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
Q5W274 UniProt NPD GO	PDR3_TOBAC	Pleiotropic drug resistance protein 3 (NtPDR3)	0.49	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1447
O75051 UniProt NPD GO	PLXA2_HUMAN	Plexin-A2 precursor (Semaphorin receptor OCT)	0.49	-	end	1	Membrane; single-pass type I membrane protein (Potential)		601054		1909
Q11207 UniProt NPD GO	PARP2_ARATH	Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30) (PARP-2) (ADPRT 2) (NAD(+) ADP-ribosyltransferase 2) (P ...	0.49	-	cyt	0	Nucleus				637
O42617 UniProt NPD GO	PAP_CANAL	Poly(A) polymerase PAPalpha (EC 2.7.7.19) (Polynucleotide adenylyltransferase alpha)	0.49	+	cyt	0	Nucleus				558
Q9VUT6 UniProt NPD GO	GALT8_DROME	Polypeptide N-acetylgalactosaminyltransferase 8 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.49	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi stack [NAS]			590
Q9R1T9 UniProt NPD GO	KCNH4_RAT	Potassium voltage-gated channel subfamily H member 4 (Voltage-gated potassium channel subunit Kv12.3 ...	0.49	-	nuc	6	Membrane; multi-pass membrane protein				1017
Q6FM43 UniProt NPD GO	PRP28_CANGA	Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 (EC 3.6.1.-)	0.49	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				582
Q752S4 UniProt NPD GO	CWC24_ASHGO	Pre-mRNA-splicing factor CWC24	0.49	-	nuc	0	Nucleus (By similarity)				250
Q6CSS6 UniProt NPD GO	CWC24_KLULA	Pre-mRNA-splicing factor CWC24	0.49	+	nuc	0	Nucleus (By similarity)				229
O60508 UniProt NPD GO	PRP17_HUMAN	Pre-mRNA-splicing factor PRP17 (hPRP17) (Cell division cycle 40 homolog) (EH-binding protein 3) (Ehb ...	0.49	-	nuc	0	Nucleus	spliceosome complex [TAS]	605585		579
Q10185 UniProt NPD GO	YAWB_SCHPO	Probable ATP-dependent permease C3F10.11c	0.49	-	end	14 *	Membrane; multi-pass membrane protein (Potential)				1478
Q9P7X8 UniProt NPD GO	RPA2_SCHPO	Probable DNA-directed RNA polymerase I polypeptide 2 (EC 2.7.7.6) (RNA polymerase I subunit 2)	0.49	-	cyt	0	Nucleus (Potential)				1227
Q9LM71 UniProt NPD GO	FKBP1_ARATH	Probable FKBP-type peptidyl-prolyl cis-trans isomerase 1, chloroplast precursor (EC 5.2.1.8) (PPIase ...	0.49	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen				232
O02108 UniProt NPD GO	CDC37_CAEEL	Probable Hsp90 co-chaperone cdc37 (Hsp90 chaperone protein kinase-targeting subunit) (Cell division ...	0.49	-	nuc	0	Cytoplasm (By similarity)				370
Q9V4Q8 UniProt NPD GO	RU2A_DROME	Probable U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.49	-	nuc	0	Nucleus (Potential)				265
Q9FL62 UniProt NPD GO	WRK30_ARATH	Probable WRKY transcription factor 30 (WRKY DNA-binding protein 30)	0.49	-	nuc	0	Nucleus (Probable)				303
P38360 UniProt NPD GO	ATU1_YEAST	Probable copper-transporting ATPase (EC 3.6.3.4) (Cu(2+)-ATPase)	0.49	+	end	7	Membrane; multi-pass membrane protein	membrane [IMP]			1216
Q9VVR9 UniProt NPD GO	C12C1_DROME	Probable cytochrome P450 12c1, mitochondrial precursor (EC 1.14.-.-) (CYPXIIC1)	0.49	-	mit	0	Mitochondrion (Potential)				524
O81053 UniProt NPD GO	FUT2_ARATH	Probable fucosyltransferase 2 (EC 2.4.1.-) (AtFUT2)	0.49	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				539
Q9XI81 UniProt NPD GO	FUT7_ARATH	Probable fucosyltransferase 7 (EC 2.4.1.-) (AtFUT7)	0.49	-	end	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				526
Q84YK8 UniProt NPD GO	LOXC2_ORYSA	Probable lipoxygenase 8, chloroplast precursor (EC 1.13.11.12)	0.49	-	mit	0	Plastid; chloroplast (Potential)				941
Q8R0N9 UniProt NPD GO	ZDHC1_MOUSE	Probable palmitoyltransferase ZDHHC1 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 1) (DH ...	0.49	+	end	4 *	Membrane; multi-pass membrane protein (Potential)				484
Q5R838 UniProt NPD GO	ZDHC5_PONPY	Probable palmitoyltransferase ZDHHC5 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 5) (DH ...	0.49	-	mit	4 *	Membrane; multi-pass membrane protein (Potential)				715
