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
O02768 UniProt NPD GO	PGH2_RABIT	Prostaglandin G/H synthase 2 precursor (EC 1.14.99.1) (Cyclooxygenase-2) (COX-2) (Prostaglandin-endo ...	0.35	-	exc	0	Microsome; microsomal membrane; peripheral membrane protein	cytoplasm [ISS] nucleus [ISS]			604
P27607 UniProt NPD GO	PGH2_CHICK	Prostaglandin G/H synthase 2 precursor (EC 1.14.99.1) (Cyclooxygenase-2) (COX-2) (Prostaglandin-endo ...	0.35	-	exc	0	Microsome; microsomal membrane; peripheral membrane protein	cytoplasm [ISS] nucleus [ISS]			603
Q8RY73 UniProt NPD GO	Y4762_ARATH	Protein At4g17620, chloroplast precursor	0.35	-	nuc	0	Plastid; chloroplast (Potential)				544
P58513 UniProt NPD GO	CU042_HUMAN	Protein C21orf42	0.35	-	mit	0					81
P58556 UniProt NPD GO	CU069_HUMAN	Protein C21orf69	0.35	-	nuc	0					163
Q8R5F3 UniProt NPD GO	CF130_MOUSE	Protein C6orf130 homolog	0.35	-	cyt	0					152
Q5TM64 UniProt NPD GO	CF136_MACMU	Protein C6orf136 homolog	0.35	-	cyt	0					172
Q9NPB0 UniProt NPD GO	CF064_HUMAN	Protein C6orf64	0.35	-	mit	1					183
Q96FA7 UniProt NPD GO	CG029_HUMAN	Protein C7orf29	0.35	-	mit	0					236
Q9Y236 UniProt NPD GO	CH001_HUMAN	Protein C8orf1 (hT41)	0.35	-	mit	0			604598		505
Q6DC60 UniProt NPD GO	CI025_BRARE	Protein C9orf25 homolog	0.35	-	nuc	0					186
P18406 UniProt NPD GO	CYR61_MOUSE	Protein CYR61 precursor (Cysteine-rich, angiogenic inducer, 61) (Insulin-like growth factor-binding ...	0.35	-	mit	0	Secreted protein				379
Q3ZBS2 UniProt NPD GO	F19A5_BOVIN	Protein FAM19A5 precursor (Chemokine-like protein TAFA-5)	0.35	-	nuc	1 *	Secreted protein (By similarity)				114
Q96KN1 UniProt NPD GO	FA84B_HUMAN	Protein FAM84B (Protein NSE2) (Breast cancer membrane protein 101)	0.35	-	nuc	0		cytoplasm [IDA] plasma membrane [IDA]			310
Q9Y334 UniProt NPD GO	G7C_HUMAN	Protein G7c precursor	0.35	-	mit	0			609693		852
Q75BI0 UniProt NPD GO	LDB19_ASHGO	Protein LDB19	0.35	-	mit	0	Cytoplasm (By similarity). Golgi apparatus (By similarity)				684
P33215 UniProt NPD GO	NEDD1_MOUSE	Protein NEDD1 (Neural precursor cell expressed developmentally down-regulated protein 1)	0.35	-	nuc	0					660
Q06144 UniProt NPD GO	ORM2_YEAST	Protein ORM2	0.35	-	end	4	Membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum	endoplasmic reticulum [IDA]			216
Q03180 UniProt NPD GO	PIR3_YEAST	Protein PIR3 precursor (Covalently-linked cell wall protein 8)	0.35	-	exc	0	Cell wall. Attached to the cell wall	cell wall (sensu Fungi) [IDA]			361
P20054 UniProt NPD GO	PYR1_DICDI	Protein PYR1-3 [Includes: Glutamine-dependent carbamoyl-phosphate synthase (EC 6.3.5.5); Aspartate c ...	0.35	-	nuc	0	Cytoplasm				2185
Q08171 UniProt NPD GO	TUBE_DROVI	Protein Tube	0.35	-	nuc	0	Cytoplasm				514
P21551 UniProt NPD GO	WNT1_AMBME	Protein Wnt-1 precursor	0.35	-	exc	0	Secreted protein; extracellular space; extracellular matrix				369
Q93097 UniProt NPD GO	WNT2B_HUMAN	Protein Wnt-2b precursor (Wnt-13)	0.35	-	mit	0	Secreted protein; extracellular space; extracellular matrix	extracellular space [TAS]	601968		391
Q8R5M2 UniProt NPD GO	WNT9A_MOUSE	Protein Wnt-9a precursor (Wnt-14)	0.35	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix				365
P39102 UniProt NPD GO	XDJ1_YEAST	Protein XDJ1	0.35	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	mitochondrion [IDA] nucleus [IDA]			459
