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
Q9UK99 UniProt NPD GO	FBX3_HUMAN	F-box only protein 3	0.64	-	cyt	0			609089		471
Q8TF61 UniProt NPD GO	FBX41_HUMAN	F-box only protein 41	0.64	-	nuc	0			609108		874
Q61554 UniProt NPD GO	FBN1_MOUSE	Fibrillin-1 precursor	0.64	-	nuc	0		microfibril [TAS]			2871
O43559 UniProt NPD GO	FRS3_HUMAN	Fibroblast growth factor receptor substrate 3 (FGFR substrate 3) (Suc1-associated neurotrophic facto ...	0.64	-	nuc	0	Membrane; lipid-anchor		607744		491
Q91738 UniProt NPD GO	FAK1_XENLA	Focal adhesion kinase 1 (EC 2.7.10.2) (FADK 1) (pp125FAK)	0.64	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion; cytoplasmic side. Constituent of focal adhesion ...				1068
P39963 UniProt NPD GO	CCNB3_CHICK	G2/mitotic-specific cyclin-B3	0.64	-	nuc	0	Nucleus				403
Q8IWJ2 UniProt NPD GO	GCC2_HUMAN	GRIP and coiled-coil domain-containing protein 2 (Golgi coiled coil protein GCC185) (CTCL tumor anti ...	0.64	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein				1583
P34512 UniProt NPD GO	GRP1_CAEEL	GTP exchange factor for ARFs 1	0.64	-	mit	0					393
P49095 UniProt NPD GO	GCSP_YEAST	Glycine dehydrogenase [decarboxylating], mitochondrial precursor (EC 1.4.4.2) (Glycine decarboxylase ...	0.64	+	mit	0	Mitochondrion (By similarity)	glycine cleavage complex [TAS] mitochondrion [IDA]			1034
P11828 UniProt NPD GO	GLYG3_SOYBN	Glycinin G3 precursor [Contains: Glycinin A subunit; Glycinin B subunit]	0.64	-	exc	0					481
Q7S3C8 UniProt NPD GO	NMT_NEUCR	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.64	+	cyt	0	Cytoplasm (By similarity)				569
Q9NZI5 UniProt NPD GO	GRHL1_HUMAN	Grainyhead-like protein 1 homolog (Transcription factor CP2-like 2) (Transcription factor LBP-32) (N ...	0.64	-	nuc	0	Nucleus		609786		618
P15509 UniProt NPD GO	CSF2R_HUMAN	Granulocyte-macrophage colony-stimulating factor receptor alpha chain precursor (GM-CSF-R-alpha) (GM ...	0.64	-	nuc	1	Cell membrane; single-pass type I membrane protein. Isoform 3, isoform 4, isoform 6: Secreted protei ...	integral to plasma membrane [TAS]	425000		400
Q8BJM3 UniProt NPD GO	GIDRP_MOUSE	Growth inhibition and differentiation-related protein 88 homolog	0.64	-	nuc	0					775
Q60779 UniProt NPD GO	GAS8_MOUSE	Growth-arrest-specific protein 8 (Growth arrest-specific 11)	0.64	-	nuc	0	Cytoplasm. Associates with microtubules. Localized to the cytoplasm of round spermatids, the tails o ...	flagellum (sensu Eukaryota) [IDA] microtubule [IDA]			478
Q63210 UniProt NPD GO	GNA12_RAT	Guanine nucleotide-binding protein alpha-12 subunit (G alpha-12)	0.64	-	mit	0	Membrane; lipid-anchor	brush border [IDA] heterotrimeric G-protein complex [TAS]			378
Q9XTB2 UniProt NPD GO	GPA13_CAEEL	Guanine nucleotide-binding protein alpha-13 subunit	0.64	-	mit	0					348
O88302 UniProt NPD GO	GNA15_RAT	Guanine nucleotide-binding protein alpha-15 subunit (G alpha-15)	0.64	-	cyt	0		heterotrimeric G-protein complex [TAS]			374
P30679 UniProt NPD GO	GNA15_HUMAN	Guanine nucleotide-binding protein alpha-15 subunit (G alpha-15) (G alpha-16)	0.64	-	mit	0		heterotrimeric G-protein complex [NAS] plasma membrane [TAS]	139314		374
P10823 UniProt NPD GO	GPA2_YEAST	Guanine nucleotide-binding protein alpha-2 subunit (GP2-alpha)	0.64	-	nuc	0		mitochondrion [IDA] plasma membrane [IDA]			449
P40615 UniProt NPD GO	DKC1_RAT	H/ACA ribonucleoprotein complex subunit 4 (EC 5.4.99.-) (Dyskerin) (Nucleolar protein family A membe ...	0.64	+	nuc	0	Nucleus; nucleolus. Nucleus; nucleoplasm; Cajal body. Also localized to Cajal bodies (coiled bodies) ...	nucleolus [IDA]			508
P60608 UniProt NPD GO	EFC2_HUMAN	HERV-F(c)2_7q36.2 provirus ancestral Env polyprotein (Envelope polyprotein) (Fc2deltaenv) [Includes: ...	0.64	-	nuc	0					527
