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
Q59XM1 UniProt NPD GO	EXO84_CANAL	Exocyst complex component EXO84	0.74	-	nuc	0	Secretory vesicle (By similarity). Cell periphery. The polarization of EXO84 requires actin cables ( ...				837
Q9JK82 UniProt NPD GO	EXT1_CRIGR	Exostosin-1 (EC 2.4.1.224) (EC 2.4.1.225) (Heparan sulfate copolymerase) (Multiple exostoses protein ...	0.74	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	integral to endoplasmic reticulum membrane [ISS]			746
Q5IGR7 UniProt NPD GO	EXT1B_BRARE	Exostosin-1b (EC 2.4.1.224) (EC 2.4.1.225) (Glucuronosyl-N-acetylglucosaminyl-proteoglycan/N-acetylg ...	0.74	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	integral to endoplasmic reticulum membrane [ISS]			741
Q9N5R9 UniProt NPD GO	SPT16_CAEEL	FACT complex subunit spt-16 (Facilitates chromatin transcription complex subunit spt-16)	0.74	+	end	0	Nucleus (By similarity)				1030
Q41276 UniProt NPD GO	AP1_SINAL	Floral homeotic protein APETALA1 (MADS C)	0.74	-	nuc	0	Nucleus (By similarity)				254
P79772 UniProt NPD GO	FOXD3_CHICK	Forkhead box protein D3 (HNF3/FH transcription factor genesis) (Winged helix protein CWH-3)	0.74	+	nuc	0	Nucleus (Probable)	nucleus [ISS]			394
Q99526 UniProt NPD GO	FOXE2_HUMAN	Forkhead box protein E2 (HNF-3/fork head-like protein 5) (HFKL5) (HFKH4)	0.74	-	nuc	0	Nucleus (Potential)		607142		500
O75593 UniProt NPD GO	FOXH1_HUMAN	Forkhead box protein H1 (Forkhead activin signal transducer 1) (Fast-1) (hFAST-1) (Forkhead activin ...	0.74	-	nuc	0	Nucleus		603621		365
Q3I5G5 UniProt NPD GO	FOXI2_MOUSE	Forkhead box protein I2	0.74	+	nuc	0	Nucleus				311
Q3BJS1 UniProt NPD GO	FOXN4_XENLA	Forkhead box protein N4	0.74	-	nuc	0	Nucleus (Potential)				506
Q9NFU0 UniProt NPD GO	FXR1_DROME	Fragile X mental retardation syndrome-related protein 1 (dFMR1) (dfxr)	0.74	-	nuc	0	Cytoplasm	RNA-induced silencing complex [IPI]			684
P24864 UniProt NPD GO	CCNE1_HUMAN	G1/S-specific cyclin-E1	0.74	-	nuc	0	Nucleus	nucleus [NAS]	123837	1W98	410
O82632 UniProt NPD GO	GAT11_ARATH	GATA transcription factor 11 (AtGATA-11)	0.74	+	nuc	0	Nucleus (Probable)				308
P23773 UniProt NPD GO	GATA3_XENLA	GATA-binding factor 3 (Transcription factor xGATA-3)	0.74	-	nuc	0	Nucleus				435
Q96CN9 UniProt NPD GO	GCC1_HUMAN	GRIP and coiled-coil domain-containing protein 1 (Golgi coiled coil protein 1)	0.74	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity)		607418		775
Q8IRI6 UniProt NPD GO	GTR1_DROME	Glucose transporter type 1	0.74	-	end	9	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [ISS] membrane [ISS] membrane fraction [ISS]			656
P97879 UniProt NPD GO	GRIP1_RAT	Glutamate receptor-interacting protein 1 (GRIP1 protein) (AMPA receptor-interacting protein GRIP1)	0.74	-	nuc	0	Cytoplasm. Intracytoplasmic membrane. Membrane-associated with vesicles, peri-Golgi complexes and en ...			1P1E	1112
Q61586 UniProt NPD GO	PLSB_MOUSE	Glycerol-3-phosphate acyltransferase, mitochondrial precursor (EC 2.3.1.15) (GPAT) (P90)	0.74	-	nuc	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			827
Q64018 UniProt NPD GO	GLRA1_MOUSE	Glycine receptor alpha-1 chain precursor (Glycine receptor 48 kDa subunit) (Strychnine-binding subun ...	0.74	-	end	3	Membrane; multi-pass membrane protein				457
P07727 UniProt NPD GO	GLRA1_RAT	Glycine receptor alpha-1 chain precursor (Glycine receptor 48 kDa subunit) (Strychnine-binding subun ...	0.74	-	end	3	Membrane; multi-pass membrane protein				457
O73754 UniProt NPD GO	GREM1_XENLA	Gremlin-1 precursor (Cysteine knot superfamily 1, BMP antagonist 1)	0.74	-	nuc	0	Secreted protein (Probable)				182
Q8JIM3 UniProt NPD GO	GHRP_RANCA	Growth hormone-releasing peptides precursor [Contains: Growth hormone-releasing peptide (GH-releasin ...	0.74	-	exc	1 *	Secreted protein	extracellular region [NAS]			221
