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
Q3USZ8 UniProt NPD GO	CC058_MOUSE	Protein C3orf58 homolog precursor	0.48	-	exc	0					444
Q9USP7 UniProt NPD GO	YHP6_SCHPO	Protein C902.06 in chromosome II	0.48	-	nuc	0	Cytoplasm	microtubule [IDA]			397
Q9D772 UniProt NPD GO	CI025_MOUSE	Protein C9orf25 homolog	0.48	-	nuc	0					157
Q8N4J0 UniProt NPD GO	CI041_HUMAN	Protein C9orf41	0.48	-	mit	0					409
Q8WUX9 UniProt NPD GO	CHMP7_HUMAN	Protein CHMP7	0.48	-	cyt	0					453
Q5R812 UniProt NPD GO	CHMP7_PONPY	Protein CHMP7	0.48	-	cyt	0					453
P25580 UniProt NPD GO	PBN1_YEAST	Protein PBN1 (Protease B Non-derepressible protein 1)	0.48	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein	endoplasmic reticulum [IDA]			416
P32567 UniProt NPD GO	SMP2_YEAST	Protein SMP2	0.48	-	nuc	0		cytoplasm [IDA] membrane fraction [IDA]			862
Q7RTT4 UniProt NPD GO	SSX8_HUMAN	Protein SSX8	0.48	-	nuc	0			300543		148
P38960 UniProt NPD GO	STN1_YEAST	Protein STN1	0.48	-	cyt	0		nuclear telomere cap complex [TAS]			494
P28132 UniProt NPD GO	WN10B_PLEJO	Protein Wnt-10b (Fragment)	0.48	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				117
P28095 UniProt NPD GO	WNT2_STRPU	Protein Wnt-2 (Fragment)	0.48	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				115
Q8AVX5 UniProt NPD GO	XRP2_XENLA	Protein XRP2	0.48	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity)				352
Q10660 UniProt NPD GO	DOM3_CAEEL	Protein dom-3	0.48	-	cyt	0					393
P15370 UniProt NPD GO	EGON_DROME	Protein embryonic gonad (Protein eagle) (Protein spready)	0.48	-	nuc	0	Nucleus (Potential)				373
P84329 UniProt NPD GO	HFW1_DROPS	Protein halfway (Protein singed wings)	0.48	-	nuc	0					595
O18326 UniProt NPD GO	HUNB_BOMMO	Protein hunchback (Fragment)	0.48	-	nuc	0	Nucleus (Probable)				385
P28178 UniProt NPD GO	PK2_DICDI	Protein kinase 2 (EC 2.7.11.1)	0.48	-	nuc	0					479
Q58EX2 UniProt NPD GO	SDK2_HUMAN	Protein sidekick-2 precursor	0.48	-	exc	1	Membrane; single-pass type I membrane protein (Potential)		607217	1WFO	2170
P19382 UniProt NPD GO	SNAI_XENLA	Protein snail homolog Sna (Protein xSna)	0.48	-	nuc	0	Nucleus (Potential)				259
Q9D662 UniProt NPD GO	SC23B_MOUSE	Protein transport protein Sec23B (SEC23-related protein B)	0.48	-	cyt	0		perinuclear region [IDA]			767
Q9Y5F9 UniProt NPD GO	PCDGI_HUMAN	Protocadherin gamma B6 precursor (PCDH-gamma-B6)	0.48	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		606303		930
Q5DRA2 UniProt NPD GO	PCDGM_PANTR	Protocadherin gamma C5 precursor (PCDH-gamma-C5)	0.48	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				944
Q8K4S3 UniProt NPD GO	S45A1_RAT	Proton-associated sugar transporter A (PAST-A) (Solute carrier family 45 member 1)	0.48	-	end	11	Membrane; multi-pass membrane protein (Potential)				751
Q9UIG5 UniProt NPD GO	PS1C1_HUMAN	Psoriasis susceptibility 1 candidate gene 1 protein (SEEK1 protein)	0.48	-	nuc	0					152
Q21122 UniProt NPD GO	F26_CAEEL	Putative 6PF-2-K/Fru-2,6-P2ASE [Includes: 6-phosphofructo-2-kinase (EC 2.7.1.105); Fructose-2,6-bisp ...	0.48	-	cyt	0					457
P24346 UniProt NPD GO	AN3_XENLA	Putative ATP-dependent RNA helicase an3 (EC 3.6.1.-)	0.48	-	cyt	0					697
