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
Q6GQL0 UniProt NPD GO	CBLBA_XENLA	E3 ubiquitin-protein ligase CBL-B-A (EC 6.3.2.-) (Signal transduction protein CBL-B-A) (SH3-binding ...	0.88	-	nuc	0	Cytoplasm (By similarity)				918
Q8BU11 UniProt NPD GO	CN092_MOUSE	Epidermal Langerhans cell protein LCP1	0.88	+	nuc	0	Nucleus (Probable)				619
Q9IAK1 UniProt NPD GO	ESR2_ICTPU	Estrogen receptor beta (ER-beta)	0.88	+	nuc	0	Nucleus				575
O54922 UniProt NPD GO	EXOC7_RAT	Exocyst complex component 7 (Exocyst complex component Exo70) (rExo70)	0.88	+	nuc	0	Cytoplasm; cytosol (By similarity). Cell membrane; peripheral membrane protein (By similarity). Tran ...				653
Q9Y2D4 UniProt NPD GO	SC15B_HUMAN	Exocyst complex component Sec15B	0.88	-	cyt	0			607880		672
Q9UIA9 UniProt NPD GO	XPO7_HUMAN	Exportin-7 (Exp7) (Ran-binding protein 16)	0.88	-	cyt	0	Cytoplasm. Nucleus. Nucleus; nuclear envelope; nuclear pore complex. Shuttles between the nucleus an ...	cytoplasm [IDA] nuclear pore [IDA] nucleus [IDA]	606140		1086
Q9EPK7 UniProt NPD GO	XPO7_MOUSE	Exportin-7 (Exp7) (Ran-binding protein 16)	0.88	-	cyt	0	Cytoplasm. Nucleus. Nucleus; nuclear envelope; nuclear pore complex. Shuttles between the nucleus an ...				1086
Q969P5 UniProt NPD GO	FBX32_HUMAN	F-box only protein 32 (Muscle atrophy F-box protein) (MAFbx) (Atrogin-1)	0.88	+	cyt	0			606604		355
Q91VS8 UniProt NPD GO	FARP2_MOUSE	FERM, RhoGEF and pleckstrin domain-containing protein 2 (FERM domain including RhoGEF) (FIR)	0.88	-	nuc	0					1065
Q9P0K8 UniProt NPD GO	FOXJ2_HUMAN	Forkhead box protein J2 (Fork head homologous X)	0.88	-	nuc	0	Nucleus				574
Q9ES18 UniProt NPD GO	FOXJ2_MOUSE	Forkhead box protein J2 (Fork head homologous X)	0.88	-	nuc	0	Nucleus				565
Q9NYZ3 UniProt NPD GO	GTSE1_HUMAN	G2 and S phase expressed protein 1 (B99 homolog)	0.88	-	nuc	0	Cytoplasm. Associated with microtubules	cytoplasmic microtubule [NAS]	607477		720
Q8R080 UniProt NPD GO	GTSE1_MOUSE	G2 and S phase expressed protein 1 (Gtse-1) (B99 protein)	0.88	-	nuc	0	Cytoplasm. Associated with microtubules				741
Q9NZM5 UniProt NPD GO	GSCR2_HUMAN	Glioma tumor suppressor candidate region gene 2 protein (p60)	0.88	+	nuc	0	Nucleus; nucleolus	intracellular [NAS]	605691		478
Q62638 UniProt NPD GO	GSLG1_RAT	Golgi apparatus protein 1 precursor (Golgi sialoglycoprotein MG-160) (E-selectin ligand 1) (ESL-1)	0.88	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type I membrane protein. Golgi medial cisternae	Golgi medial cisterna [IDA]			1171
Q9QYE6 UniProt NPD GO	GOGA5_MOUSE	Golgin subfamily A member 5 (Golgin-84) (Sumiko protein) (Ret-II protein)	0.88	+	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity). Found through ...	Golgi apparatus [ISS] Golgi membrane [IDA]			729
Q9NYA3 UniProt NPD GO	GOGA6_HUMAN	Golgin subfamily A member 6 (Golgin linked to PML) (Golgin-like protein)	0.88	-	nuc	0					693
Q76IQ7 UniProt NPD GO	GCX1_RAT	Granulosa cell HMG box protein 1 (GCX-1)	0.88	-	nuc	0	Nucleus				473
O73755 UniProt NPD GO	GREM1_CHICK	Gremlin-1 precursor	0.88	+	nuc	1 *	Secreted protein (Potential)				184
Q8SPE7 UniProt NPD GO	G45IP_CERAE	Growth arrest and DNA-damage-inducible proteins-interacting protein 1 (Papillomavirus L2-interacting ...	0.88	-	mit	0	Nucleus (By similarity)				222
P63117 UniProt NPD GO	GFC1_HUMAN	HERV-F(c)1_Xq21.33 provirus ancestral Gag polyprotein (Gag polyprotein) [Contains: Matrix protein; C ...	0.88	-	nuc	0	Cell membrane (Potential)				469
Q8BGA5 UniProt NPD GO	HRB2_MOUSE	HIV-1 Rev-binding protein 2 homolog	0.88	-	nuc	0	Nucleus; nucleolus (By similarity)				380
P22813 UniProt NPD GO	HSF_DROME	Heat shock factor protein (HSF) (Heat shock transcription factor) (HSTF)	0.88	-	nuc	0	Nucleus	nucleus [IDA] polytene chromosome [IDA]		1HKT	691
