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
Q922E6 UniProt NPD GO	FAKD2_MOUSE	FAST kinase domains-containing protein 2	0.54	-	mit	0					689
Q05040 UniProt NPD GO	FAR8_YEAST	Factor arrest protein 8	0.54	-	nuc	0	Cytoplasm. Endoplasmic reticulum				523
Q96NZ1 UniProt NPD GO	FOXN4_HUMAN	Forkhead box protein N4	0.54	-	nuc	0	Nucleus (Potential)		609429		517
Q09537 UniProt NPD GO	GRK1_CAEEL	G protein-coupled receptor kinase 1 (EC 2.7.11.16)	0.54	+	cyt	0					642
Q09639 UniProt NPD GO	GRK2_CAEEL	G protein-coupled receptor kinase 2 (EC 2.7.11.16)	0.54	-	cyt	0					707
Q9Y4H4 UniProt NPD GO	GPSM3_HUMAN	G-protein signaling modulator 3 (Activator of G-protein signaling 4) (Protein G18) (G18.1b)	0.54	-	nuc	0	Cytoplasm				160
O49743 UniProt NPD GO	GATA4_ARATH	GATA transcription factor 4 (AtGATA-4)	0.54	-	nuc	0	Nucleus (Probable)				240
Q9NPZ5 UniProt NPD GO	B3GA2_HUMAN	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2 (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.54	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	integral to membrane [ISS]	607497		323
P59270 UniProt NPD GO	B3GA2_MOUSE	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2 (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.54	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to membrane [ISS]			324
Q9VLA1 UniProt NPD GO	B3G2S_DROME	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase S (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.54	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)	Golgi apparatus [NAS]			409
O88871 UniProt NPD GO	GABR2_RAT	Gamma-aminobutyric acid type B receptor, subunit 2 precursor (GABA-B receptor 2) (GABA-B-R2) (Gb2) ( ...	0.54	-	end	7	Cell membrane; multi-pass membrane protein. Moreover coexpression of GABA-B-R1 and GABA-B-R2 appears ...	integral to membrane [TAS]			940
Q9XYP7 UniProt NPD GO	GCP2_DROME	Gamma-tubulin complex component 2 homolog (Gamma ring complex protein 84) (dGrip84) (d84p)	0.54	-	nuc	0	Centrosome (Potential)	gamma-tubulin small complex [IDA]			852
P02891 UniProt NPD GO	BAB2_BABBO	Gene BABR protein 2	0.54	-	nuc	0					183
Q8R4T5 UniProt NPD GO	GRASP_RAT	General receptor for phosphoinositides 1-associated scaffold protein (GRP1-associated scaffold prote ...	0.54	-	nuc	0	Cytoplasm; perinuclear region. Cell membrane; peripheral membrane protein; cytoplasmic side. Postsyn ...	plasma membrane [IDA]			394
P05110 UniProt NPD GO	GLUC_CAVPO	Glucagon precursor [Contains: Glicentin; Glicentin-related polypeptide (GRPP); Oxyntomodulin (OXY) ( ...	0.54	-	exc	0	Secreted protein				180
Q04739 UniProt NPD GO	GAL83_YEAST	Glucose repression protein GAL83 (Protein SPM1)	0.54	-	nuc	0		nucleus [IDA]			417
O93869 UniProt NPD GO	GYS_NEUCR	Glycogen [starch] synthase (EC 2.4.1.11)	0.54	-	nuc	0					706
Q9QZF2 UniProt NPD GO	GPC1_MOUSE	Glypican-1 precursor	0.54	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				557
Q91XA2 UniProt NPD GO	GP73_MOUSE	Golgi phosphoprotein 2 (Golgi membrane protein GP73)	0.54	-	nuc	1 *	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; single-pass type II membrane protein ...				393
Q9GKI7 UniProt NPD GO	C43BP_BOVIN	Goodpasture antigen-binding protein (EC 2.7.11.9) (GPBP) (Collagen type IV alpha-3-binding protein) ...	0.54	+	cyt	0					624
Q9XZV4 UniProt NPD GO	GNAQ_GEOCY	Guanine nucleotide-binding protein G(q) subunit alpha (Guanine nucleotide-binding protein alpha-q)	0.54	-	cyt	0					355
P45645 UniProt NPD GO	GNA11_MELGA	Guanine nucleotide-binding protein alpha-11 subunit	0.54	-	cyt	0					359
P38408 UniProt NPD GO	GNA14_BOVIN	Guanine nucleotide-binding protein alpha-14 subunit (GL1)	0.54	-	cyt	0					355
