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
P83294 UniProt NPD GO	GR64B_DROME	Putative gustatory receptor 64b	0.12	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			406
P09565 UniProt NPD GO	IG2R_HUMAN	Putative insulin-like growth factor 2-associated protein (Insulin-like growth factor II-associated p ...	0.12	-	nuc	0					84
O13805 UniProt NPD GO	YE08_SCHPO	Putative mitochondrial carrier C17H9.08	0.12	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				326
Q9I816 UniProt NPD GO	OR19A_DROME	Putative odorant receptor 19a	0.12	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			387
Q9VVF3 UniProt NPD GO	OR74A_DROME	Putative odorant receptor 74a	0.12	-	end	5	Membrane; multi-pass membrane protein (Potential)				404
P82986 UniProt NPD GO	OR82A_DROME	Putative odorant receptor 82a	0.12	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				385
Q9C8G4 UniProt NPD GO	PEL4_ARATH	Putative pectate lyase 4 precursor (EC 4.2.2.2)	0.12	-	exc	0					368
Q9V9A7 UniProt NPD GO	PCCB_DROME	Putative propionyl-CoA carboxylase beta chain, mitochondrial precursor (EC 6.4.1.3) (PCCase subunit ...	0.12	-	mit	0	Mitochondrion; mitochondrial matrix				578
Q9FM41 UniProt NPD GO	DGP13_ARATH	Putative protease Do-like 13 (EC 3.4.21.-)	0.12	-	nuc	0					486
O62251 UniProt NPD GO	RRMJ1_CAEEL	Putative ribosomal RNA methyltransferase F45G2.9 (EC 2.1.1.-) (rRNA (uridine-2'-O-)-methyltransferas ...	0.12	-	mit	0					214
O78436 UniProt NPD GO	MIND_GUITH	Putative septum site-determining protein minD	0.12	-	cyt	0	Plastid; chloroplast				269
P34528 UniProt NPD GO	YM67_CAEEL	Putative serine protease K12H4.7 precursor (EC 3.4.-.-)	0.12	-	exc	0					510
Q08579 UniProt NPD GO	THIY_YEAST	Putative thiamine transporter YOR192C	0.12	-	end	10 *	Membrane; multi-pass membrane protein				599
P38215 UniProt NPD GO	YBM3_YEAST	Putative uncharacterized protein YBR013C precursor	0.12	-	exc	0					129
P53113 UniProt NPD GO	YGP2_YEAST	Putative uncharacterized protein YGL152C	0.12	-	end	3	Membrane; multi-pass membrane protein (Potential)				225
O13578 UniProt NPD GO	YL415_YEAST	Putative uncharacterized protein YLR415C, mitochondrial precursor	0.12	-	mit	0	Mitochondrion (Potential)				112
Q6YXZ1 UniProt NPD GO	CAX4_ORYSA	Putative vacuolar cation/proton exchanger 4 (Ca(2+)/H(+) exchanger 4) (OsCAX4)	0.12	-	end	9	Vacuole; vacuolar membrane; multi-pass membrane protein (Potential). Tonoplast				447
P40483 UniProt NPD GO	YIK8_YEAST	Putative zinc metalloproteinase YIL108W (EC 3.4.24.-)	0.12	-	cyt	0		cytoplasm [IDA]			696
P60487 UniProt NPD GO	PLPP_MOUSE	Pyridoxal phosphate phosphatase (EC 3.1.3.74) (PLP phosphatase)	0.12	-	cyt	0					292
P36597 UniProt NPD GO	THI3_SCHPO	Pyrimidine precursor biosynthesis enzyme thi3 (No message in thiamine protein 1)	0.12	-	cyt	0					346
P37362 UniProt NPD GO	PYRRH_PYRAP	Pyrrhocoricin	0.12	-		0	Secreted protein				20
Q8HXW9 UniProt NPD GO	ODPA_MACFA	Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor (EC 1.2.4.1 ...	0.12	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				390
P11636 UniProt NPD GO	QAY_NEUCR	Quinate permease (Quinate transporter)	0.12	-	end	11 *	Membrane; multi-pass membrane protein				537
Q98TY9 UniProt NPD GO	AKT1_XENLA	RAC-alpha serine/threonine-protein kinase (EC 2.7.11.1) (RAC-PK-alpha) (Protein kinase Akt-1) (Prote ...	0.12	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Nucleus after activation by integrin-linked prot ...	cytoplasm [ISS]			481
P31749 UniProt NPD GO	AKT1_HUMAN	RAC-alpha serine/threonine-protein kinase (EC 2.7.11.1) (RAC-PK-alpha) (Protein kinase B) (PKB) (C-A ...	0.12	-	cyt	0	Cytoplasm. Nucleus. Nucleus after activation by integrin-linked protein kinase 1 (ILK1)	cytoplasm [ISS]	164730	1UNR	480
