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
Q00939 UniProt NPD GO	FOXGB_RAT	Forkhead box protein G1B (Forkhead-related protein FKHL1) (Transcription factor BF-1) (Brain factor ...	0.71	-	nuc	0	Nucleus				480
P48755 UniProt NPD GO	FOSL1_MOUSE	Fos-related antigen 1 (FRA-1)	0.71	+	nuc	0	Nucleus				273
P29119 UniProt NPD GO	FURI1_XENLA	Furin-1 precursor (EC 3.4.21.75) (Paired basic amino acid residue cleaving enzyme) (PACE) (Dibasic-p ...	0.71	+	end	1					783
Q10654 UniProt NPD GO	CCNB3_CAEEL	G2/mitotic-specific cyclin-B3	0.71	-	mit	0	Nucleus				384
Q8LC59 UniProt NPD GO	GAT22_ARATH	GATA transcription factor 22	0.71	-	nuc	0	Nucleus (Probable)				120
P23824 UniProt NPD GO	GATA2_CHICK	GATA-binding factor 2 (GATA-2) (Transcription factor NF-E1B)	0.71	-	nuc	0	Nucleus				466
Q5R8N8 UniProt NPD GO	GRAM3_PONPY	GRAM domain-containing protein 3	0.71	-	nuc	1					446
O35929 UniProt NPD GO	REM1_MOUSE	GTP-binding protein REM 1 (Rad and Gem-like GTP-binding protein 1)	0.71	-	nuc	0					297
P18721 UniProt NPD GO	ZG44_XENLA	Gastrula zinc finger protein XLCGF44.2 (Fragment)	0.71	-	nuc	0	Nucleus (Potential)				138
Q8BX17 UniProt NPD GO	GEMI5_MOUSE	Gem-associated protein 5 (Gemin5)	0.71	+	nuc	0	Nucleus (By similarity). Found both in the nucleoplasm and in nuclear bodies called gems (Gemini of ...				1502
Q5JLY8 UniProt NPD GO	GOGA5_ORYSA	Golgin-84	0.71	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)				709
Q5RAR8 UniProt NPD GO	GRHL1_PONPY	Grainyhead-like protein 1 homolog (Transcription factor CP2-like 2)	0.71	-	nuc	0	Nucleus (By similarity)				618
Q03160 UniProt NPD GO	GRB7_MOUSE	Growth factor receptor-bound protein 7 (GRB7 adapter protein) (Epidermal growth factor receptor GRB- ...	0.71	-	nuc	0		cytosol [TAS]			535
P38411 UniProt NPD GO	GNAQ_LYMST	Guanine nucleotide-binding protein G(q) subunit alpha (Guanine nucleotide-binding protein alpha-q)	0.71	-	cyt	0					353
Q9BIG5 UniProt NPD GO	GPA4_CAEEL	Guanine nucleotide-binding protein alpha-4 subunit	0.71	-	nuc	0					358
Q758V8 UniProt NPD GO	HDA3_ASHGO	HDA1 complex subunit 3 (Histone deacetylase complex 1 subunit 3)	0.71	-	nuc	0	Nucleus (By similarity)				637
Q9H583 UniProt NPD GO	HEAT1_HUMAN	HEAT repeat-containing protein 1 (Protein BAP28)	0.71	-	end	0	Nucleus; nucleolus				2144
P24724 UniProt NPD GO	HSP90_THEPA	Heat shock protein 90 (HSP90)	0.71	+	cyt	0					721
Q8BKN6 UniProt NPD GO	OST3A_MOUSE	Heparan sulfate glucosamine 3-O-sulfotransferase 3A1 (EC 2.8.2.23) (Heparan sulfate D-glucosaminyl 3 ...	0.71	+	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				393
Q99LI8 UniProt NPD GO	HGS_MOUSE	Hepatocyte growth factor-regulated tyrosine kinase substrate	0.71	-	nuc	0	Cytoplasm. Endosome; early endosome; early endosomal membrane; peripheral membrane protein. Endosome ...	cytoplasm [IDA]			775
O14964 UniProt NPD GO	HGS_HUMAN	Hepatocyte growth factor-regulated tyrosine kinase substrate (Protein pp110) (Hrs)	0.71	-	nuc	0	Cytoplasm. Endosome; early endosome; early endosomal membrane; peripheral membrane protein	endosome [TAS]	604375	2D3G	777
P15257 UniProt NPD GO	HNF1A_RAT	Hepatocyte nuclear factor 1-alpha (HNF-1A) (Liver-specific transcription factor LF-B1) (LFB1)	0.71	-	nuc	0	Nucleus			2LFB	628
Q9Y3E1 UniProt NPD GO	HDGR3_HUMAN	Hepatoma-derived growth factor-related protein 3 (HRP-3) (Hepatoma-derived growth factor 2)	0.71	-	nuc	0	Nucleus	nucleus [IDA]			203
P48557 UniProt NPD GO	H2B_HOLTU	Histone H2B	0.71	-	nuc	0	Nucleus				123
P14837 UniProt NPD GO	HM8_XENLA	Homeobox protein 8 (XlHbox-8)	0.71	+	nuc	0	Nucleus				271