P46441 UniProt NPD GO	N2B_HAEIR	Putative ATPase N2B (HFN2B)	0.48	-	mit	0					464
Q497M3 UniProt NPD GO	ABEC4_MOUSE	Putative C->U-editing enzyme APOBEC-4 (EC 3.5.4.-) (Apolipoprotein B mRNA-editing enzyme catalytic p ...	0.48	-	nuc	0					374
Q9STE7 UniProt NPD GO	R13L3_ARATH	Putative disease resistance RPP13-like protein 3	0.48	-	cyt	0					847
P58954 UniProt NPD GO	GR22F_DROME	Putative gustatory receptor 22f	0.48	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			378
Q9VM09 UniProt NPD GO	GR28A_DROME	Putative gustatory receptor 28a	0.48	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			450
Q6L3Z7 UniProt NPD GO	R1B14_SOLDE	Putative late blight resistance protein homolog R1B-14	0.48	-	cyt	0	Cytoplasm (By similarity)				1317
Q10490 UniProt NPD GO	SYLC_SCHPO	Putative leucyl-tRNA synthetase, cytoplasmic (EC 6.1.1.4) (Leucine--tRNA ligase) (LeuRS)	0.48	-	cyt	0	Cytoplasm (By similarity)				1111
P78920 UniProt NPD GO	YB31_SCHPO	Putative nucleosome assembly protein C2D10.11C	0.48	-	nuc	0	Nucleus (Potential)				379
O59797 UniProt NPD GO	YCO6_SCHPO	Putative nucleosome assembly protein C364.06	0.48	+	nuc	0	Nucleus (Potential)				393
Q9SGG3 UniProt NPD GO	ALA5_ARATH	Putative phospholipid-transporting ATPase 5 (EC 3.6.3.1) (Aminophospholipid flippase 5)	0.48	-	end	10	Membrane; multi-pass membrane protein				1228
Q21734 UniProt NPD GO	KS6A1_CAEEL	Putative ribosomal protein S6 kinase alpha-1 (EC 2.7.11.1)	0.48	-	cyt	0					784
O23100 UniProt NPD GO	APRR8_ARATH	Putative two-component response regulator-like APRR8 (Pseudo-response regulator 8)	0.48	-	nuc	0	Nucleus (Probable)				367
Q12454 UniProt NPD GO	OCA6_YEAST	Putative tyrosine-protein phosphatase OCA6 (EC 3.1.3.48) (Oxidant-induced cell-cycle arrest protein ...	0.48	-	nuc	0	Cytoplasm	cytoplasm [IDA]			224
P25572 UniProt NPD GO	YCE2_YEAST	Putative uncharacterized protein YCL042W	0.48	-	nuc	0		cytoplasm [IDA]			119
Q9LK50 UniProt NPD GO	WBC27_ARATH	Putative white-brown complex homolog protein 27	0.48	-	end	6	Membrane; multi-pass membrane protein (By similarity)				693
Q9FF46 UniProt NPD GO	WBC29_ARATH	Putative white-brown complex homolog protein 29	0.48	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				1109
Q9UBS8 UniProt NPD GO	RNF14_HUMAN	RING finger protein 14 (Androgen receptor-associated protein 54) (Triad2 protein) (HFB30)	0.48	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]	605675		474
P38239 UniProt NPD GO	YBR2_YEAST	RING finger protein YBR062C	0.48	-	nuc	0					180
Q4IEV5 UniProt NPD GO	REXO4_GIBZE	RNA exonuclease 4 (EC 3.1.-.-)	0.48	+	nuc	0	Nucleus (By similarity)				319
Q6CMT3 UniProt NPD GO	REXO4_KLULA	RNA exonuclease 4 (EC 3.1.-.-)	0.48	+	nuc	0	Nucleus (By similarity)				294
O13759 UniProt NPD GO	CSX1_SCHPO	RNA-binding post-transcriptional regulator csx1	0.48	-	nuc	0	Cytoplasm	cytoplasm [IDA]			632
Q9D9S3 UniProt NPD GO	RWDD2_MOUSE	RWD domain-containing protein 2	0.48	-	cyt	0					292
Q8IZJ4 UniProt NPD GO	RGDSR_HUMAN	Ral-GDS-related protein (hRGR)	0.48	-	exc	0	Cytoplasmic vesicle (By similarity)				473

You are viewing entries 26501 to 26550 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.