O42581 UniProt NPD GO	RDS1_XENLA	RDS/peripherin-like protein xRDS35	0.12	-	end	3 *	Membrane; multi-pass membrane protein				345
Q7TQ33 UniProt NPD GO	RGMB_MOUSE	RGM domain family member B precursor	0.12	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	anchored to plasma membrane [IDA] ER-Golgi intermediate compartment [IDA]			436
Q08096 UniProt NPD GO	RCL1_YEAST	RNA 3'-terminal phosphate cyclase-like protein	0.12	-	mit	0	Nucleus; nucleolus	nucleolus [IDA]			367
O43251 UniProt NPD GO	RBM9_HUMAN	RNA-binding protein 9 (RNA-binding motif protein 9) (Hexaribonucleotide-binding protein 2) (Represso ...	0.12	-	cyt	0		nucleus [IDA]		2CQ3	390
Q61474 UniProt NPD GO	MSI1H_MOUSE	RNA-binding protein Musashi homolog 1 (Musashi-1)	0.12	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA] polysome [IDA]		2MST	362
Q8K3P4 UniProt NPD GO	MSI1H_RAT	RNA-binding protein Musashi homolog 1 (Musashi-1)	0.12	-	cyt	0	Cytoplasm. Nucleus				362
Q9W6I1 UniProt NPD GO	RBPMS_CHICK	RNA-binding protein with multiple splicing homolog (RBP-MS) (HEart, RRM Expressed Sequence) (Hermes) ...	0.12	-	cyt	0					200
Q38903 UniProt NPD GO	RAC2_ARATH	Rac-like GTP-binding protein ARAC2 (GTPase protein ROP7)	0.12	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				201
P87018 UniProt NPD GO	RAS_BOTCI	Ras-like protein	0.12	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				212
P28775 UniProt NPD GO	RAS_LENED	Ras-like protein	0.12	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				217
Q5ZJN2 UniProt NPD GO	RB11A_CHICK	Ras-related protein Rab-11A	0.12	-	cyt	0	Cell membrane; lipid-anchor (By similarity). Endosome; recycling endosome; recycling endosomal membr ...				216
P62822 UniProt NPD GO	RAB1A_CANFA	Ras-related protein Rab-1A	0.12	-	cyt	0	Golgi apparatus				204
Q52NJ2 UniProt NPD GO	RAB1A_PIG	Ras-related protein Rab-1A	0.12	-	cyt	0	Golgi apparatus				204
Q6NYB7 UniProt NPD GO	RAB1A_RAT	Ras-related protein Rab-1A	0.12	-	cyt	0	Golgi apparatus				204
P62820 UniProt NPD GO	RAB1A_HUMAN	Ras-related protein Rab-1A (YPT1-related protein)	0.12	-	cyt	0	Golgi apparatus		179508	2FOL	204
P62821 UniProt NPD GO	RAB1A_MOUSE	Ras-related protein Rab-1A (YPT1-related protein)	0.12	-	cyt	0	Golgi apparatus	Golgi apparatus [IDA]			204
P51156 UniProt NPD GO	RAB26_RAT	Ras-related protein Rab-26	0.12	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				257
Q9CZE3 UniProt NPD GO	RAB32_MOUSE	Ras-related protein Rab-32	0.12	-	cyt	0	Mitochondrion (By similarity)				222
Q9H082 UniProt NPD GO	RB33B_HUMAN	Ras-related protein Rab-33B	0.12	-	mit	0	Golgi apparatus; Golgi membrane; lipid-anchor (By similarity)		605950		229
Q96DA2 UniProt NPD GO	RB39B_HUMAN	Ras-related protein Rab-39B	0.12	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
Q8BHC1 UniProt NPD GO	RB39B_MOUSE	Ras-related protein Rab-39B	0.12	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
P20336 UniProt NPD GO	RAB3A_HUMAN	Ras-related protein Rab-3A	0.12	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	synaptic vesicle [TAS]	179490		220
Q4R4R9 UniProt NPD GO	RAB3A_MACFA	Ras-related protein Rab-3A	0.12	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				220
Q5JT25 UniProt NPD GO	RAB41_HUMAN	Ras-related protein Rab-41	0.12	-	cyt	0					212
P34213 UniProt NPD GO	RAB6A_CAEEL	Ras-related protein Rab-6.1	0.12	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				205

You are viewing entries 61801 to 61850 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.