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
Q99PV0 UniProt NPD GO	PRP8_MOUSE	Pre-mRNA-processing-splicing factor 8 (Splicing factor Prp8)	0.76	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle				2335
Q6P2Q9 UniProt NPD GO	PRP8_HUMAN	Pre-mRNA-processing-splicing factor 8 (Splicing factor Prp8) (PRP8 homolog) (220 kDa U5 snRNP-specif ...	0.76	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)		607300		2335
P53131 UniProt NPD GO	PRP43_YEAST	Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 (EC 3.6.1.-) (Helicase JA1)	0.76	-	nuc	0	Nucleus	mitochondrion [IDA] spliceosome complex [TAS]			767
Q75AR4 UniProt NPD GO	CWC25_ASHGO	Pre-mRNA-splicing factor CWC25	0.76	-	nuc	0	Nucleus (By similarity)				138
Q6FR30 UniProt NPD GO	ISY1_CANGA	Pre-mRNA-splicing factor ISY1	0.76	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				203
Q06461 UniProt NPD GO	SECA_ANTSP	Preprotein translocase secA subunit	0.76	-	nuc	0	Plastid; chloroplast				878
Q92841 UniProt NPD GO	DDX17_HUMAN	Probable ATP-dependent RNA helicase DDX17 (EC 3.6.1.-) (DEAD box protein 17) (RNA-dependent helicase ...	0.76	+	nuc	0	Nucleus	nucleus [TAS]			650
P60705 UniProt NPD GO	ABEC3_RAT	Probable DNA dC->dU-editing enzyme APOBEC3 (EC 3.5.4.-)	0.76	-	nuc	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				429
Q18775 UniProt NPD GO	YYI3_CAEEL	Probable G-protein coupled receptor C52B11.3	0.76	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				517
P34217 UniProt NPD GO	YBF1_YEAST	Probable RNA-binding protein YBL051C	0.76	-	nuc	0		cytoplasm [IDA]		2A0T	668
Q93WT0 UniProt NPD GO	WRK31_ARATH	Probable WRKY transcription factor 31 (WRKY DNA-binding protein 31)	0.76	-	nuc	0	Nucleus (Potential)				538
Q5A1Q5 UniProt NPD GO	NUF2_CANAL	Probable kinetochore protein NUF2	0.76	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				485
Q09879 UniProt NPD GO	UBP5_SCHPO	Probable ubiquitin carboxyl-terminal hydrolase 5 (EC 3.1.2.15) (Ubiquitin thioesterase 5) (Ubiquitin ...	0.76	-	cyt	0					1108
Q9HC23 UniProt NPD GO	PROK2_HUMAN	Prokineticin-2 precursor (PK2) (Protein Bv8 homolog)	0.76	+	exc	0	Secreted protein	extracellular region [TAS]	607002		129
Q04592 UniProt NPD GO	PCSK5_MOUSE	Proprotein convertase subtilisin/kexin type 5 precursor (EC 3.4.21.-) (Proprotein convertase PC5) (S ...	0.76	-	end	1	PC5A is secreted through the regulated secretory pathway. PC5B is a type I membrane protein localize ...				1877
Q6S8J7 UniProt NPD GO	POTE8_HUMAN	Prostate, ovary, testis-expressed protein on chromosome 8	0.76	-	nuc	0			608915		498
P08130 UniProt NPD GO	PRTB_MUGCE	Protamine-M6/M7 (Mugiline beta)	0.76	+	nuc	0	Nucleus				33
Q9H7T3 UniProt NPD GO	CJ095_HUMAN	Protein C10orf95	0.76	-	nuc	0					257
Q8K3X4 UniProt NPD GO	CN004_MOUSE	Protein C14orf4 homolog	0.76	-	nuc	0	Nucleus (Potential)				775
Q5ZLN7 UniProt NPD GO	CI042_CHICK	Protein C9orf42 homolog	0.76	-	nuc	0					284
Q5ZI27 UniProt NPD GO	CI090_CHICK	Protein C9orf90 homolog	0.76	-	nuc	0					330
Q06632 UniProt NPD GO	CFT1_YEAST	Protein CFT1 (Cleavage factor two protein 1)	0.76	+	nuc	0	Nucleus	mitochondrion [IDA] mRNA cleavage and polyadenylation specifici... [IPI]			1357
P59074 UniProt NPD GO	CG301_HUMAN	Protein CGI-301	0.76	-	nuc	0					171
Q8K4I6 UniProt NPD GO	PGEA1_RAT	Protein Chibby (PKD2 interactor, Golgi and endoplasmic reticulum associated 1) (PIGEA-14) (Cytosolic ...	0.76	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Nuclear, in a punctate manner. Golgi apparatu ...				127
Q7TNV0 UniProt NPD GO	DEK_MOUSE	Protein DEK	0.76	-	nuc	0	Nucleus (Potential)				380
Q3T026 UniProt NPD GO	F112A_BOVIN	Protein FAM112A	0.76	-	nuc	0					169
Q5E9L2 UniProt NPD GO	FAM5A_BOVIN	Protein FAM5A precursor	0.76	-	nuc	0	Secreted protein (Potential)				761
