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
Q9V521 UniProt NPD GO	PRPP1_DROME	Probable phenoloxidase subunit CG8193 precursor (EC 1.14.18.1)	0.44	-	cyt	0	Secreted protein	extracellular region [IDA]			684
O81439 UniProt NPD GO	PAP1_ARATH	Probable plastid-lipid-associated protein 1, chloroplast precursor (AtPap1) (Fibrillin-1)	0.44	-	mit	0	Plastid; chloroplast (Potential)	thylakoid membrane (sensu Viridiplantae) [IDA]			318
O81016 UniProt NPD GO	PDR4_ARATH	Probable pleiotropic drug resistance protein 4	0.44	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1420
Q18409 UniProt NPD GO	RSP6_CAEEL	Probable splicing factor, arginine/serine-rich 6 (RNA-binding protein srp-1) (CeSRp20)	0.44	+	nuc	0	Nucleus	nucleus [IDA]			179
Q9FLX5 UniProt NPD GO	WBC8_ARATH	Probable white-brown complex homolog protein 8	0.44	-	end	7	Membrane; multi-pass membrane protein (By similarity)				589
P04094 UniProt NPD GO	PENK_RAT	Proenkephalin A precursor [Contains: Synenkephalin; Met-enkephalin (Opioid growth factor) (OGF); Met ...	0.44	-	exc	0	Secreted protein				269
O93337 UniProt NPD GO	PRL_SPAAU	Prolactin precursor (PRL)	0.44	-	exc	0	Secreted protein				212
O62781 UniProt NPD GO	PRL_TRIVU	Prolactin precursor (PRL)	0.44	-	exc	0	Secreted protein				228
Q16378 UniProt NPD GO	PROL4_HUMAN	Proline-rich protein 4 precursor (Lacrimal proline-rich protein) (Nasopharyngeal carcinoma-associate ...	0.44	-	exc	0	Secreted protein	extracellular space [TAS]	605359		134
Q60541 UniProt NPD GO	TKN1_MESAU	Protachykinin 1 precursor (PPT) [Contains: Substance P; Neurokinin A (NKA) (Substance K) (Neuromedin ...	0.44	-	exc	0	Secreted protein				130
P40529 UniProt NPD GO	AGE2_YEAST	Protein AGE2	0.44	-	nuc	0	Cytoplasm. Golgi apparatus. Associates with the Golgi complex				298
Q9CWT2 UniProt NPD GO	BEX4_MOUSE	Protein BEX4 (Brain-expressed X-linked protein 4 homolog) (BEX1-like 1)	0.44	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				118
Q9NVP4 UniProt NPD GO	CT012_HUMAN	Protein C20orf12	0.44	-	nuc	0					579
P57060 UniProt NPD GO	CU006_HUMAN	Protein C21orf6	0.44	-	cyt	0				2DAX	319
Q9UKZ1 UniProt NPD GO	CB029_HUMAN	Protein C2orf29	0.44	-	nuc	0					510
Q8IV03 UniProt NPD GO	CI150_HUMAN	Protein C9orf150	0.44	-	nuc	0					231
Q8IW50 UniProt NPD GO	CI025_HUMAN	Protein C9orf25	0.44	-	nuc	0					157
Q9CQ90 UniProt NPD GO	CI085_MOUSE	Protein C9orf85 homolog	0.44	-	nuc	0					155
Q96MF6 UniProt NPD GO	CQ10A_HUMAN	Protein COQ10 A, mitochondrial precursor	0.44	-	mit	0	Mitochondrion (Potential)				247
P54858 UniProt NPD GO	DOS2_YEAST	Protein DOS2	0.44	-	nuc	0		cytoplasm [IDA]			310
Q5R9Q6 UniProt NPD GO	F103A_PONPY	Protein FAM103A1	0.44	-	nuc	0					118
P40569 UniProt NPD GO	GAT4_YEAST	Protein GAT4	0.44	-	nuc	0					121
O43299 UniProt NPD GO	K0415_HUMAN	Protein KIAA0415 (Fragment)	0.44	-	cyt	0					634
P40850 UniProt NPD GO	MKT1_YEAST	Protein MKT1	0.44	-	nuc	0		cytoplasm [IDA] polysome [IDA]			830
Q00539 UniProt NPD GO	NAM8_YEAST	Protein NAM8	0.44	-	nuc	0	Nucleus	commitment complex [IPI] snRNP U1 [IDA]			523
P50109 UniProt NPD GO	PSP2_YEAST	Protein PSP2 (Mitochondrial regulator of splicing 15)	0.44	-	nuc	0		cytoplasm [IDA]			578
Q9H9A7 UniProt NPD GO	RMI1_HUMAN	Protein RMI1 homolog	0.44	-	nuc	0					625
