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
P58511 UniProt NPD GO	CU051_HUMAN	Protein C21orf51	0.38	-	nuc	1 *					58
Q80UY1 UniProt NPD GO	CI041_MOUSE	Protein C9orf41 homolog	0.38	-	mit	0					400
Q5I0I9 UniProt NPD GO	CQ10B_RAT	Protein COQ10 B, mitochondrial precursor	0.38	-	mit	0	Mitochondrion (Potential)				240
Q01197 UniProt NPD GO	E6_GOSHI	Protein E6	0.38	-	exc	1 *					238
P35682 UniProt NPD GO	G10C_ORYSA	Protein G10 homolog 3	0.38	-	nuc	0	Nucleus (Potential)				145
Q4R4P6 UniProt NPD GO	MTO1_MACFA	Protein MTO1 homolog, mitochondrial precursor	0.38	-	mit	0	Mitochondrion (By similarity)				692
Q3B7M6 UniProt NPD GO	NEDD1_BOVIN	Protein NEDD1	0.38	-	nuc	0					659
Q5XIN7 UniProt NPD GO	PMGT1_RAT	Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (EC 2.4.1.-) (POMGnT1)	0.38	-	end	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				660
Q6FV52 UniProt NPD GO	OS9_CANGA	Protein OS-9 homolog precursor	0.38	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				696
O13374 UniProt NPD GO	PT122_SACBA	Protein PET122, mitochondrial precursor	0.38	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				260
Q9C0L9 UniProt NPD GO	SEY1_CANAL	Protein SEY1	0.38	-	end	2	Membrane; multi-pass membrane protein (Potential)				790
Q96G75 UniProt NPD GO	U2508_HUMAN	Protein UNQ2508/PRO5996	0.38	-	cyt	0					393
P51891 UniProt NPD GO	WNT11_COTJA	Protein Wnt-11 precursor	0.38	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix				354
O70283 UniProt NPD GO	WNT2B_MOUSE	Protein Wnt-2b precursor (Wnt-13)	0.38	-	mit	0	Secreted protein; extracellular space; extracellular matrix				389
O14905 UniProt NPD GO	WNT9B_HUMAN	Protein Wnt-9b precursor (Wnt-15) (Wnt-14b)	0.38	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix	extracellular region [NAS]	602864		357
Q7XIM7 UniProt NPD GO	YAB1_ORYSA	Protein YABBY (OsYAB1) (Filamentous flower protein 1)	0.38	-	nuc	0	Nucleus				169
P23241 UniProt NPD GO	ELAV_DROVI	Protein elav (Embryonic lethal abnormal visual protein)	0.38	-	nuc	0					519
Q61239 UniProt NPD GO	PFTA_MOUSE	Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit (EC 2.5.1.58) (EC 2.5.1.5 ...	0.38	-	cyt	0					377
P13360 UniProt NPD GO	GLAS_DROME	Protein glass	0.38	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			604
Q8N2W9 UniProt NPD GO	PIAS4_HUMAN	Protein inhibitor of activated STAT protein 4 (Protein inhibitor of activated STAT protein gamma) (P ...	0.38	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Colocalizes with promyelocytic leukemia nucle ...	nucleus [IDA]	605989		510
P24723 UniProt NPD GO	KPCL_HUMAN	Protein kinase C eta type (EC 2.7.11.13) (nPKC-eta) (PKC-L)	0.38	-	cyt	0			605437		682
P09217 UniProt NPD GO	KPCZ_RAT	Protein kinase C zeta type (EC 2.7.11.13) (nPKC-zeta)	0.38	-	cyt	0	Cytoplasm. In the retina, localizes in the terminals of the rod bipolar cells				592
P18502 UniProt NPD GO	PTC_DROME	Protein patched (Hedgehog receptor)	0.38	-	end	11	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			1286
P49597 UniProt NPD GO	PP2C1_ARATH	Protein phosphatase 2C ABI1 (EC 3.1.3.16) (PP2C) (Abscisic acid-insensitive 1)	0.38	+	nuc	0					434
Q12702 UniProt NPD GO	2ABA_SCHPO	Protein phosphatase PP2A regulatory subunit B (PR55) (Protein phosphatase 2A 55 kDa regulatory subun ...	0.38	-	pox	0					463
Q9D1C3 UniProt NPD GO	PREY_MOUSE	Protein preY, mitochondrial precursor	0.38	-	mit	0	Mitochondrion (Potential)	endoplasmic reticulum membrane [ISS] glycosylphosphatidylinositol-N-acetylglucos... [ISS]			112
Q74ZD2 UniProt NPD GO	SEC22_ASHGO	Protein transport protein SEC22	0.38	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)				214
Q3SZN2 UniProt NPD GO	SC23B_BOVIN	Protein transport protein Sec23B (SEC23-related protein B)	0.38	-	cyt	0					767