Q9EPK2 UniProt NPD GO	XRP2_MOUSE	Protein XRP2	0.35	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity)				346
Q8ML92 UniProt NPD GO	AVE_DROME	Protein aveugle	0.35	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	cytoplasm [IDA]			106
P82116 UniProt NPD GO	BCN92_DROSU	Protein bcn92	0.35	-	mit	0					92
O22025 UniProt NPD GO	CFXQ_CYAME	Protein cfxQ homolog	0.35	-	cyt	0	Plastid; chloroplast				293
Q9MS99 UniProt NPD GO	CFXQ_GALSU	Protein cfxQ homolog	0.35	-	nuc	0	Plastid; chloroplast				305
P13678 UniProt NPD GO	KPC3_DROME	Protein kinase C (EC 2.7.11.13) (PKC) (dPKC98F)	0.35	-	cyt	0					634
P36616 UniProt NPD GO	DSK1_SCHPO	Protein kinase dsk1 (EC 2.7.11.1) (Dis1-suppressing protein kinase)	0.35	-	nuc	0	Cytoplasm. Nucleus. Enriched in the nucleus in mitotically arrested mutant and wild-type mitotic cel ...	cytoplasm [IDA] nucleus [IDA]			544
P82147 UniProt NPD GO	L2EFL_DROME	Protein lethal(2)essential for life (Protein Efl21)	0.35	-	nuc	0					187
Q9W349 UniProt NPD GO	LOZEN_DROME	Protein lozenge	0.35	-	nuc	0		nucleus [IC]			826
O46040 UniProt NPD GO	MSTAA_DROME	Protein msta, isoform A	0.35	-	cyt	0					462
Q9DDD5 UniProt NPD GO	NBEA_CHICK	Protein neurobeachin (Fragment)	0.35	-	mit	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				793
Q3T135 UniProt NPD GO	OSR2_BOVIN	Protein odd-skipped-related 2	0.35	-	nuc	0	Nucleus (Potential)				276
Q6AY34 UniProt NPD GO	OSR2_RAT	Protein odd-skipped-related 2	0.35	-	nuc	0	Nucleus (Potential)				276
Q90693 UniProt NPD GO	PTC1_CHICK	Protein patched homolog 1 (PTC1) (PTC)	0.35	-	end	12	Membrane; multi-pass membrane protein				1442
P48612 UniProt NPD GO	PELO_DROME	Protein pelota	0.35	-	cyt	0	Nucleus (Potential)				395
Q9VMD6 UniProt NPD GO	RETM_DROME	Protein real-time	0.35	-	cyt	0	Mitochondrion	mitochondrion [IDA]			659
O42899 UniProt NPD GO	SCO1_SCHPO	Protein sco1	0.35	-	mit	0					263
Q22795 UniProt NPD GO	SET1_CAEEL	Protein set-1	0.35	-	nuc	0	Nucleus				242
P55085 UniProt NPD GO	PAR2_HUMAN	Proteinase-activated receptor 2 precursor (PAR-2) (Thrombin receptor-like 1) (Coagulation factor II ...	0.35	-	end	8 *	Membrane; multi-pass membrane protein	Golgi apparatus [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	600933		397
P55086 UniProt NPD GO	PAR2_MOUSE	Proteinase-activated receptor 2 precursor (PAR-2) (Thrombin receptor-like 1) (Coagulation factor II ...	0.35	-	end	7	Membrane; multi-pass membrane protein				399
Q9Y5I0 UniProt NPD GO	PCDAD_HUMAN	Protocadherin alpha 13 precursor (PCDH-alpha13)	0.35	+	nuc	0	Membrane; single-pass type I membrane protein (By similarity)		606319		950
Q9Y5H7 UniProt NPD GO	PCDA5_HUMAN	Protocadherin alpha 5 precursor (PCDH-alpha5)	0.35	+	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606311		936
Q5DRE7 UniProt NPD GO	PCDA5_PANTR	Protocadherin alpha 5 precursor (PCDH-alpha5)	0.35	+	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				936
Q9H158 UniProt NPD GO	PCDC1_HUMAN	Protocadherin alpha C1 precursor (PCDH-alpha-C1)	0.35	+	end	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606320		963
Q5DRE2 UniProt NPD GO	PCDC1_PANTR	Protocadherin alpha C1 precursor (PCDH-alpha-C1)	0.35	+	end	1	Membrane; single-pass type I membrane protein (By similarity)				963

You are viewing entries 36151 to 36200 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.