Q9D4G9 UniProt NPD GO	RMI1_MOUSE	Protein RMI1 homolog	0.44	-	nuc	0					616
Q6CPQ2 UniProt NPD GO	SIA1_KLULA	Protein SIA1 precursor	0.44	-	mit	1 *					578
P39926 UniProt NPD GO	SSO2_YEAST	Protein SSO2	0.44	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)	cytoplasm [IDA] endoplasmic reticulum [IDA] integral to plasma membrane [TAS]			295
P50273 UniProt NPD GO	TCM10_YEAST	Protein TCM10	0.44	-	mit	0		mitochondrial inner membrane [IDA]			684
Q96LA8 UniProt NPD GO	ANM6_HUMAN	Protein arginine N-methyltransferase 6 (EC 2.1.1.-) (Heterogeneous nuclear ribonucleoprotein methylt ...	0.44	-	cyt	0	Nucleus		608274		375
Q10322 UniProt NPD GO	DMA1_SCHPO	Protein dma1	0.44	-	nuc	0					267
P22007 UniProt NPD GO	RAM1_YEAST	Protein farnesyltransferase subunit beta (EC 2.5.1.58) (CAAX farnesyltransferase subunit beta) (RAS ...	0.44	-	mit	0		protein farnesyltransferase complex [IDA]			431
O46234 UniProt NPD GO	HUNB_DROAA	Protein hunchback (Fragments)	0.44	-	nuc	0	Nucleus (By similarity)				196
O46254 UniProt NPD GO	HUNB_SCAAL	Protein hunchback (Fragments)	0.44	-	nuc	0	Nucleus (By similarity)				171
Q9Z0W5 UniProt NPD GO	PACN1_RAT	Protein kinase C and casein kinase substrate in neurons protein 1 (Synaptic, dynamin-associated prot ...	0.44	-	nuc	0	Cytoplasm. Colocalizes with dynamin I at vesicular structures in the cell body and neurites				441
Q96D31 UniProt NPD GO	ORAI1_HUMAN	Protein orai-1	0.44	-	mit	3	Cell membrane; multi-pass membrane protein				301
Q9Y7L0 UniProt NPD GO	SEC22_SCHPO	Protein transport protein sec22	0.44	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)				209
Q9VYB7 UniProt NPD GO	TPST_DROME	Protein-tyrosine sulfotransferase (EC 2.8.2.20) (Tyrosylprotein sulfotransferase) (TPST) (Transport ...	0.44	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				499
P08941 UniProt NPD GO	ROS_CHICK	Proto-oncogene tyrosine-protein kinase ROS precursor (EC 2.7.10.1) (c-ros-1)	0.44	-	nuc	1	Membrane; single-pass type I membrane protein				2311
P02854 UniProt NPD GO	VCLB_PEA	Provicilin precursor (Type B) (Fragment)	0.44	-	exc	0	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies				410
Q8IVA1 UniProt NPD GO	PCP2_HUMAN	Purkinje cell protein 2 homolog	0.44	-	nuc	0					99
O14181 UniProt NPD GO	YDS5_SCHPO	Putative 60S ribosomal protein C4F8.05c	0.44	-	nuc	0					118
Q8WW27 UniProt NPD GO	ABEC4_HUMAN	Putative C->U-editing enzyme APOBEC-4 (EC 3.5.4.-) (Apolipoprotein B mRNA-editing enzyme catalytic p ...	0.44	-	nuc	0			609908		367
Q9P7W6 UniProt NPD GO	MLH1_SCHPO	Putative MutL protein homolog 1 (DNA mismatch repair protein MLH1)	0.44	-	nuc	0	Nucleus (Potential)				684
Q9M0R4 UniProt NPD GO	ATL4D_ARATH	Putative RING-H2 finger protein ATL4D precursor	0.44	-	end	2 *					357
Q5G8B4 UniProt NPD GO	AP5_TITCO	Putative antimicrobial peptide clone 5 precursor	0.44	-	end	1 *	Secreted protein				73
Q7SI68 UniProt NPD GO	CRYD_NEUCR	Putative cryptochrome DASH, mitochondrial precursor	0.44	+	mit	0	Mitochondrion (Potential)				745
Q9VKJ7 UniProt NPD GO	GR32A_DROME	Putative gustatory receptor 32a	0.44	-	vac	6	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			461

You are viewing entries 29201 to 29250 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.