Q10439 UniProt NPD GO	YDE5_SCHPO	Probable peptidase C12B10.05 (EC 3.4.-.-)	0.49	-	mit	0					486
O44568 UniProt NPD GO	RF1M_CAEEL	Probable peptide chain release factor 1, mitochondrial precursor (MRF-1)	0.49	-	mit	0	Mitochondrion (Potential)				389
P34335 UniProt NPD GO	KPBA_CAEEL	Probable phosphorylase b kinase regulatory subunit alpha (Phosphorylase kinase subunit alpha)	0.49	-	cyt	0					1226
Q7PC84 UniProt NPD GO	PDR11_ARATH	Probable pleiotropic drug resistance protein 11	0.49	-	end	12	Membrane; multi-pass membrane protein (By similarity)				1454
Q7PC83 UniProt NPD GO	PDR13_ARATH	Probable pleiotropic drug resistance protein 13	0.49	-	end	11	Membrane; multi-pass membrane protein (By similarity)				1397
O42945 UniProt NPD GO	DHX15_SCHPO	Probable pre-mRNA-splicing factor ATP-dependent RNA helicase prp43 (EC 3.6.1.-)	0.49	-	cyt	0	Nucleus (By similarity)				735
Q96B02 UniProt NPD GO	UBE2W_HUMAN	Probable ubiquitin-conjugating enzyme E2 W (EC 6.3.2.19) (Ubiquitin-protein ligase W) (Ubiquitin car ...	0.49	-	nuc	0				2A7L	151
Q38908 UniProt NPD GO	XTH30_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 30 precursor (EC 2.4.1.207) (At-XTH30) (X ...	0.49	-	exc	0	Secreted protein; extracellular space; apoplast (Probable)				343
Q28409 UniProt NPD GO	PENK_FELCA	Proenkephalin A [Contains: Synenkephalin; Met-enkephalin; Leu-enkephalin] (Fragment)	0.49	-	nuc	0	Secreted protein				187
Q9WU78 UniProt NPD GO	PDC6I_MOUSE	Programmed cell death 6-interacting protein (ALG-2-interacting protein X) (ALG-2-interacting protein ...	0.49	-	nuc	0	Cytoplasm; cytosol (By similarity)	cytosol [IDA]			869
P48249 UniProt NPD GO	PRL_DICLA	Prolactin precursor (PRL)	0.49	-	exc	1 *	Secreted protein				212
P20646 UniProt NPD GO	PPAP_RAT	Prostatic acid phosphatase precursor (EC 3.1.3.2)	0.49	-	exc	0				1RPT	381
Q2TBV0 UniProt NPD GO	BEX2_BOVIN	Protein BEX2 (Brain-expressed X-linked protein 2 homolog)	0.49	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				128
Q3MKP9 UniProt NPD GO	BEX4_RAT	Protein BEX4 (Brain-expressed X-linked protein 4 homolog) (BEX1-like 1)	0.49	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				118
Q8NDZ4 UniProt NPD GO	CC058_HUMAN	Protein C3orf58 precursor	0.49	-	mit	0					430
Q63HQ0 UniProt NPD GO	CD016_HUMAN	Protein C4orf16	0.49	-	nuc	0					302
Q9Z1R4 UniProt NPD GO	CF047_MOUSE	Protein C6orf47 homolog	0.49	-	end	0					293
P39715 UniProt NPD GO	ECM1_YEAST	Protein ECM1 (Extracellular matrix protein 1) (Protein SIM1)	0.49	-	nuc	0	Nucleus	nucleolus [IDA] nucleoplasm [IDA] nucleus [IDA]			212
Q12497 UniProt NPD GO	FMP16_YEAST	Protein FMP16, mitochondrial precursor (Found in mitochondrial proteome protein 16)	0.49	-	mit	0	Mitochondrion	mitochondrion [IDA]			93
Q9P305 UniProt NPD GO	IGO2_YEAST	Protein IGO2	0.49	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			130
Q9NPB8 UniProt NPD GO	K1434_HUMAN	Protein KIAA1434	0.49	-	cyt	0					672
Q00246 UniProt NPD GO	RHO4_YEAST	Protein RHO4	0.49	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	intracellular [TAS]			291
Q92734 UniProt NPD GO	TFG_HUMAN	Protein TFG (TRK-fused gene protein)	0.49	-	nuc	0		cytoplasm [NAS]	602498		400
P40040 UniProt NPD GO	THO1_YEAST	Protein THO1	0.49	-	nuc	0		nucleus [IDA]		1H1J	218
Q7KRW1 UniProt NPD GO	TRC8_DROME	Protein TRC8 homolog	0.49	-	end	11	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			809
P34889 UniProt NPD GO	WNT2_CAEEL	Protein Wnt-2 precursor	0.49	-	exc	0	Secreted protein; extracellular space; extracellular matrix				360
P51029 UniProt NPD GO	WNT8B_BRARE	Protein Wnt-8b precursor	0.49	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				358

You are viewing entries 25801 to 25850 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.