL6_ARATH	COBRA-like protein 6 precursor	0.19	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)				454
P39706 UniProt NPD GO	SWD1_YEAST	COMPASS component SWD1 (Complex proteins associated with SET1 protein SWD1) (Set1C component SWD1)	0.19	-	cyt	0	Nucleus	COMPASS complex [IPI]			426
Q59PG6 UniProt NPD GO	CSN5_CANAL	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	0.19	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				213

You are viewing entries 51601 to 51650 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.