Q9WJR5 UniProt NPD GO	POK3_HUMAN	HERV-K_19q12 provirus ancestral Pol protein (HERV-K(C19) Pol protein) [Includes: Reverse transcripta ...	0.64	-	nuc	0					959
P41154 UniProt NPD GO	HSF_XENLA	Heat shock factor protein (HSF) (Heat shock transcription factor) (HSTF)	0.64	-	nuc	0	Nucleus				451
Q9S7U5 UniProt NPD GO	HSF5_ARATH	Heat shock factor protein 5 (HSF 5) (Heat shock transcription factor 5) (HSTF 5)	0.64	-	nuc	0	Nucleus (By similarity)				374
P07901 UniProt NPD GO	HS90A_MOUSE	Heat shock protein HSP 90-alpha (HSP 86) (Tumor-specific transplantation 86 kDa antigen) (TSTA)	0.64	-	nuc	0	Cytoplasm	cytosol [TAS]			732
P17945 UniProt NPD GO	HGF_RAT	Hepatocyte growth factor precursor (Scatter factor) (SF) (Hepatopoeitin A) [Contains: Hepatocyte gro ...	0.64	+	exc	1 *					728
P22449 UniProt NPD GO	HNF4A_RAT	Hepatocyte nuclear factor 4-alpha (HNF-4-alpha) (Transcription factor HNF-4) (Transcription factor 1 ...	0.64	-	nuc	0	Nucleus	transcription factor complex [IDA]		1M7W	465
Q15651 UniProt NPD GO	HMGN3_HUMAN	High mobility group nucleosome-binding domain-containing protein 3 (Thyroid receptor-interacting pro ...	0.64	-	nuc	0	Nucleus	nucleus [NAS]	604502		99
P40626 UniProt NPD GO	HMGB_TETTH	High mobility group protein B (Nonhistone chromosomal protein LG-2)	0.64	-	nuc	0	Nucleus. Macronuclei				143
P02285 UniProt NPD GO	H2B_MARGL	Histone H2B, sperm	0.64	+	nuc	0	Nucleus				120
P22845 UniProt NPD GO	H5B_XENLA	Histone H5B (XLH5B) (H1E) (H1-SB)	0.64	+	nuc	0	Nucleus				194
P70436 UniProt NPD GO	DLX4_MOUSE	Homeobox protein DLX-4 (DLX-7)	0.64	+	nuc	0	Nucleus (Potential)				240
P15859 UniProt NPD GO	SCR_APIME	Homeobox protein H55 (Fragment)	0.64	+	nuc	0	Nucleus				86
P46606 UniProt NPD GO	HD1_BRANA	Homeobox protein HD1	0.64	-	cyt	0	Nucleus (Probable)				294
P09022 UniProt NPD GO	HXA1_MOUSE	Homeobox protein Hox-A1 (Hox-1.6) (Homeotic protein ERA-1-993) (Early retinoic acid 1) (Homeoboxless ...	0.64	+	nuc	0	Nucleus				331
P49639 UniProt NPD GO	HXA1_HUMAN	Homeobox protein Hox-A1 (Hox-1F)	0.64	+	nuc	0	Nucleus		142955		335
P79724 UniProt NPD GO	HXADB_BRARE	Homeobox protein Hox-A13b (Hox-A13)	0.64	+	nuc	0	Nucleus (By similarity)				289
Q98SI1 UniProt NPD GO	HXA1A_BRARE	Homeobox protein Hox-A1a (Hox-A1)	0.64	+	nuc	0	Nucleus (By similarity)				329
P31246 UniProt NPD GO	HXA2_RAT	Homeobox protein Hox-A2 (Hox-1.11)	0.64	+	nuc	0	Nucleus				372
Q90346 UniProt NPD GO	HXB1_CYPCA	Homeobox protein Hox-B1	0.64	+	nuc	0	Nucleus				315
O42367 UniProt NPD GO	HXB2A_BRARE	Homeobox protein Hox-B2a (Hox-B2)	0.64	+	nuc	0	Nucleus				390
P09024 UniProt NPD GO	HXB7_MOUSE	Homeobox protein Hox-B7 (Hox-2.3) (MUB1) (MH-22B)	0.64	+	nuc	0	Nucleus				217
P09629 UniProt NPD GO	HXB7_HUMAN	Homeobox protein Hox-B7 (Hox-2C) (HHO.C1)	0.64	+	nuc	0	Nucleus	nucleus [NAS]	142962		217
Q08820 UniProt NPD GO	HXD1_XENLA	Homeobox protein Hox-D1 (Hox.lab1)	0.64	+	nuc	0	Nucleus				300
P28357 UniProt NPD GO	HXD9_MOUSE	Homeobox protein Hox-D9 (Hox-4.4) (Hox-5.2)	0.64	+	nuc	0	Nucleus				339
Q60954 UniProt NPD GO	MEIS1_MOUSE	Homeobox protein Meis1 (Myeloid ecotropic viral integration site 1)	0.64	-	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			390
O95475 UniProt NPD GO	SIX6_HUMAN	Homeobox protein SIX6 (Sine oculis homeobox homolog 6) (Optic homeobox 2) (Homeodomain protein OPTX2 ...	0.64	-	nuc	0	Nucleus (By similarity)		606326		246
P20271 UniProt NPD GO	HM14_CAEEL	Homeobox protein ceh-14	0.64	+	nuc	0	Nucleus	nucleus [IDA]			351
P56663 UniProt NPD GO	KNOX5_MAIZE	Homeobox protein knotted-1-like 5 (Fragment)	0.64	+	nuc	0	Nucleus (Probable)				85

You are viewing entries 16851 to 16900 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.