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
Q8TF62 UniProt NPD GO	AT8B4_HUMAN	Probable phospholipid-transporting ATPase IM (EC 3.6.3.1) (ATPase class I type 8B member 4)	0.40	+	end	9	Membrane; multi-pass membrane protein		609123		1192
Q12222 UniProt NPD GO	KOM8_YEAST	Probable serine/threonine-protein kinase YOL128C (EC 2.7.11.1)	0.40	-	cyt	0					375
Q09444 UniProt NPD GO	UBH4_CAEEL	Probable ubiquitin carboxyl-terminal hydrolase ubh-4 (EC 3.4.19.12) (Ubiquitin C-terminal hydrolase ...	0.40	-	cyt	0					321
Q22494 UniProt NPD GO	VATH2_CAEEL	Probable vacuolar ATP synthase subunit H 2 (EC 3.6.3.14) (V-ATPase H subunit 2) (Vacuolar proton pum ...	0.40	-	cyt	0					470
P93046 UniProt NPD GO	XTH31_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 31 precursor (EC 2.4.1.207) (At-XTH31) (X ...	0.40	-	nuc	0	Secreted protein; extracellular space; apoplast (Probable)				293
O08628 UniProt NPD GO	PCOC1_RAT	Procollagen C-endopeptidase enhancer 1 precursor (Procollagen COOH-terminal proteinase enhancer 1) ( ...	0.40	-	nuc	0	Secreted protein				468
P37044 UniProt NPD GO	GON2_HAPBU	Progonadoliberin-2 precursor (Progonadoliberin II) [Contains: Gonadoliberin-2 (Gonadoliberin II) (Lu ...	0.40	-	end	0	Secreted protein	extracellular region [NAS]			85
Q28632 UniProt NPD GO	PRL_RABIT	Prolactin precursor (PRL)	0.40	-	exc	0	Secreted protein			1AN3	227
Q8CG71 UniProt NPD GO	P3H2_MOUSE	Prolyl 3-hydroxylase 2 precursor (EC 1.14.11.7) (Leprecan-like protein 1)	0.40	-	end	0	Endoplasmic reticulum. Golgi apparatus (By similarity)				703
P29121 UniProt NPD GO	PCSK4_MOUSE	Proprotein convertase subtilisin/kexin type 4 precursor (EC 3.4.21.-) (PC4) (Neuroendocrine converta ...	0.40	+	exc	0					655
P46069 UniProt NPD GO	PE2R3_RABIT	Prostaglandin E2 receptor, EP3 subtype (Prostanoid EP3 receptor) (PGE receptor, EP3 subtype)	0.40	+	end	6 *	Membrane; multi-pass membrane protein				411
P70682 UniProt NPD GO	PGH2_CAVPO	Prostaglandin G/H synthase 2 precursor (EC 1.14.99.1) (Cyclooxygenase-2) (COX-2) (Prostaglandin-endo ...	0.40	-	exc	0	Microsome; microsomal membrane; peripheral membrane protein	cytoplasm [ISS] nucleus [ISS]			604
P35355 UniProt NPD GO	PGH2_RAT	Prostaglandin G/H synthase 2 precursor (EC 1.14.99.1) (Cyclooxygenase-2) (COX-2) (Prostaglandin-endo ...	0.40	-	vac	0	Microsome; microsomal membrane; peripheral membrane protein	cytoplasm [ISS] endoplasmic reticulum [TAS] nuclear envelope [TAS] nucleus [ISS]			604
P06767 UniProt NPD GO	TKN1_RAT	Protachykinin 1 precursor (PPT) [Contains: Substance P; Neurokinin A (NKA) (Substance K) (Neuromedin ...	0.40	-	exc	0	Secreted protein				130
P32195 UniProt NPD GO	PG2_PIG	Protegrin-2 precursor (PG-2)	0.40	-	mit	1 *	Secreted protein				147
O80543 UniProt NPD GO	Y1280_ARATH	Protein At1g22800	0.40	-	mit	0					355
Q00994 UniProt NPD GO	BEX3_HUMAN	Protein BEX3 (Brain-expressed X-linked protein 3) (p75NTR-associated cell death executor) (Nerve gro ...	0.40	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the cytoplasm and the nucleus. Associates with replicating mito ...		300361	1SA6	111
Q3ZBJ9 UniProt NPD GO	BEX5_BOVIN	Protein BEX5 (Brain-expressed X-linked protein 5 homolog) (NGFRAP1-like 1)	0.40	-	nuc	0	Cytoplasm (By similarity)				112
Q8VC42 UniProt NPD GO	MIC1_MOUSE	Protein C18orf8 homolog (Colon cancer-associated protein Mic1) (Mic-1)	0.40	-	cyt	0					657
Q32LB9 UniProt NPD GO	CD014_BOVIN	Protein C4orf14 homolog	0.40	-	mit	0					694
Q9CQY6 UniProt NPD GO	CF125_MOUSE	Protein C6orf125 homolog	0.40	-	nuc	0					136
Q5BJW5 UniProt NPD GO	CI150_RAT	Protein C9orf150 homolog	0.40	-	nuc	0					221
Q6PBN4 UniProt NPD GO	CQ10B_BRARE	Protein COQ10 B, mitochondrial precursor	0.40	-	nuc	0	Mitochondrion (Potential)				233