Q99332 UniProt NPD GO	HPH1_YEAST	Protein HPH1 (High pH protein 1) (Functionally related to TCP1 protein 1)	0.76	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Punctate foci a ...	endoplasmic reticulum [IDA]			602
Q5JTH9 UniProt NPD GO	K0690_HUMAN	Protein KIAA0690	0.76	-	nuc	0	Nucleus; nucleolus				1297
Q8CDJ3 UniProt NPD GO	K0831_MOUSE	Protein KIAA0831	0.76	-	nuc	0					492
Q9VTK2 UniProt NPD GO	POMT1_DROME	Protein O-mannosyltransferase 1 (EC 2.4.1.109) (Dolichyl-phosphate-mannose--protein mannosyltransfer ...	0.76	-	vac	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum membrane [ISS]			886
Q01105 UniProt NPD GO	SET_HUMAN	Protein SET (Phosphatase 2A inhibitor I2PP2A) (I-2PP2A) (Template-activating factor I) (TAF-I) (HLA- ...	0.76	-	nuc	0	Cytoplasm; cytosol. Endoplasmic reticulum. Nucleus; nucleoplasm. In the cytoplasm, found both in the ...	endoplasmic reticulum [IDA] nucleus [IDA] perinuclear region [IDA]	600960		290
O13472 UniProt NPD GO	SPT3_KLULA	Protein SPT3	0.76	-	nuc	0	Nucleus				328
P06844 UniProt NPD GO	SPT3_YEAST	Protein SPT3 (Positive regulator of Ty transcription)	0.76	-	nuc	0	Nucleus (Probable)	SAGA complex [IDA] SLIK (SAGA-like) complex [IPI]			337
Q7RTT6 UniProt NPD GO	SSX6_HUMAN	Protein SSX6	0.76	-	nuc	0			300541		188
Q24523 UniProt NPD GO	BUN2_DROME	Protein bunched, class 2 isoform (Protein shortsighted)	0.76	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA]			1206
Q8MSX1 UniProt NPD GO	ENC_DROME	Protein encore	0.76	-	nuc	0	Cytoplasm. Colocalizes with grk	cytoplasm [IDA]			1818
P54360 UniProt NPD GO	FOJO_DROME	Protein four-jointed	0.76	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type II membrane protein. Golgi apparatus, in the wing ...	plasma membrane [IDA]			583
P09082 UniProt NPD GO	GSB_DROME	Protein gooseberry (Protein gooseberry distal) (BSH9)	0.76	+	nuc	0	Nucleus				427
Q9FZ92 UniProt NPD GO	RH44_ARATH	Putative DEAD-box ATP-dependent RNA helicase 44 (EC 3.6.1.-)	0.76	-	nuc	0					622
P41754 UniProt NPD GO	CUTI_PHYCP	Putative cutinase (EC 3.1.1.74) (Cutin hydrolase)	0.76	-	mit	2					210
Q9LD40 UniProt NPD GO	CNG13_ARATH	Putative cyclic nucleotide-gated ion channel 13 (Cyclic nucleotide-and calmodulin-regulated ion chan ...	0.76	-	end	5	Cell membrane; multi-pass membrane protein (Potential)				696
P91928 UniProt NPD GO	IMMT_DROME	Putative mitochondrial inner membrane protein	0.76	-	nuc	0	Mitochondrion; mitochondrial inner membrane (By similarity)	mitochondrial inner membrane [ISS]			841
P40851 UniProt NPD GO	AXL1_YEAST	Putative protease AXL1 (EC 3.4.99.-)	0.76	-	nuc	0	Mother-bud neck and division site remnants of haploid cells	bud neck [IDA] integral to membrane [TAS] mating projection tip [IDA]			1208
Q8MYQ1 UniProt NPD GO	Y31E_CAEEL	Putative serine/threonine-protein kinase F31E3.2 (EC 2.7.11.1)	0.76	+	nuc	0					441
Q9CAA4 UniProt NPD GO	BIM2_ARATH	Putative transcription factor BIM2 (BES1-interacting Myc-like protein 2) (Transcription factor EN 12 ...	0.76	-	nuc	0	Nucleus (Probable)				311
Q9P2K3 UniProt NPD GO	RCOR3_HUMAN	REST corepressor 3	0.76	-	nuc	0	Nucleus (By similarity)				495
Q9R1A8 UniProt NPD GO	RFWD2_MOUSE	RING finger and WD repeat domain protein 2 (EC 6.3.2.-) (Ubiquitin-protein ligase COP1) (Constitutiv ...	0.76	-	mit	0	Nucleus; nucleoplasm; nuclear speckle. Cytoplasm. In the nucleus, it forms nuclear speckles				733
P32569 UniProt NPD GO	MED17_YEAST	RNA polymerase II mediator complex subunit 17 (Suppressor of RNA polymerase B 4)	0.76	-	nuc	0	Nucleus	mediator complex [IDA]			687
Q6CT73 UniProt NPD GO	TFB3_KLULA	RNA polymerase II transcription factor B subunit 3 (RNA polymerase II transcription factor B p38 sub ...	0.76	-	nuc	0	Nucleus (By similarity)				318

You are viewing entries 11001 to 11050 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.