P31260 UniProt NPD GO	HXA10_HUMAN	Homeobox protein Hox-A10 (Hox-1H) (Hox-1.8) (PL)	0.71	+	nuc	0	Nucleus		142957		393
Q9IA21 UniProt NPD GO	HXA3_HETFR	Homeobox protein Hox-A3	0.71	+	nuc	0	Nucleus (By similarity)				410
Q9PWD2 UniProt NPD GO	HXA4_MORSA	Homeobox protein Hox-A4	0.71	+	nuc	0	Nucleus				248
P70321 UniProt NPD GO	HXB13_MOUSE	Homeobox protein Hox-B13	0.71	+	nuc	0	Nucleus				286
P09079 UniProt NPD GO	HXB5_MOUSE	Homeobox protein Hox-B5 (Hox-2.1) (MU-1) (H24.1)	0.71	+	nuc	0	Nucleus				269
P09067 UniProt NPD GO	HXB5_HUMAN	Homeobox protein Hox-B5 (Hox-2A) (HHO.C10) (HU-1)	0.71	+	nuc	0	Nucleus		142960		269
P24341 UniProt NPD GO	HXD10_CHICK	Homeobox protein Hox-D10 (Chox-4.5) (Chox-4D) (Fragment)	0.71	+	nuc	0	Nucleus				95
Q90472 UniProt NPD GO	HXDDA_BRARE	Homeobox protein Hox-D13a (Hox-D13)	0.71	+	nuc	0	Nucleus				256
Q9IA11 UniProt NPD GO	HXD5_HETFR	Homeobox protein Hox-D5	0.71	+	nuc	0	Nucleus (By similarity)				252
P23463 UniProt NPD GO	HXD8_MOUSE	Homeobox protein Hox-D8 (Hox-4.3) (Hox-5.4)	0.71	+	nuc	0	Nucleus				289
Q03357 UniProt NPD GO	MSXA_BRARE	Homeobox protein MSH-A	0.71	+	nuc	0	Nucleus				257
Q01704 UniProt NPD GO	MSXD_BRARE	Homeobox protein MSH-D	0.71	+	nuc	0	Nucleus				226
P97368 UniProt NPD GO	MEIS3_MOUSE	Homeobox protein Meis3 (Meis1-related protein 2)	0.71	-	nuc	0	Nucleus (Probable)				378
Q9H2Z4 UniProt NPD GO	NKX24_HUMAN	Homeobox protein Nkx-2.4 (Homeobox protein NKX2.4) (Homeobox protein NK-2 homolog D)	0.71	-	nuc	0	Nucleus (By similarity)		607808		353
Q9NPC8 UniProt NPD GO	SIX2_HUMAN	Homeobox protein SIX2 (Sine oculis homeobox homolog 2)	0.71	-	nuc	0	Nucleus		604994		291
O93307 UniProt NPD GO	SIX6_CHICK	Homeobox protein SIX6 (Sine oculis homeobox homolog 6) (Optic homeobox 2) (Six9 protein)	0.71	-	nuc	0	Nucleus (By similarity)				246
Q26430 UniProt NPD GO	ABDA_MANSE	Homeobox protein abdominal-A homolog (Fragment)	0.71	+	mit	0	Nucleus (Probable)				97
Q24248 UniProt NPD GO	ARA_DROME	Homeobox protein araucan	0.71	-	nuc	0	Nucleus (Probable)				717
Q93356 UniProt NPD GO	HM37_CAEEL	Homeobox protein ceh-37	0.71	-	mit	0	Nucleus (Probable)	chromosome, telomeric region [IDA]			278
P19622 UniProt NPD GO	HME2_HUMAN	Homeobox protein engrailed-2 (Hu-En-2)	0.71	+	nuc	0	Nucleus		131310		333
P97458 UniProt NPD GO	PROP1_MOUSE	Homeobox protein prophet of Pit-1 (PROP-1) (Pituitary-specific homeodomain factor)	0.71	+	nuc	0	Nucleus (By similarity)				223
Q9NSB8 UniProt NPD GO	HOME2_HUMAN	Homer protein homolog 2 (Homer-2) (Cupidin)	0.71	-	nuc	0	Cytoplasm. Postsynaptic density of neuronal cells. The stabilization and clustering of the metabotro ...		604799		354
Q9QWW1 UniProt NPD GO	HOME2_MOUSE	Homer protein homolog 2 (Homer-2) (Cupidin) (VASP/Ena-related gene up-regulated during seizure and L ...	0.71	-	nuc	0	Cytoplasm. Postsynaptic density of neuronal cells. The stabilization and clustering of the metabotro ...	cytoplasm [IDA]		1I7A	354
O88801 UniProt NPD GO	HOME2_RAT	Homer protein homolog 2 (Homer-2) (Cupidin) (VASP/Ena-related gene up-regulated during seizure and L ...	0.71	-	nuc	0	Cytoplasm. Postsynaptic density of neuronal cells. The stabilization and clustering of the metabotro ...				354
Q8BIL5 UniProt NPD GO	HOOK1_MOUSE	Hook homolog 1	0.71	-	nuc	0	Cytoplasm. Does not associate with the Golgi complex. During spermiogenesis, it localizes to the man ...	microtubule [IDA]		1WIX	728

You are viewing entries 13251 to 13300 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.