P52924 UniProt NPD GO	COS10_YEAST	Protein COS10	0.40	-	cyt	2 *	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA] endoplasmic reticulum [IDA] nuclear envelope [IDA]			374
P43542 UniProt NPD GO	COS4_YEAST	Protein COS4	0.40	-	vac	4 *	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			379
P36075 UniProt NPD GO	CUE2_YEAST	Protein CUE2	0.40	-	nuc	0				1OTR	443
Q9JHA8 UniProt NPD GO	G7C_MOUSE	Protein G7c precursor	0.40	-	mit	0					891
P40531 UniProt NPD GO	GVP36_YEAST	Protein GVP36 (36 kDa Golgi vesicle protein)	0.40	-	nuc	0	Golgi apparatus; Golgi membrane; peripheral membrane protein	cytoplasm [IDA] integral to Golgi membrane [IDA]			326
Q14154 UniProt NPD GO	K0141_HUMAN	Protein KIAA0141	0.40	-	mit	0		mitochondrion [IDA]			515
P34253 UniProt NPD GO	KTI12_YEAST	Protein KTI12	0.40	-	nuc	0		DNA-directed RNA polymerase II, holoenzyme [TAS]			313
Q8WZA1 UniProt NPD GO	PMGT1_HUMAN	Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (EC 2.4.1.-) (POMGnT1) (UDP-GlcN ...	0.40	-	end	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)		606822		660
Q6CV11 UniProt NPD GO	PBN1_KLULA	Protein PBN1	0.40	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				414
Q3SYG4 UniProt NPD GO	PTHB1_HUMAN	Protein PTHB1 (Parathyroid hormone-responsive B1 gene protein) (Bardet-Biedl syndrome 9 protein)	0.40	-	cyt	0			607968		887
Q96WL3 UniProt NPD GO	URE2_CANAL	Protein URE2	0.40	-	nuc	0					344
Q96X43 UniProt NPD GO	URE2_KLULA	Protein URE2	0.40	-	nuc	0					389
O73864 UniProt NPD GO	WNT11_BRARE	Protein Wnt-11 precursor	0.40	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix	plasma membrane [IMP]			354
P28123 UniProt NPD GO	WNT72_EPTST	Protein Wnt-7(II) (Fragment)	0.40	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				126
Q5ZHN4 UniProt NPD GO	XRP2_CHICK	Protein XRP2	0.40	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity)				356
P32793 UniProt NPD GO	YSC84_YEAST	Protein YSC84 (LAS seventeen-binding protein 4)	0.40	-	nuc	0	Actin patch. Cortical actin patches	actin cortical patch [IDA]			468
O96566 UniProt NPD GO	A37C_DROSI	Protein anon-37Cs (Fragment)	0.40	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			501
Q9UT16 UniProt NPD GO	ATP12_SCHPO	Protein atp12, mitochondrial precursor	0.40	-	mit	0	Mitochondrion (By similarity)				287
Q99316 UniProt NPD GO	MPD2_YEAST	Protein disulfide isomerase MPD2 precursor (EC 5.3.4.1)	0.40	-	nuc	1 *	Endoplasmic reticulum	endoplasmic reticulum [TAS]			277
Q5I0H9 UniProt NPD GO	PDIA5_RAT	Protein disulfide-isomerase A5 precursor (EC 5.3.4.1)	0.40	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				517
Q24732 UniProt NPD GO	GLAS_DROVI	Protein glass	0.40	-	nuc	0	Nucleus (Probable)	nucleus [ISS]			598
P17276 UniProt NPD GO	PH4H_DROME	Protein henna [Includes: Phenylalanine-4-hydroxylase (EC 1.14.16.1) (PAH) (Phe-4-monooxygenase); Try ...	0.40	-	nuc	0					452
O46258 UniProt NPD GO	HUNB_DROSO	Protein hunchback (Fragments)	0.40	-	nuc	0	Nucleus (By similarity)				159
Q02111 UniProt NPD GO	KPCT_MOUSE	Protein kinase C theta type (EC 2.7.11.13) (nPKC-theta)	0.40	-	cyt	0		cytoplasm [IDA] immunological synapse [IDA] plasma membrane [IDA]			707
P13677 UniProt NPD GO	KPC2_DROME	Protein kinase C, eye isozyme (EC 2.7.11.13) (PKC) (dPKC53E(EY)) (Protein INAC) (Inactivation no aft ...	0.40	-	cyt	0		inaD signaling complex [TAS]			700
Q23536 UniProt NPD GO	LGG2_CAEEL	Protein lgg-2	0.40	-	nuc	0					130
Q61115 UniProt NPD GO	PTC1_MOUSE	Protein patched homolog 1 (PTC1) (PTC)	0.40	-	end	12	Membrane; multi-pass membrane protein	extracellular region [TAS] integral to plasma membrane [TAS]			1434

You are viewing entries 32101 to 32150 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.