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
O54749 UniProt NPD GO	CP2J5_MOUSE	Cytochrome P450 2J5 (EC 1.14.14.1) (CYPIIJ5) (Arachidonic acid epoxygenase)	0.34	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				501
Q8AXY5 UniProt NPD GO	C356_FUNHE	Cytochrome P450 3A56 (EC 1.14.14.1) (CYPIIIA56)	0.34	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				496
Q9EP75 UniProt NPD GO	CP4FE_MOUSE	Cytochrome P450 4F14 (EC 1.14.13.30) (Leukotriene-B4 omega-hydroxylase) (Leukotriene-B4 20-monooxyge ...	0.34	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				524
O44221 UniProt NPD GO	CP4E5_DROMT	Cytochrome P450 4e5, mitochondrial precursor (EC 1.14.-.-) (CYPIVE5)	0.34	-	cyt	1 *	Mitochondrion (Probable)				522
Q9VYY4 UniProt NPD GO	C4G15_DROME	Cytochrome P450 4g15 (EC 1.14.-.-) (CYPIVG15)	0.34	-	cyt	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				574
P93596 UniProt NPD GO	CP51_WHEAT	Cytochrome P450 51 (EC 1.14.13.70) (CYPLI) (P450-LIA1) (Obtusifoliol 14-alpha demethylase) (Fragment ...	0.34	-	cyt	0					453
Q42716 UniProt NPD GO	C71A8_MENPI	Cytochrome P450 71A8 (EC 1.14.-.-)	0.34	-	nuc	0					502
P50266 UniProt NPD GO	CYB5R_DROVI	Cytochrome b5-related protein	0.34	-	cyt	0					142
Q91W29 UniProt NPD GO	COX42_MOUSE	Cytochrome c oxidase subunit 4 isoform 2, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxidase ...	0.34	-	nuc	1	Mitochondrion; mitochondrial inner membrane				172
Q03571 UniProt NPD GO	CPB1_CAEEL	Cytoplasmic polyadenylation element-binding protein 1	0.34	-	nuc	0		cytoplasm [IDA]			372
P19020 UniProt NPD GO	DRD3_RAT	D(3) dopamine receptor	0.34	-	end	7 *	Membrane; multi-pass membrane protein				446
Q9NYX4 UniProt NPD GO	D1IP_HUMAN	D1 dopamine receptor-interacting protein calcyon	0.34	-	nuc	1	Membrane; single-pass type III membrane protein (Potential)	integral to plasma membrane [TAS]	604647		217
Q694B7 UniProt NPD GO	ABC3G_PAPAN	DNA dC->dU-editing enzyme APOBEC-3G (EC 3.5.4.-)	0.34	-	mit	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				383
Q694C0 UniProt NPD GO	ABC3G_PONPY	DNA dC->dU-editing enzyme APOBEC-3G (EC 3.5.4.-)	0.34	-	cyt	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				384
Q8K409 UniProt NPD GO	DPOLB_MOUSE	DNA polymerase beta (EC 2.7.7.7) (EC 4.2.99.-)	0.34	-	nuc	0	Nucleus (By similarity)	synaptonemal complex [TAS]			334
O93610 UniProt NPD GO	DPOD2_XENLA	DNA polymerase subunit delta 2 (EC 2.7.7.7) (XlCDC1)	0.34	-	cyt	0	Nucleus				463
O15315 UniProt NPD GO	RA51B_HUMAN	DNA repair protein RAD51 homolog 2 (R51H2) (RAD51-like protein 1) (Rad51B)	0.34	-	cyt	0	Nucleus (Probable)	nucleus [TAS]	602948		384
Q14691 UniProt NPD GO	PSF1_HUMAN	DNA replication complex GINS protein PSF1	0.34	-	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			196
O78483 UniProt NPD GO	RPOC2_GUITH	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.34	-	cyt	0	Plastid; chloroplast				1286
O43542 UniProt NPD GO	XRCC3_HUMAN	DNA-repair protein XRCC3 (X-ray repair cross-complementing protein 3)	0.34	-	cyt	0	Nucleus (Probable)		600675		346
P87064 UniProt NPD GO	DODA_AMAMU	DOPA 4,5-dioxygenase (EC 1.14.99.-)	0.34	-	mit	0	Cytoplasm				228
Q32LH1 UniProt NPD GO	DYDC1_BOVIN	DPY30 domain-containing protein 1	0.34	-	cyt	0					175
O01901 UniProt NPD GO	DDL1_CAEEL	Daf-16-dependent longevity protein 1	0.34	-	nuc	0					189
Q6VY05 UniProt NPD GO	DND1_MOUSE	Dead end protein homolog 1 (RNA-binding motif, single-stranded-interacting protein 4)	0.34	-	cyt	0					352
O13851 UniProt NPD GO	DLP1_SCHPO	Decaprenyl-diphosphate synthase subunit 2 (EC 2.5.1.-) (Decaprenyl pyrophosphate synthetase subunit ...	0.34	-	nuc	0					294
P22913 UniProt NPD GO	DH16D_ORYSA	Dehydrin Rab16D	0.34	-	nuc	0					151
Q9Z110 UniProt NPD GO	P5CS_MOUSE	Delta 1-pyrroline-5-carboxylate synthetase (P5CS) (Aldehyde dehydrogenase 18 family member A1) [Incl ...	0.34	-	mit	0	Mitochondrion; mitochondrial inner membrane				795