O55148 UniProt NPD GO	GAS7_RAT	Growth-arrest-specific protein 7 (GAS-7)	0.74	-	nuc	0	Cytoplasm (By similarity)				422
P55106 UniProt NPD GO	GDF6_BOVIN	Growth/differentiation factor 6 precursor (GDF-6) (Cartilage-derived morphogenetic protein 2) (CDMP- ...	0.74	-	nuc	0	Secreted protein (Probable)				436
Q9BXR3 UniProt NPD GO	POK2_HUMAN	HERV-K_7p22.1 provirus ancestral Pol protein (HERV-K(HML-2.HOM) Pol protein) (HERV-K108 Pol protein) ...	0.74	-	nuc	0					956
Q96QV1 UniProt NPD GO	HHIP_HUMAN	Hedgehog-interacting protein precursor (HHIP) (HIP)	0.74	+	exc	0	Cell membrane; peripheral membrane protein (By similarity). Secreted protein (By similarity). The la ...		606178		700
Q9NQZ6 UniProt NPD GO	HC127_HUMAN	Hepatocellular carcinoma-associated antigen 127	0.74	-	nuc	0					224
Q68FG0 UniProt NPD GO	HC127_MOUSE	Hepatocellular carcinoma-associated antigen 127 homolog	0.74	-	nuc	0					224
Q91910 UniProt NPD GO	HNF1B_XENLA	Hepatocyte nuclear factor 1-beta (HNF-1B) (LFB3) (XLFB3)	0.74	+	nuc	0	Nucleus (By similarity)				561
Q7RYU8 UniProt NPD GO	HAT1_NEUCR	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.74	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				508
Q9UTM7 UniProt NPD GO	HAT1_SCHPO	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.74	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				378
O35085 UniProt NPD GO	ARX_MOUSE	Homeobox protein ARX (Aristaless-related homeobox)	0.74	+	nuc	0	Nucleus (By similarity)				564
P31310 UniProt NPD GO	HXA10_MOUSE	Homeobox protein Hox-A10 (Hox-1.8)	0.74	+	nuc	0	Nucleus				399
Q9PWD3 UniProt NPD GO	HXA5_MORSA	Homeobox protein Hox-A5	0.74	+	nuc	0	Nucleus (By similarity)				281
Q9IA25 UniProt NPD GO	HXA7_HETFR	Homeobox protein Hox-A7	0.74	+	nuc	0	Nucleus (By similarity)				208
O43248 UniProt NPD GO	HXC11_HUMAN	Homeobox protein Hox-C11	0.74	+	nuc	0	Nucleus		605559		304
P10629 UniProt NPD GO	HXC6_MOUSE	Homeobox protein Hox-C6 (Hox-3.3) (Hox-6.1)	0.74	+	nuc	0	Nucleus				235
P15862 UniProt NPD GO	HXC6A_BRARE	Homeobox protein Hox-C6a (Hox-C6) (Zf-61)	0.74	+	nuc	0	Nucleus (By similarity)				231
P09025 UniProt NPD GO	HXC8_MOUSE	Homeobox protein Hox-C8 (Hox-3.1) (M31)	0.74	+	nuc	0	Nucleus	nucleus [IDA]			242
P31273 UniProt NPD GO	HXC8_HUMAN	Homeobox protein Hox-C8 (Hox-3A)	0.74	+	nuc	0	Nucleus	nucleus [NAS]	142970		242
P17278 UniProt NPD GO	HXD4_CHICK	Homeobox protein Hox-D4 (Chox-A)	0.74	+	nuc	0	Nucleus				235
P52952 UniProt NPD GO	NKX25_HUMAN	Homeobox protein Nkx-2.5 (Homeobox protein NK-2 homolog E) (Cardiac-specific homeobox) (Homeobox pro ...	0.74	+	nuc	0	Nucleus (Probable)	transcription factor complex [ISS]	600584		324
Q26417 UniProt NPD GO	OTX_STRPU	Homeobox protein OTX (SPOTX)	0.74	-	nuc	0	Nucleus				371
P80206 UniProt NPD GO	OTX2_MOUSE	Homeobox protein OTX2	0.74	-	nuc	0	Nucleus (Probable)	nucleus [IC]			289
Q03014 UniProt NPD GO	HHEX_HUMAN	Homeobox protein PRH (Hematopoietically expressed homeobox) (Homeobox protein HEX)	0.74	+	nuc	0	Nucleus (Probable)		604420		270
P29555 UniProt NPD GO	ABDA_DROME	Homeobox protein abdominal-A	0.74	+	mit	0	Nucleus (Probable)				590
Q07961 UniProt NPD GO	ABDA_TRICA	Homeobox protein abdominal-A homolog	0.74	+	nuc	0	Nucleus (Probable)				343
Q05007 UniProt NPD GO	ABDA_ARTSF	Homeobox protein abdominal-A homolog (Fragment)	0.74	+	nuc	0	Nucleus (Probable)				139
O95076 UniProt NPD GO	ALX3_HUMAN	Homeobox protein aristaless-like 3 (Proline-rich transcription factor ALX3)	0.74	+	nuc	0	Nucleus (By similarity)		606014		343
Q05916 UniProt NPD GO	HME1_CHICK	Homeobox protein engrailed-1 (Gg-En-1)	0.74	+	nuc	0	Nucleus				333

You are viewing entries 11801 to 11850 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.