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
Q08162 UniProt NPD GO	RRP44_YEAST	Exosome complex exonuclease RRP44 (EC 3.1.13.-) (Ribosomal RNA-processing protein 44) (Protein DIS3) ...	0.75	-	nuc	0	Cytoplasm. Nucleus; nucleolus	cytoplasmic exosome (RNase complex) [IDA] mitochondrion [IDA] nuclear exosome (RNase complex) [IDA]			1001
Q924C1 UniProt NPD GO	XPO5_MOUSE	Exportin-5 (Exp5) (Ran-binding protein 21)	0.75	+	end	0	Nucleus. Cytoplasm. Shuttles between the nucleus and the cytoplasm (By similarity)				1204
Q704U0 UniProt NPD GO	XPO7A_XENLA	Exportin-7-A	0.75	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1087
Q569Z2 UniProt NPD GO	XPO7B_XENLA	Exportin-7-B	0.75	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1087
O74991 UniProt NPD GO	POF3_SCHPO	F-box/TPR-repeat protein pof3	0.75	-	nuc	0	Nucleus				577
Q9JL70 UniProt NPD GO	FANCA_MOUSE	Fanconi anemia group A protein homolog (Protein FACA)	0.75	-	vac	0	Nucleus (By similarity). Major form. Cytoplasm (By similarity). Minor form				1439
P22315 UniProt NPD GO	HEMH_MOUSE	Ferrochelatase, mitochondrial precursor (EC 4.99.1.1) (Protoheme ferro-lyase) (Heme synthetase)	0.75	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side	mitochondrial inner membrane [TAS]			420
Q3YA36 UniProt NPD GO	HEMH_PANTR	Ferrochelatase, mitochondrial precursor (EC 4.99.1.1) (Protoheme ferro-lyase) (Heme synthetase)	0.75	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity). Bound to the mitochondrial ...				423
Q8TAT2 UniProt NPD GO	FGFP3_HUMAN	Fibroblast growth factor-binding protein 3 precursor (FGF-binding protein 3) (FGF-BP3) (FGFBP-3)	0.75	+	exc	0	Secreted protein (Probable)				258
P17839 UniProt NPD GO	AG_ARATH	Floral homeotic protein AGAMOUS	0.75	-	nuc	0	Nucleus				252
Q01540 UniProt NPD GO	AG_BRANA	Floral homeotic protein AGAMOUS	0.75	-	nuc	0	Nucleus				252
Q40885 UniProt NPD GO	AG_PETHY	Floral homeotic protein AGAMOUS (pMADS3)	0.75	-	nuc	0	Nucleus (By similarity)				242
Q63249 UniProt NPD GO	FOXD4_RAT	Forkhead box protein D4 (Forkhead-related protein FKHL9) (Forkhead-related transcription factor 5) ( ...	0.75	-	mit	0	Nucleus				101
Q12952 UniProt NPD GO	FOXL1_HUMAN	Forkhead box protein L1 (Forkhead-related protein FKHL11) (Forkhead-related transcription factor 7) ...	0.75	-	nuc	0	Nucleus	nucleus [NAS]	603252		345
Q66J77 UniProt NPD GO	FOXN2_XENLA	Forkhead box protein N2	0.75	-	nuc	0	Nucleus (Potential)				430
P51116 UniProt NPD GO	FXR2_HUMAN	Fragile X mental retardation syndrome-related protein 2	0.75	-	nuc	0	Cytoplasm	cytoplasm [TAS] cytosolic large ribosomal subunit (sensu Eu... [TAS] nucleus [TAS]	605339		673
O43952 UniProt NPD GO	TGP1_TETTH	G-quartet DNA-binding protein TGP1	0.75	-	nuc	0	Nucleus (Potential)				725
P38794 UniProt NPD GO	PCL5_YEAST	G1/S-specific cyclin PCL5	0.75	-	nuc	0		cyclin-dependent protein kinase holoenzyme ... [TAS]			229
Q62997 UniProt NPD GO	GFRA1_RAT	GDNF family receptor alpha-1 precursor (GFR-alpha-1) (GDNF receptor alpha) (GDNFR-alpha) (TGF-beta-r ...	0.75	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [TAS]		1Q8D	468
O13157 UniProt NPD GO	GFRA2_CHICK	GDNF family receptor alpha-2 precursor (GFR-alpha-2) (Neurturin receptor alpha) (NTNR-alpha) (NRTNR- ...	0.75	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				465
Q9D4H2 UniProt NPD GO	GCC1_MOUSE	GRIP and coiled-coil domain-containing protein 1 (Golgi coiled coil protein 1)	0.75	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity)				778
Q9NUV9 UniProt NPD GO	GIMA4_HUMAN	GTPase, IMAP family member 4 (Immunity-associated protein 4) (Immunity-associated nucleotide 1 prote ...	0.75	-	nuc	0			608087		329
P07733 UniProt NPD GO	GS17_XENLA	Gastrula-specific protein 17	0.75	-	nuc	0					147
Q9Y5Q9 UniProt NPD GO	TF3C3_HUMAN	General transcription factor 3C polypeptide 3 (Transcription factor IIIC-subunit gamma) (TF3C-gamma) ...	0.75	-	nuc	0	Nucleus	transcription factor TFIIIC complex [TAS]	604888		886
Q8R2T8 UniProt NPD GO	TF3C5_MOUSE	General transcription factor 3C polypeptide 5 (Transcription factor IIIC-epsilon subunit) (TF3C-epsi ...	0.75	-	nuc	0	Nucleus (By similarity)				520
