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
Q9UTQ0 UniProt NPD GO	CCA1_SCHPO	Probable tRNA nucleotidyltransferase (EC 2.7.7.25) (tRNA adenylyltransferase) (tRNA CCA-pyrophosphor ...	0.31	-	cyt	0					500
O74533 UniProt NPD GO	UCR7_SCHPO	Probable ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2) (Complex III subunit ...	0.31	-	nuc	0	Mitochondrion; mitochondrial inner membrane (Potential)				137
P51925 UniProt NPD GO	GON2_SPAAU	Progonadoliberin-2 precursor (Progonadoliberin II) [Contains: Gonadoliberin-2 (Gonadoliberin II) (Lu ...	0.31	-	end	0	Secreted protein				85
Q9DD49 UniProt NPD GO	GON3_ORYLA	Progonadoliberin-3 precursor (Progonadoliberin III) (Salmon-type gonadotropin-releasing hormone) (sG ...	0.31	-	exc	1 *	Secreted protein	extracellular region [ISS]			90
Q9IA09 UniProt NPD GO	GON3_DICLA	Progonadoliberin-3 precursor (Progonadoliberin III) [Contains: Gonadoliberin-3 (Gonadoliberin III) ( ...	0.31	-	exc	0	Secreted protein				90
Q8HXS1 UniProt NPD GO	PRL_AILME	Prolactin precursor (PRL)	0.31	-	exc	0	Secreted protein				229
Q6JTA8 UniProt NPD GO	PRLR_PIG	Prolactin receptor precursor (PRL-R)	0.31	-	exc	2 *	Membrane; single-pass type I membrane protein (By similarity)	cell surface [ISS]			625
P09368 UniProt NPD GO	PUT1_YEAST	Proline oxidase, mitochondrial precursor (EC 1.5.3.-) (Proline dehydrogenase)	0.31	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			476
P05979 UniProt NPD GO	PGH1_SHEEP	Prostaglandin G/H synthase 1 precursor (EC 1.14.99.1) (Cyclooxygenase-1) (COX-1) (Prostaglandin-endo ...	0.31	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Microsome; micro ...	cytoplasm [ISS] microsome [ISS] nucleus [ISS]		2AYL	600
P54120 UniProt NPD GO	AIG1_ARATH	Protein AIG1	0.31	-	cyt	0					353
Q9Z1Q2 UniProt NPD GO	BAT5_MOUSE	Protein BAT5 (HLA-B-associated transcript 5)	0.31	-	mit	2	Membrane; multi-pass membrane protein (Potential)				557
Q9NYP9 UniProt NPD GO	CU045_HUMAN	Protein C21orf45	0.31	-	nuc	0					233
P57076 UniProt NPD GO	CU059_HUMAN	Protein C21orf59	0.31	-	cyt	0					290
Q9BRT2 UniProt NPD GO	CF125_HUMAN	Protein C6orf125 (Breast cancer-associated protein SGA-81M)	0.31	-	nuc	0					126
Q9P2X8 UniProt NPD GO	CI027_HUMAN	Protein C9orf27 (Protein EST-YD1)	0.31	-	nuc	0					86
Q9D217 UniProt NPD GO	CI065_MOUSE	Protein C9orf65 homolog	0.31	-	nuc	0					263
Q496M8 UniProt NPD GO	CI094_HUMAN	Protein C9orf94 precursor	0.31	-	nuc	1 *					467
Q00371 UniProt NPD GO	CAP22_COLGL	Protein CAP22	0.31	-	exc	0	Located on the wall of the appressorium				227
P53822 UniProt NPD GO	COS1_YEAST	Protein COS1	0.31	-	vac	4 *	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			381
Q3SZU0 UniProt NPD GO	F112B_BOVIN	Protein FAM112B	0.31	-	nuc	0					167
Q86XJ0 UniProt NPD GO	FA26A_HUMAN	Protein FAM26A	0.31	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				350
Q9CY86 UniProt NPD GO	G7D_MOUSE	Protein G7d	0.31	-	cyt	0					146
Q86YS7 UniProt NPD GO	K0528_HUMAN	Protein KIAA0528	0.31	-	nuc	0					1000
Q7TPS5 UniProt NPD GO	K0528_MOUSE	Protein KIAA0528	0.31	-	nuc	0					1016
Q5PR98 UniProt NPD GO	NDRG2_BRARE	Protein NDRG2	0.31	-	nuc	0	Cytoplasm (By similarity)				368
P42642 UniProt NPD GO	NOV_COTJA	Protein NOV precursor (Nephroblastoma overexpressed gene protein)	0.31	-	nuc	0	Secreted protein (By similarity)				353
Q7L099 UniProt NPD GO	RUFY3_HUMAN	Protein RUFY3 (Rap2-interacting protein x) (RIPx)	0.31	-	nuc	0					469
P14359 UniProt NPD GO	SNA3_YEAST	Protein SNA3	0.31	-	end	2 *	Membrane; multi-pass membrane protein (Potential). Sorted via late endosomes to the vacuolar lumen i ...	membrane [IDA] vacuolar lumen (sensu Fungi) [IDA]			133
