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
Q9TYK1 UniProt NPD GO	NOLA1_CAEEL	Putative H/ACA ribonucleoprotein complex subunit 1-like protein	0.20	+	cyt	0	Nucleus; nucleolus (By similarity)				244
Q9M290 UniProt NPD GO	NAC61_ARATH	Putative NAC domain-containing protein 61 (ANAC061)	0.20	-	nuc	0	Nucleus (Potential)				228
P34492 UniProt NPD GO	YMQ1_CAEEL	Putative NipSnap protein K02D10.1	0.20	-	cyt	0					526
O00398 UniProt NPD GO	P2Y10_HUMAN	Putative P2Y purinoceptor 10 (P2Y10) (P2Y-like receptor)	0.20	-	end	7 *	Membrane; multi-pass membrane protein		300529		339
O43865 UniProt NPD GO	SAHH2_HUMAN	Putative adenosylhomocysteinase 2 (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase 2) (AdoHcyase 2) ...	0.20	-	cyt	0			607826		530
Q80SW1 UniProt NPD GO	SAHH2_MOUSE	Putative adenosylhomocysteinase 2 (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase 2) (AdoHcyase 2) ...	0.20	-	cyt	0					530
Q9FMA0 UniProt NPD GO	EXP14_ARATH	Putative alpha-expansin 14 precursor (AtEXPA14) (At-EXP14) (AtEx14) (Ath-ExpAlpha-1.5)	0.20	-	cyt	0	Cell wall; peripheral membrane protein				255
P42168 UniProt NPD GO	YKL1_CAEEL	Putative casein kinase I C03C10.1 (EC 2.7.11.1)	0.20	-	cyt	0					341
P94017 UniProt NPD GO	CAP9_ARATH	Putative clathrin assembly protein At1g14910	0.20	-	cyt	0					692
Q20893 UniProt NPD GO	CDO_CAEEL	Putative cysteine dioxygenase (EC 1.13.11.20) (CDO)	0.20	-	cyt	0					190
P07915 UniProt NPD GO	EGGS_FASHE	Putative eggshell protein precursor	0.20	-	exc	0					197
Q9VM08 UniProt NPD GO	GR28B_DROME	Putative gustatory receptor 28b	0.20	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			470
Q9W1N5 UniProt NPD GO	GR59F_DROME	Putative gustatory receptor 59f	0.20	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			406
P87118 UniProt NPD GO	IPYR2_SCHPO	Putative inorganic pyrophosphatase C3A12.02 (EC 3.6.1.1) (Pyrophosphate phosphohydrolase) (PPase)	0.20	-	nuc	0	Cytoplasm (By similarity)				286
Q9LSJ6 UniProt NPD GO	MDR19_ARATH	Putative multidrug resistance protein 19 (P-glycoprotein 17)	0.20	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				1240
Q9VYZ1 UniProt NPD GO	OR10A_DROME	Putative odorant receptor 10a	0.20	-	cyt	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			406
Q07530 UniProt NPD GO	YD114_YEAST	Putative oxidoreductase YDL114W (EC 1.-.-.-)	0.20	-	mit	0					308
Q92247 UniProt NPD GO	BLI4_NEUCR	Putative oxidoreductase bli-4, mitochondrial precursor (EC 1.-.-.-)	0.20	-	mit	0	Mitochondrion				412
Q944H0 UniProt NPD GO	PEAM2_ARATH	Putative phosphoethanolamine N-methyltransferase 2 (EC 2.1.1.103)	0.20	-	cyt	0	Cytoplasm (By similarity)				475
P83855 UniProt NPD GO	ACLP_MOUSE	Putative sperm adenylate cyclase (EC 4.6.1.1) (Fragment)	0.20	-	nuc	0					21
Q9UAY4 UniProt NPD GO	ASM3_CAEEL	Putative sphingomyelin phosphodiesterase asm-3 precursor (EC 3.1.4.12)	0.20	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS]			589
Q04487 UniProt NPD GO	YM07_YEAST	Putative succinate dehydrogenase cytochrome B subunit, mitochondrial precursor	0.20	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				196
Q8NAJ2 UniProt NPD GO	CI106_HUMAN	Putative uncharacterized protein C9orf106	0.20	-	nuc	0					232
Q3E732 UniProt NPD GO	YL264_YEAST	Putative uncharacterized protein YLR264C-A	0.20	-	nuc	0					38
P53862 UniProt NPD GO	YNW8_YEAST	Putative uncharacterized protein YNL228W precursor	0.20	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				258
Q8J136 UniProt NPD GO	P2OX_PENSG	Pyranose 2-oxidase precursor (EC 1.1.3.10) (P2Ox) (Pyranose oxidase) (PROD) (POD) (POx) (Pyranose:ox ...	0.20	-	cyt	0	Hyphal periplasmic space (By similarity)			2F5V	623