Q40152 UniProt NPD GO	HSF8_LYCES	Heat shock factor protein HSF8 (Heat shock transcription factor 8) (HSTF 8) (Heat stress transcripti ...	0.88	+	nuc	0	Nucleus				527
Q9UGU5 UniProt NPD GO	HM2L1_HUMAN	High mobility group protein 2-like 1 (Protein HMGBCG)	0.88	+	nuc	0	Nucleus (Potential)	nucleus [NAS]	604702		601
Q5ZKF4 UniProt NPD GO	HM20A_CHICK	High mobility group protein 20A (HMG box-containing protein 20A)	0.88	+	nuc	0	Nucleus (By similarity)				348
Q6DRA6 UniProt NPD GO	H2B2D_HUMAN	Histone H2B type 2-D	0.88	+	nuc	0	Nucleus				163
Q14493 UniProt NPD GO	SLBP_HUMAN	Histone RNA hairpin-binding protein (Histone stem-loop-binding protein)	0.88	-	nuc	0	Cytoplasm. Nucleus. Polyribosome-associated	ribonucleoprotein complex [TAS]	602422		270
Q75BY2 UniProt NPD GO	ESA1_ASHGO	Histone acetyltransferase ESA1 (EC 2.3.1.48)	0.88	-	cyt	0	Nucleus (By similarity)				520
Q8VZJ1 UniProt NPD GO	ATXR5_ARATH	Histone-lysine N-methyltransferase ATXR5 (EC 2.1.1.43) (Trithorax-related protein 5) (TRX-related pr ...	0.88	+	nuc	0	Nucleus (By similarity)				352
Q96KQ7 UniProt NPD GO	EHMT2_HUMAN	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 (EC 2.1.1.43) (Histone H3-K9 methyltransf ...	0.88	+	nuc	0	Nucleus. Associates with euchromatic regions. Does not associate with heterochromatin		604599		1210
Q9Z148 UniProt NPD GO	EHMT2_MOUSE	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 (EC 2.1.1.43) (Histone H3-K9 methyltransf ...	0.88	+	nuc	0	Nucleus. Almost excluded form nucleoli. Associates with euchromatic regions. Does not associate with ...	nucleus [IDA]			1263
Q8K3E9 UniProt NPD GO	HOMEZ_RAT	Homeobox and leucine zipper protein Homez (Homeodomain leucine zipper-containing factor)	0.88	-	nuc	0	Nucleus (By similarity)				513
P31311 UniProt NPD GO	HXA11_MOUSE	Homeobox protein Hox-A11 (Hox-1.9)	0.88	+	nuc	0	Nucleus				313
P31270 UniProt NPD GO	HXA11_HUMAN	Homeobox protein Hox-A11 (Hox-1I)	0.88	+	nuc	0	Nucleus		142958		313
P28358 UniProt NPD GO	HXD10_HUMAN	Homeobox protein Hox-D10 (Hox-4D) (Hox-4E)	0.88	+	nuc	0	Nucleus		192950		340
P41936 UniProt NPD GO	HM22_CAEEL	Homeobox protein ceh-22	0.88	+	nuc	0	Nucleus				346
P53565 UniProt NPD GO	CUTL1_RAT	Homeobox protein cut-like 1 (CCAAT displacement protein) (CDP) (CDP2) (Fragment)	0.88	-	nuc	0	Nucleus				862
P48000 UniProt NPD GO	KNAT3_ARATH	Homeobox protein knotted-1-like 3 (KNAT3)	0.88	-	nuc	0	Nucleus (Probable)				431
O22300 UniProt NPD GO	LET12_LYCES	Homeobox protein knotted-1-like LET12	0.88	-	nuc	0	Nucleus (Probable)				426
P10181 UniProt NPD GO	ROUGH_DROME	Homeobox protein rough	0.88	+	nuc	0	Nucleus (Probable)				350
Q6NT76 UniProt NPD GO	HMBX1_HUMAN	Homeobox-containing protein 1	0.88	-	nuc	0	Nucleus (Potential)			2CUF	420
Q12751 UniProt NPD GO	YM48_YEAST	Hypothetical 113.2 kDa protein in SSO2-HSC82 intergenic region	0.88	-	cyt	0					981
P38851 UniProt NPD GO	YHV5_YEAST	Hypothetical 143.6 kDa protein in SPO16-REC104 intergenic region	0.88	-	nuc	2		mitochondrion [IDA]			1228
P53317 UniProt NPD GO	YG5C_YEAST	Hypothetical 22.3 kDa protein in MGA1-GCN4 intergenic region	0.88	+	nuc	0		nucleolus [IDA] nucleus [IDA]			196
P93318 UniProt NPD GO	M660_ARATH	Hypothetical mitochondrial protein AtMg00660 (ORF149)	0.88	-	mit	0	Mitochondrion (Potential)				149
Q10342 UniProt NPD GO	YBLE_SCHPO	Hypothetical protein C106.14c in chromosome II	0.88	-	nuc	0					719
Q10273 UniProt NPD GO	YD39_SCHPO	Hypothetical protein C13G7.09c in chromosome I	0.88	+	nuc	0					135
O13894 UniProt NPD GO	YF32_SCHPO	Hypothetical protein C22A12.02c in chromosome I	0.88	-	nuc	0					124
O74504 UniProt NPD GO	YJD1_SCHPO	Hypothetical protein C594.01 in chromosome III	0.88	-	nuc	0					791

You are viewing entries 5101 to 5150 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.