Q6BM74 UniProt NPD GO	URE2_DEBHA	Protein URE2	0.31	-	mit	0					308
Q94981 UniProt NPD GO	ARI1_DROME	Protein ariadne-1 (Ari-1)	0.31	-	nuc	0	Cytoplasm. Mainly				503
Q9TLY2 UniProt NPD GO	CFXQ1_CYACA	Protein cfxQ homolog	0.31	-	cyt	0	Plastid; chloroplast				301
Q94481 UniProt NPD GO	CIGB_DICDI	Protein cigB (Fragment)	0.31	-	nuc	0					735
Q24139 UniProt NPD GO	COMM_DROME	Protein commissureless	0.31	-	nuc	1	Cytoplasmic vesicle; cytoplasmic vesicle membrane; single-pass membrane protein (Potential). Cell me ...	Golgi apparatus [IDA] integral to membrane [NAS] plasma membrane [IDA]			370
Q14554 UniProt NPD GO	PDIA5_HUMAN	Protein disulfide-isomerase A5 precursor (EC 5.3.4.1) (Protein disulfide isomerase-related protein)	0.31	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum lumen [TAS]			519
Q94554 UniProt NPD GO	ER_DROVI	Protein enhancer of rudimentary	0.31	-	nuc	0					104
Q9Y765 UniProt NPD GO	RAM2_CANAL	Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit (EC 2.5.1.58) (EC 2.5.1.5 ...	0.31	-	cyt	0					306
Q19266 UniProt NPD GO	KPC3_CAEEL	Protein kinase C-like 3 (EC 2.7.11.13) (Atypical protein kinase C-3) (aPKC3)	0.31	-	cyt	0	Targeted and anchored at the apical surface (villi) of intestinal and pharyngeal cells, and in proxi ...	cortical actin cytoskeleton [IDA] plasma membrane [IDA]			597
P21965 UniProt NPD GO	MCK1_YEAST	Protein kinase MCK1 (EC 2.7.11.1) (Meiosis and centromere regulatory kinase)	0.31	-	nuc	0		soluble fraction [IDA]			375
Q8BXR6 UniProt NPD GO	PELI3_MOUSE	Protein pellino homolog 3 (Pellino-3)	0.31	-	nuc	0					445
Q62084 UniProt NPD GO	PP14B_MOUSE	Protein phosphatase 1 regulatory subunit 14B (Phosphatase holoenzyme inhibitor 1) (PHI-1) (Phospholi ...	0.31	-	nuc	0	Cytoplasm (Probable)				147
Q8K3F3 UniProt NPD GO	PP14B_RAT	Protein phosphatase 1 regulatory subunit 14B (Phosphatase holoenzyme inhibitor 1) (PHI-1) (Ubiquitou ...	0.31	-	nuc	0	Cytoplasm (Probable)				147
Q6TGC4 UniProt NPD GO	PADI6_HUMAN	Protein-arginine deiminase type-6 (EC 3.5.3.15) (Protein-arginine deiminase type VI) (Peptidylargini ...	0.31	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				686
P10650 UniProt NPD GO	MOS_CERAE	Proto-oncogene serine/threonine-protein kinase mos (EC 2.7.11.1) (c-mos) (Oocyte maturation factor m ...	0.31	-	cyt	0					346
Q5DRE9 UniProt NPD GO	PCDA3_PANTR	Protocadherin alpha 3 precursor (PCDH-alpha3)	0.31	+	nuc	0	Membrane; single-pass type I membrane protein (By similarity)				950
Q08174 UniProt NPD GO	PCDH1_HUMAN	Protocadherin-1 precursor (Protocadherin-42) (PC42) (Cadherin-like protein 1)	0.31	-	nuc	1	Cell membrane; cell-cell junction; single-pass type I membrane protein. Cell membrane; cell-matrix j ...	integral to plasma membrane [TAS] intercellular junction [TAS] plasma membrane [TAS]	603626		1026
Q96PZ0 UniProt NPD GO	PUS7_HUMAN	Pseudouridylate synthase 7 homolog (EC 5.4.99.-)	0.31	-	cyt	0					661
P53100 UniProt NPD GO	YGT5_YEAST	Putative 2-hydroxyacid dehydrogenase YGL185C (EC 1.-.-.-)	0.31	-	nuc	0		cytoplasm [IDA]			379
P51205 UniProt NPD GO	YCF30_PORPU	Putative HTH-type transcriptional regulator ycf30	0.31	-	cyt	0	Plastid; chloroplast				317
O82198 UniProt NPD GO	LBD9_ARATH	Putative LOB domain-containing protein 9	0.31	-	nuc	0					124
O80507 UniProt NPD GO	CSK2E_ARATH	Putative casein kinase II subunit beta-4 (CK II beta-4)	0.31	-	nuc	0					283

You are viewing entries 39751 to 39800 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.