O44081 UniProt NPD GO	DKC1_DROME	H/ACA ribonucleoprotein complex subunit 4 (EC 5.4.99.-) (Nucleolar protein AT band 60B) (Protein min ...	0.54	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			508
Q8LEM6 UniProt NPD GO	HA22H_ARATH	HVA22-like protein h (AtHVA22h)	0.54	-	nuc	0					315
Q9UBI9 UniProt NPD GO	HDC_HUMAN	Headcase protein homolog (hHDC)	0.54	-	nuc	0			607977		543
P46598 UniProt NPD GO	HSP90_CANAL	Heat shock protein 90 homolog	0.54	-	cyt	0					707
P11501 UniProt NPD GO	HS90A_CHICK	Heat shock protein HSP 90-alpha	0.54	-	cyt	0	Cytoplasm	cytoplasm [IDA] soluble fraction [IDA]			728
P06660 UniProt NPD GO	HSP85_TRYCR	Heat shock-like 85 kDa protein	0.54	-	cyt	0	Cytoplasm				704
Q86BJ3 UniProt NPD GO	PIPE_DROME	Heparan sulfate 2-O-sulfotransferase pipe (EC 2.8.2.-)	0.54	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein. Wbl is required for its proce ...	chromosome [IDA] Golgi apparatus [IDA] integral to Golgi membrane [NAS] nucleus [IDA]			514
P51991 UniProt NPD GO	ROA3_HUMAN	Heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3)	0.54	+	nuc	0	Nucleus (By similarity). Component of ribonucleosomes (By similarity)	ribonucleoprotein complex [TAS]	605372		378
Q8BG05 UniProt NPD GO	ROA3_MOUSE	Heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3)	0.54	+	nuc	0	Nucleus (By similarity). Component of ribonucleosomes (By similarity)				379
Q6URK4 UniProt NPD GO	ROA3_RAT	Heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3)	0.54	+	nuc	0	Nucleus (By similarity). Component of ribonucleosomes (By similarity)				379
O76083 UniProt NPD GO	PDE9A_HUMAN	High-affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35)	0.54	-	nuc	0			602973	2HD1	593
O00479 UniProt NPD GO	HMGN4_HUMAN	High-mobility group nucleosome-binding domain-containing protein 4 (Nonhistone chromosomal protein H ...	0.54	-	nuc	0	Nucleus (By similarity)				89
P98176 UniProt NPD GO	H2AFB_HUMAN	Histone H2A-Bbd (H2A Barr body-deficient) (H2A.Bbd)	0.54	+	mit	0	Nucleus. Associated with the active X chromosome and with autosomes, while it is absent from the ina ...		300445		115
Q75VN4 UniProt NPD GO	H2B_RHASC	Histone H2B	0.54	+	nuc	0	Nucleus. Secreted protein	extracellular region [IDA] nucleosome [NAS]			125
P06900 UniProt NPD GO	H2B12_XENLA	Histone H2B 1.2 (H2B1.2)	0.54	+	nuc	0	Nucleus				125
O60814 UniProt NPD GO	H2B1K_HUMAN	Histone H2B type 1-K (H2B K) (HIRA-interacting protein 1)	0.54	+	nuc	0	Nucleus	nucleosome [ISS]		2CV5	125
Q6CK60 UniProt NPD GO	H2B1_KLULA	Histone H2B.1	0.54	-	nuc	0	Nucleus (By similarity)				131
P61832 UniProt NPD GO	H3_ASPFU	Histone H3	0.54	-	nuc	0	Nucleus (By similarity)				135
Q2UCQ0 UniProt NPD GO	H3_ASPOR	Histone H3	0.54	-	nuc	0	Nucleus (By similarity)				135
P23753 UniProt NPD GO	H3_EMENI	Histone H3	0.54	-	nuc	0	Nucleus (By similarity)				135
P61834 UniProt NPD GO	H3_PENFN	Histone H3	0.54	-	nuc	0	Nucleus (By similarity)				135
Q6FTW5 UniProt NPD GO	GCN5_CANGA	Histone acetyltransferase GCN5 (EC 2.3.1.48)	0.54	+	nuc	0	Nucleus (By similarity)				546
O88574 UniProt NPD GO	SAP30_MOUSE	Histone deacetylase complex subunit SAP30 (Sin3-associated polypeptide, 30 kDa) (Sin3 corepressor co ...	0.54	-	nuc	0	Nucleus				220
P79775 UniProt NPD GO	ANF1_CHICK	Homeobox protein ANF-1 (GANF)	0.54	+	nuc	0	Nucleus (Probable)				196
P47902 UniProt NPD GO	CDX1_HUMAN	Homeobox protein CDX-1 (Caudal-type homeobox protein 1)	0.54	+	nuc	0	Nucleus		600746		265
Q98878 UniProt NPD GO	DLX4B_BRARE	Homeobox protein Dlx4b (DLX-7) (Distal-less homeobox protein 4b)	0.54	+	nuc	0	Nucleus (Potential)				254
P82976 UniProt NPD GO	GBX1_MOUSE	Homeobox protein GBX-1 (Gastrulation and brain-specific homeobox protein 1)	0.54	+	nuc	0	Nucleus (By similarity)				418

You are viewing entries 22501 to 22550 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.