Q91XF4 UniProt NPD GO	RN167_MOUSE	RING finger protein 167 precursor	0.20	-	end	1	Membrane; single-pass membrane protein (Potential)				347
Q38919 UniProt NPD GO	RAC4_ARATH	Rac-like GTP-binding protein ARAC4 (GTPase protein ROP2)	0.20	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				195
Q38937 UniProt NPD GO	RAC5_ARATH	Rac-like GTP-binding protein ARAC5 (GTPase protein ROP4)	0.20	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Associated with the membrane when activated				196
P22280 UniProt NPD GO	RAS3_RHIRA	Ras-like protein 3	0.20	-	cyt	0	Cell membrane; lipid-anchor				205
P28186 UniProt NPD GO	ARA3_ARATH	Ras-related protein ARA-3	0.20	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				216
P35289 UniProt NPD GO	RAB15_RAT	Ras-related protein Rab-15	0.20	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	membrane [TAS]			212
P10949 UniProt NPD GO	RAB3C_BOVIN	Ras-related protein Rab-3C (SMG P25C)	0.20	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				227
P35279 UniProt NPD GO	RAB6A_MOUSE	Ras-related protein Rab-6A (Rab-6)	0.20	-	cyt	0	Golgi apparatus; Golgi membrane; lipid-anchor	Golgi apparatus [IDA]			207
Q9WVB1 UniProt NPD GO	RAB6A_RAT	Ras-related protein Rab-6A (Rab-6) (Fragment)	0.20	-	cyt	0	Golgi apparatus; Golgi membrane; lipid-anchor				140
O04157 UniProt NPD GO	RAB7_ARATH	Ras-related protein Rab7 (AtRab75)	0.20	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				203
Q61527 UniProt NPD GO	ERBB4_MOUSE	Receptor tyrosine-protein kinase erbB-4 (EC 2.7.10.1) (Fragments)	0.20	-	nuc	0	Membrane; single-pass type I membrane protein				95
O46471 UniProt NPD GO	RGS16_BOVIN	Regulator of G-protein signaling 16 (RGS16) (Retinally abundant regulator of G-protein signaling) (R ...	0.20	-	nuc	0					202
P49808 UniProt NPD GO	RGS2_CAEEL	Regulator of G-protein signaling rgs-2	0.20	-	cyt	0					169
Q6PCX7 UniProt NPD GO	RGMA_MOUSE	Repulsive guidance molecule A precursor (RGM domain family member A)	0.20	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	cell surface [IDA]			454
P61249 UniProt NPD GO	CNCG_MOUSE	Retinal cone rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase gamma-subunit (EC 3.1.4.17) (GM ...	0.20	-	nuc	0					83
P61250 UniProt NPD GO	CNCG_RAT	Retinal cone rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase gamma-subunit (EC 3.1.4.17) (GM ...	0.20	-	nuc	0					83
P04972 UniProt NPD GO	CNRG_BOVIN	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase gamma-subunit (EC 3.1.4.17) (GMP ...	0.20	-	cyt	0				1FQJ	87
O57414 UniProt NPD GO	RHG06_FUGRU	Rho-GTPase-activating protein 6 (Rho-type GTPase-activating protein RhoGAPX-1) (Fragment)	0.20	-	mit	0	Cytoplasm (Potential)				53
Q9U6P6 UniProt NPD GO	RNHL_CAEEL	Ribonuclease HI large subunit (EC 3.1.26.4) (RNase HI large subunit) (RNase H(35))	0.20	-	cyt	0					297
O46527 UniProt NPD GO	RNAS6_PAPHA	Ribonuclease K6 precursor (EC 3.1.27.-) (RNase K6)	0.20	-	nuc	1 *	Secreted protein				150
P67926 UniProt NPD GO	RNAS1_CAPHI	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.20	-	nuc	0	Secreted protein				124
P67927 UniProt NPD GO	RNAS1_SHEEP	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.20	-	nuc	0	Secreted protein				124
P00684 UniProt NPD GO	RNS1B_RAT	Ribonuclease pancreatic beta-type precursor (EC 3.1.27.5) (RNase 1 gamma) (RNase A) (RL1)	0.20	-	exc	0	Secreted protein			1RRA	152
Q9WUV3 UniProt NPD GO	RNAS1_MICNV	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.20	-	exc	0	Secreted protein				148

You are viewing entries 51151 to 51200 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.