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
P28098 UniProt NPD GO	WNT7_STRPU	Protein Wnt-7 (Fragment)	0.42	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P10040 UniProt NPD GO	CRB_DROME	Protein crumbs precursor (95F)	0.42	-	nuc	1	Cell membrane; apical cell membrane; single-pass type I membrane protein. Specifically localized to ...	apical plasma membrane [TAS] apicolateral plasma membrane [IDA] integral to membrane [TAS] plasma membrane [IDA] subapical complex [TAS]			2146
O43125 UniProt NPD GO	CSH3_SCHPO	Protein csh3	0.42	-	nuc	0					296
O74352 UniProt NPD GO	HOB1_SCHPO	Protein hob1 (Homolog of Bin1)	0.42	-	nuc	0		cell cortex of cell tip [TAS] medial ring [TAS]			466
O46238 UniProt NPD GO	HUNB_DROCY	Protein hunchback (Fragments)	0.42	-	nuc	0	Nucleus (By similarity)				198
O46240 UniProt NPD GO	HUNB_DRODS	Protein hunchback (Fragments)	0.42	-	nuc	0	Nucleus (By similarity)				198
O46252 UniProt NPD GO	HUNB_DROPO	Protein hunchback (Fragments)	0.42	-	nuc	0	Nucleus (By similarity)				193
O46260 UniProt NPD GO	HUNB_DROTA	Protein hunchback (Fragments)	0.42	-	nuc	0	Nucleus (By similarity)				192
Q05513 UniProt NPD GO	KPCZ_HUMAN	Protein kinase C zeta type (EC 2.7.11.13) (nPKC-zeta)	0.42	-	nuc	0	Cytoplasm. In the retina, localizes in the terminals of the rod bipolar cells (By similarity). Endos ...	cytoplasm [TAS] membrane fraction [TAS] plasma membrane [TAS]	176982		592
P16912 UniProt NPD GO	KDC2_DROME	Protein kinase DC2 (EC 2.7.11.1)	0.42	-	nuc	0					583
Q10452 UniProt NPD GO	GSK3_SCHPO	Protein kinase gsk3 (EC 2.7.11.1) (Protein kinase skp1)	0.42	-	nuc	0					387
Q58DV0 UniProt NPD GO	PELO_BOVIN	Protein pelota homolog	0.42	-	cyt	0	Nucleus (Potential)				386
Q9BRX2 UniProt NPD GO	PELO_HUMAN	Protein pelota homolog	0.42	-	cyt	0	Nucleus (Potential)		605757	1X52	385
Q5RCE3 UniProt NPD GO	PELO_PONPY	Protein pelota homolog	0.42	-	cyt	0	Nucleus (Potential)				385
Q12511 UniProt NPD GO	PP2C5_YEAST	Protein phosphatase 2C homolog 5 (EC 3.1.3.16) (PP2C-5)	0.42	-	nuc	0	Mitochondrion	mitochondrion [IDA]			572
Q6FNL6 UniProt NPD GO	PPME1_CANGA	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.42	-	cyt	0					386
Q96I23 UniProt NPD GO	PREY_HUMAN	Protein preY, mitochondrial precursor	0.42	-	mit	0	Mitochondrion (Potential)				114
Q24668 UniProt NPD GO	SXL_DROSU	Protein sex-lethal	0.42	-	nuc	0					354
Q9P5X6 UniProt NPD GO	SEY1_NEUCR	Protein sey-1	0.42	-	cyt	2	Membrane; multi-pass membrane protein (Potential)				862
Q27K34 UniProt NPD GO	PLA2_ORYSA	Protein terminal ear1 homolog (Protein PLASTOCHRON2) (Protein LEAFY HEAD2)	0.42	+	nuc	0					683
P52871 UniProt NPD GO	SC6B2_YEAST	Protein transport protein SEB2 (Ssh1 complex subunit SEB2) (Ssh1 complex subunit beta)	0.42	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein	endoplasmic reticulum [TAS] translocon complex [TAS]			88
P15303 UniProt NPD GO	SEC23_YEAST	Protein transport protein SEC23	0.42	-	nuc	0	Cytoplasm	COPII vesicle coat [TAS] cytoplasm [IDA]		1M2V	768
Q92837 UniProt NPD GO	FRAT1_HUMAN	Proto-oncogene FRAT1 (Frequently rearranged in advanced T-cell lymphomas) (Frat-1)	0.42	-	nuc	0	Cytoplasm		602503	1GNG	279
P04426 UniProt NPD GO	WNT1_MOUSE	Proto-oncogene protein Wnt-1 precursor	0.42	-	exc	0	Secreted protein; extracellular space; extracellular matrix				370
P12931 UniProt NPD GO	SRC_HUMAN	Proto-oncogene tyrosine-protein kinase Src (EC 2.7.10.2) (p60-Src) (c-Src) (pp60c-src)	0.42	-	nuc	0			190090	2SRC	535
Q9BZA7 UniProt NPD GO	PC11X_HUMAN	Protocadherin-11 X-linked precursor (Protocadherin-11) (Protocadherin on the X chromosome) (PCDH-X) ...	0.42	+	nuc	0	Membrane; single-pass type I membrane protein (Potential)		300246		1347
P48271 UniProt NPD GO	YCF30_CYAPA	Putative HTH-type transcriptional regulator ycf30	0.42	-	cyt	0	Plastid; cyanelle				324