O14266 UniProt NPD GO	SEC39_SCHPO	Protein transport protein sec39	0.38	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				769
Q8K3V4 UniProt NPD GO	PADI6_MOUSE	Protein-arginine deiminase type-6 (EC 3.5.3.15) (Protein-arginine deiminase type VI) (Peptidylargini ...	0.38	-	cyt	0	Cytoplasm. Nucleus. Predominantly cytoplasmic (oocyte cytoplasmic sheets), also nuclear	cytoplasm [IDA] intermediate filament cytoskeleton [IDA]			682
Q9Y5F0 UniProt NPD GO	PCDBD_HUMAN	Protocadherin beta 13 precursor (PCDH-beta13)	0.38	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	integral to membrane [NAS]	606339		798
Q5DRB0 UniProt NPD GO	PCDGD_PANTR	Protocadherin gamma B1 precursor (PCDH-gamma-B1)	0.38	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				927
Q5DRA8 UniProt NPD GO	PCDGG_PANTR	Protocadherin gamma B4 precursor (PCDH-gamma-B4)	0.38	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				923
Q9UN71 UniProt NPD GO	PCDGG_HUMAN	Protocadherin gamma B4 precursor (PCDH-gamma-B4) (Cadherin-20) (Fibroblast cadherin 2)	0.38	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	membrane [NAS]	604968		923
P12660 UniProt NPD GO	PCP2_MOUSE	Purkinje cell protein 2 (Protein PCD-5) (Purkinje cell-specific protein L7)	0.38	-	nuc	0					99
Q84L32 UniProt NPD GO	RD23B_ARATH	Putative DNA repair protein RAD23-2 (RAD23-like protein 2) (AtRAD23-2)	0.38	-	nuc	0	Nucleus (Probable)				368
Q9XVR8 UniProt NPD GO	NOLA3_CAEEL	Putative H/ACA ribonucleoprotein complex subunit 3-like protein	0.38	-	nuc	0	Nucleus; nucleolus (By similarity)				64
Q9M0M4 UniProt NPD GO	MO25M_ARATH	Putative MO25-like protein At4g17270	0.38	-	mit	0					343
P30642 UniProt NPD GO	IF37_CAEEL	Putative eukaryotic translation initiation factor 3 subunit 7 (eIF-3 zeta) (eIF3d)	0.38	-	nuc	0					570
Q92215 UniProt NPD GO	TOXC_COCCA	Putative fatty acid synthase subunit TOXC [Includes: 3-hydroxypalmitoyl-[acyl-carrier-protein] dehyd ...	0.38	-	cyt	0					2080
O81007 UniProt NPD GO	GT7_ARATH	Putative glycosyltransferase 7 (EC 2.4.-.-) (AtGT7)	0.38	+	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				449
P58951 UniProt NPD GO	GR22A_DROME	Putative gustatory receptor 22a	0.38	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			394
O81893 UniProt NPD GO	ITPK3_ARATH	Putative inositol-tetrakisphosphate 1-kinase 3 (EC 2.7.1.134) (Inositol-triphosphate 5/6-kinase 3) ( ...	0.38	-	nuc	0					333
Q6L3N7 UniProt NPD GO	R1C3_SOLDE	Putative late blight resistance protein homolog R1C-3	0.38	-	mit	0	Cytoplasm (By similarity)				1292
Q08548 UniProt NPD GO	YO175_YEAST	Putative membrane-bound O-acyltransferase YOR175C (EC 2.3.1.-)	0.38	-	end	7 *		endoplasmic reticulum [IDA]			619
O76997 UniProt NPD GO	TRK1_LYMST	Putative neurotrophin receptor LTRK 1 precursor (EC 2.7.10.1)	0.38	-	end	1 *	Membrane; single-pass type I membrane protein				794
Q9LK90 UniProt NPD GO	ALA8_ARATH	Putative phospholipid-transporting ATPase 8 (EC 3.6.3.1) (Aminophospholipid flippase 8)	0.38	+	end	10	Membrane; multi-pass membrane protein				1189
Q8IA41 UniProt NPD GO	GLT11_DROME	Putative polypeptide N-acetylgalactosaminyltransferase 11 (EC 2.4.1.41) (Protein-UDP acetylgalactosa ...	0.38	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi stack [ISS]			557
Q8IA44 UniProt NPD GO	GLT12_DROME	Putative polypeptide N-acetylgalactosaminyltransferase 12 (EC 2.4.1.41) (Protein-UDP acetylgalactosa ...	0.38	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi stack [ISS]			563
O42980 UniProt NPD GO	YBE1_SCHPO	Putative thiol protease C17D11.01 (EC 3.4.22.-)	0.38	-	nuc	0		cytoplasm [IDA]			420

You are viewing entries 33701 to 33750 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.