Q9JI57 UniProt NPD GO	GT2D1_MOUSE	General transcription factor II-I repeat domain-containing protein 1 (GTF2I repeat domain-containing ...	0.75	-	nuc	0	Nucleus	nucleus [ISS]			1104
P49843 UniProt NPD GO	GCR_ONCMY	Glucocorticoid receptor (GR)	0.75	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in the absence of ligand; nuclear af ...				758
P49844 UniProt NPD GO	GCR_XENLA	Glucocorticoid receptor (GR)	0.75	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in the absence of ligand; nuclear af ...				776
Q7TT51 UniProt NPD GO	GLUD1_RAT	Glutamate--ammonia ligase domain-containing protein 1 (Lengsin) (Lens glutamine synthase-like)	0.75	-	nuc	0					561
Q9LMP7 UniProt NPD GO	GOS11_ARATH	Golgi SNARE 11 protein (AtGOS11) (Golgi SNAP receptor complex member 1-1)	0.75	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				223
Q02391 UniProt NPD GO	GSLG1_CHICK	Golgi apparatus protein 1 precursor (Cysteine-rich fibroblast growth factor receptor)	0.75	-	end	1	Golgi apparatus; Golgi membrane; single-pass type I membrane protein				1142
Q62839 UniProt NPD GO	GOGA2_RAT	Golgin subfamily A member 2 (Cis-Golgi matrix protein GM130)	0.75	+	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein. Peripheral membrane ...	Golgi apparatus [IDA] Golgi cis cisterna [IDA]			986
Q7SXE4 UniProt NPD GO	GOGA5_BRARE	Golgin subfamily A member 5 (Golgin-84)	0.75	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)	Golgi apparatus [ISS]			760
Q6ISB3 UniProt NPD GO	GRHL2_HUMAN	Grainyhead-like protein 2 homolog (Brother of mammalian grainyhead) (Transcription factor CP2-like 3 ...	0.75	-	nuc	0	Nucleus		608641		625
O70326 UniProt NPD GO	GREM1_MOUSE	Gremlin-1 precursor (Cysteine knot superfamily 1, BMP antagonist 1) (Down-regulated in Mos-transform ...	0.75	-	exc	0	Secreted protein (Probable)				184
Q9JLM9 UniProt NPD GO	GRB14_MOUSE	Growth factor receptor-bound protein 14 (GRB14 adapter protein)	0.75	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein (By similari ...				538
Q99988 UniProt NPD GO	GDF15_HUMAN	Growth/differentiation factor 15 precursor (GDF-15) (Placental bone morphogenetic protein) (Placenta ...	0.75	-	exc	0	Secreted protein (Probable)	extracellular region [TAS]	605312		308
Q4VT39 UniProt NPD GO	GPA13_CAEBR	Guanine nucleotide-binding protein alpha-13 subunit	0.75	-	mit	0					349
Q9N2V6 UniProt NPD GO	GPA16_CAEEL	Guanine nucleotide-binding protein alpha-16 subunit	0.75	-	cyt	0					356
Q61B55 UniProt NPD GO	GPA4_CAEBR	Guanine nucleotide-binding protein alpha-4 subunit	0.75	-	cyt	0					358
Q5R7I3 UniProt NPD GO	HBP1_PONPY	HMG box-containing protein 1 (HMG box transcription factor 1) (High mobility group box transcription ...	0.75	-	nuc	0	Nucleus (By similarity)				514
Q02577 UniProt NPD GO	HEN2_HUMAN	Helix-loop-helix protein 2 (HEN2) (Nescient helix loop helix 2) (NSCL-2)	0.75	+	nuc	0			162361		135
P20823 UniProt NPD GO	HNF1A_HUMAN	Hepatocyte nuclear factor 1-alpha (HNF-1A) (Liver-specific transcription factor LF-B1) (LFB1) (Trans ...	0.75	-	nuc	0	Nucleus		142410	1IC8	631
Q9UPZ3 UniProt NPD GO	HPS5_HUMAN	Hermansky-Pudlak syndrome 5 protein (Alpha-integrin-binding protein 63) (Ruby-eye protein 2 homolog) ...	0.75	-	nuc	0			607521		1129
Q7Z2G1 UniProt NPD GO	H2BWT_HUMAN	Histone H2B type W-T (H2B histone family member W testis-specific)	0.75	-	nuc	0	Nucleus; nuclear membrane		300507		175
Q27750 UniProt NPD GO	H2BS2_PSAMI	Histone H2B.2, sperm	0.75	+	nuc	0	Nucleus				142
P52951 UniProt NPD GO	GBX2_HUMAN	Homeobox protein GBX-2 (Gastrulation and brain-specific homeobox protein 2)	0.75	+	nuc	0	Nucleus (Probable)		601135		348
P17277 UniProt NPD GO	HXA4_CHICK	Homeobox protein Hox-A4 (Chox-1.4)	0.75	+	nuc	0	Nucleus				309
Q6B3N0 UniProt NPD GO	HXA5_CHICK	Homeobox protein Hox-A5	0.75	+	nuc	0	Nucleus (By similarity)				270
Q9PWL7 UniProt NPD GO	HXBAA_BRARE	Homeobox protein Hox-B10a (Hox-B10) (Fragment)	0.75	+	nuc	0	Nucleus (By similarity)				85

You are viewing entries 11301 to 11350 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.