Q10334 UniProt NPD GO	ALAT_SCHPO	Putative alanine aminotransferase (EC 2.6.1.2) (Glutamic--pyruvic transaminase) (GPT) (Glutamic--ala ...	0.42	-	cyt	0	Cytoplasm (Potential)				505
Q23688 UniProt NPD GO	FCA1_CRIFA	Putative flagellar calcium-binding protein (Fragment)	0.42	-	nuc	0	Flagellum (Potential)				63
P83101 UniProt NPD GO	GSK3H_DROME	Putative glycogen synthase kinase-3 homolog (EC 2.7.11.26) (GSK-3) (Protein gasket)	0.42	-	nuc	0					501
Q9V568 UniProt NPD GO	OR45A_DROME	Putative odorant receptor 45a	0.42	+	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			378
Q7TT15 UniProt NPD GO	GLTL3_MOUSE	Putative polypeptide N-acetylgalactosaminyltransferase-like protein 3 (EC 2.4.1.41) (Protein-UDP ace ...	0.42	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				598
Q8K1B9 UniProt NPD GO	GLTL4_MOUSE	Putative polypeptide N-acetylgalactosaminyltransferase-like protein 4 (EC 2.4.1.41) (Protein-UDP ace ...	0.42	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				622
Q09474 UniProt NPD GO	T23O_CAEEL	Putative tryptophan 2,3-dioxygenase (EC 1.13.11.11) (TO) (Tryptophan pyrrolase) (Tryptophanase) (Try ...	0.42	-	cyt	0					403
Q9SJJ7 UniProt NPD GO	ATL2E_ARATH	RING-H2 finger protein ATL2E	0.42	-	nuc	1 *					237
Q8SV03 UniProt NPD GO	FCP1_ENCCU	RNA polymerase II subunit A C-terminal domain phosphatase (EC 3.1.3.16) (CTD phosphatase FCP1)	0.42	+	cyt	0	Nucleus (Probable)				411
Q94901 UniProt NPD GO	LARK_DROME	RNA-binding protein lark	0.42	-	nuc	0	Cytoplasm. Nucleus. The precise location within neurons varies according to the type of neuron, bein ...	cytoplasm [IDA] nucleus [IDA]			352
Q9H446 UniProt NPD GO	RWDD1_HUMAN	RWD domain-containing protein 1	0.42	-	cyt	0					243
Q9BYM8 UniProt NPD GO	UB7I3_HUMAN	RanBP-type and C3HC4-type zinc finger-containing protein 1 (Ubiquitin-conjugating enzyme 7-interacti ...	0.42	-	nuc	0				2CRC	500
Q9DD19 UniProt NPD GO	RASF7_MOUSE	Ras association domain-containing protein 7	0.42	+	nuc	0					359
Q62132 UniProt NPD GO	PTPRR_MOUSE	Receptor-type tyrosine-protein phosphatase R precursor (EC 3.1.3.48) (Protein-tyrosine-phosphatase S ...	0.42	-	end	1	Isoform alpha: Cell membrane; single-pass type I membrane protein. Isoform beta, isoform gamma: Cyto ...	cell surface [ISS]		1JLN	656
O94810 UniProt NPD GO	RGS11_HUMAN	Regulator of G-protein signaling 11 (RGS11)	0.42	-	mit	0			603895		467
Q09843 UniProt NPD GO	RFC2_SCHPO	Replication factor C subunit 2 (Activator 1 41 kDa subunit) (Replication factor C2)	0.42	-	nuc	0	Nucleus (By similarity)	Ctf18 RFC-like complex [TAS] Elg1 RFC-like complex [IDA] Rad17 RFC-like complex [TAS]			340
Q9CZQ6 UniProt NPD GO	RAE1E_MOUSE	Retinoic acid early inducible protein 1 epsilon precursor (RAE-1epsilon)	0.42	-	nuc	1	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	anchored to plasma membrane [ISS]			251
Q9DCH2 UniProt NPD GO	POP7_MOUSE	Ribonuclease P protein subunit p20 (EC 3.1.26.5) (RNaseP protein p20)	0.42	-	nuc	0	Nucleus; nucleolus (Potential)				140
Q6PEE3 UniProt NPD GO	RIR2B_MOUSE	Ribonucleoside-diphosphate reductase M2 subunit B (EC 1.17.4.1) (TP53-inducible ribonucleotide reduc ...	0.42	-	cyt	1	Cytoplasm. Translocates from cytoplasm to nucleus in response to DNA damage (By similarity)				351
Q9WUT3 UniProt NPD GO	KS6A2_MOUSE	Ribosomal protein S6 kinase alpha-2 (EC 2.7.11.1) (S6K-alpha 2) (90 kDa ribosomal protein S6 kinase ...	0.42	+	mit	0	Nucleus (By similarity)	cytoplasm [IDA] spindle [IDA]			733
Q5R5X9 UniProt NPD GO	SMYD4_PONPY	SET and MYND domain-containing protein 4	0.42	-	nuc	0					804
P54214 UniProt NPD GO	SFAS_DUNBI	SF-assemblin	0.42	-	nuc	0					277
P34714 UniProt NPD GO	SPRC_CAEEL	SPARC precursor (Secreted protein acidic and rich in cysteine) (Osteonectin) (ON) (Basement-membrane ...	0.42	-	exc	0	Secreted protein; extracellular space; extracellular matrix				264

You are viewing entries 30651 to 30700 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.