P23227 UniProt NPD GO	ECTP_TRIGR	Developmentally-regulated ectodermal protein precursor	0.34	+	vac	0					87
Q9Y272 UniProt NPD GO	RASD1_HUMAN	Dexamethasone-induced Ras-related protein 1 (Activator of G-protein signaling 1)	0.34	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		605550		281
Q9JMC3 UniProt NPD GO	DNJA4_MOUSE	DnaJ homolog subfamily A member 4 (MmDjA4)	0.34	-	cyt	0	Membrane; lipid-anchor (Potential)				397
Q64237 UniProt NPD GO	DOPO_MOUSE	Dopamine beta-hydroxylase precursor (EC 1.14.17.1) (Dopamine beta-monooxygenase)	0.34	-	mit	0	Exists as both a soluble and membrane-bound form in chromaffin granules (the membrane-bound form may ...				621
Q9PUE0 UniProt NPD GO	DMRT1_ALLMI	Doublesex- and mab-3-related transcription factor 1 (Fragment)	0.34	-	nuc	0	Nucleus (Potential)				101
O61213 UniProt NPD GO	DUOX1_CAEEL	Dual oxidase 1 precursor (EC 1.6.3.1) (EC 1.11.1.-) (DUOX1) (NADPH thyroid oxidase 1) (Blistered cut ...	0.34	-	end	7	Membrane; multi-pass membrane protein (By similarity)				1497
Q16690 UniProt NPD GO	DUS5_HUMAN	Dual specificity protein phosphatase 5 (EC 3.1.3.48) (EC 3.1.3.16) (Dual specificity protein phospha ...	0.34	-	nuc	0	Nucleus (Potential)		603069		384
Q9UHF1 UniProt NPD GO	EGFL7_HUMAN	EGF-like domain-containing protein 7 precursor (Multiple EGF-like domain protein 7) (Multiple epider ...	0.34	-	nuc	0	Secreted protein (By similarity)	extracellular region [ISS]	608582		273
Q9H4M9 UniProt NPD GO	EHD1_HUMAN	EH-domain-containing protein 1 (Testilin) (hPAST1)	0.34	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side. Endosome; early endosome; early endosome membrane; li ...		605888		534
Q9WVK4 UniProt NPD GO	EHD1_MOUSE	EH-domain-containing protein 1 (mPAST1)	0.34	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Endosome; early endosome; early endos ...	early endosome [IDA] endocytic vesicle [IDA] plasma membrane [IDA]			534
O09032 UniProt NPD GO	ELAV4_RAT	ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)	0.34	-	nuc	0					373
P17639 UniProt NPD GO	EMB1_DAUCA	EMB-1 protein	0.34	-	nuc	0					92
Q7L775 UniProt NPD GO	EPMIP_HUMAN	EPM2A-interacting protein 1 (Laforin-interacting protein)	0.34	-	cyt	0	Endoplasmic reticulum		607911		607
P61562 UniProt NPD GO	ENW1_HYLPI	ERV-W1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (ERVWE1 envelope protein) ...	0.34	-	end	1	TM: Cell membrane; single-pass type I membrane protein. SU: Cell membrane; peripheral membrane prote ...				538
Q15723 UniProt NPD GO	ELF2_HUMAN	ETS-related transcription factor Elf-2 (E74-like factor 2) (New ETS-related factor)	0.34	+	nuc	0	Nucleus	nucleus [IC]			593
P13060 UniProt NPD GO	EF2_DROME	Elongation factor 2 (EF-2)	0.34	-	nuc	0	Cytoplasm				843
Q64355 UniProt NPD GO	EFS_MOUSE	Embryonal Fyn-associated substrate (SRC-interacting protein) (Signal-integrating protein)	0.34	-	nuc	0					560
P52403 UniProt NPD GO	CHI1_SOLTU	Endochitinase 1 precursor (EC 3.2.1.14) (Fragment)	0.34	-	cyt	0	Vacuole (By similarity). Vacuolar and protoplast (By similarity)				318
Q39785 UniProt NPD GO	CHI2_GOSHI	Endochitinase 2 precursor (EC 3.2.1.14) (Fragment)	0.34	-	nuc	0					302
P52405 UniProt NPD GO	CHI3_SOLTU	Endochitinase 3 precursor (EC 3.2.1.14) (Fragment)	0.34	-	nuc	0	Vacuole (By similarity). Vacuolar and protoplast (By similarity)				318
P36361 UniProt NPD GO	CHI5_PHAVU	Endochitinase CH5B precursor (EC 3.2.1.14)	0.34	-	vac	1 *	Vacuole (By similarity). Vacuolar and protoplast (By similarity)				327
Q8TC29 UniProt NPD GO	ENKUR_HUMAN	Enkurin	0.34	-	nuc	0	Sperm acrosomal crescent and flagellar principal piece				256
P47778 UniProt NPD GO	ECP_GORGO	Eosinophil cationic protein precursor (EC 3.1.27.-) (ECP) (Ribonuclease 3) (RNase 3)	0.34	-	exc	0	Matrix of eosinophil's large specific granule				160

You are viewing entries 36601 to 36650 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.