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
Q4WJ02 UniProt NPD GO	SPT16_ASPFU	FACT complex subunit spt16 (Facilitates chromatin transcription complex subunit spt16)	0.68	+	mit	1	Nucleus (By similarity)				1019
P54731 UniProt NPD GO	FAF1_MOUSE	FAS-associated factor 1 (Protein FAF1)	0.68	-	nuc	0	Nucleus (Potential)	CD95 death-inducing signaling complex [ISS] cytosol [ISS] nucleus [ISS] perinuclear region [ISS]			649
Q14331 UniProt NPD GO	FRG1_HUMAN	FRG1 protein (FSHD region gene 1 protein)	0.68	-	nuc	0	Nucleus; nucleoplasm; Cajal body. Nucleus; nucleoplasm; nuclear speckle. First expressed in Cajal bo ...		601278		258
O15287 UniProt NPD GO	FANCG_HUMAN	Fanconi anemia group G protein (Protein FACG) (DNA-repair protein XRCC9)	0.68	-	mit	0	Nucleus. Major form. Cytoplasm. Minor form		602956		622
P97578 UniProt NPD GO	FEZ2_RAT	Fasciculation and elongation protein zeta 2 (Zygin-2) (Zygin II) (Zygin-related protein types I/II)	0.68	-	nuc	0					375
O57478 UniProt NPD GO	HEMH_XENLA	Ferrochelatase, mitochondrial precursor (EC 4.99.1.1) (Protoheme ferro-lyase) (Heme synthetase)	0.68	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side (By similarity ...				411
P39748 UniProt NPD GO	FEN1_HUMAN	Flap endonuclease 1 (EC 3.1.-.-) (Flap structure-specific endonuclease 1) (FEN-1) (Maturation factor ...	0.68	-	nuc	0	Nucleus	nucleus [IDA]	600393	1UL1	380
Q07474 UniProt NPD GO	MADS2_PETHY	Floral homeotic protein PMADS 2	0.68	-	nuc	0	Nucleus				212
Q64731 UniProt NPD GO	FOXL1_MOUSE	Forkhead box protein L1 (Forkhead-related protein FKHL11) (Transcription factor FKH-6)	0.68	-	nuc	0	Nucleus				337
P15407 UniProt NPD GO	FOSL1_HUMAN	Fos-related antigen 1 (FRA-1)	0.68	+	nuc	0	Nucleus	nucleus [TAS]	136515		271
Q61584 UniProt NPD GO	FXR1_MOUSE	Fragile X mental retardation syndrome-related protein 1 (mFxr1p)	0.68	-	nuc	0	Cytoplasm (By similarity)	costamere [IDA]			677
P24867 UniProt NPD GO	PCL1_YEAST	G1/S-specific cyclin PCL1 (Cyclin HCS26)	0.68	-	nuc	0		cyclin-dependent protein kinase holoenzyme ... [TAS]			279
Q61457 UniProt NPD GO	CCNE1_MOUSE	G1/S-specific cyclin-E1	0.68	-	nuc	0	Nucleus (By similarity)	cyclin-dependent protein kinase holoenzyme ... [IPI]			491
Q9SV30 UniProt NPD GO	GAT10_ARATH	GATA transcription factor 10 (AtGATA-10)	0.68	+	nuc	0	Nucleus (Probable)				322
Q9LIB5 UniProt NPD GO	GAT17_ARATH	GATA transcription factor 17	0.68	+	nuc	0	Nucleus (Probable)				190
O49741 UniProt NPD GO	GATA2_ARATH	GATA transcription factor 2 (AtGATA-2)	0.68	-	nuc	0	Nucleus (Probable)				264
P29794 UniProt NPD GO	GLUC_CANFA	Glucagon precursor [Contains: Glicentin; Glicentin-related polypeptide (GRPP); Oxyntomodulin (OXY) ( ...	0.68	-	vac	0	Secreted protein				180
P31384 UniProt NPD GO	CCR4_YEAST	Glucose-repressible alcohol dehydrogenase transcriptional effector (EC 3.1.13.4) (Cytoplasmic deaden ...	0.68	-	nuc	0	Cytoplasm. Nucleus	CCR4-NOT core complex [IPI] Cdc73/Paf1 complex [IPI] cytoplasm [IDA]			837
P33438 UniProt NPD GO	GLT_DROME	Glutactin precursor	0.68	-	exc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane	basement membrane [IDA]			1026
Q13224 UniProt NPD GO	NMDE2_HUMAN	Glutamate [NMDA] receptor subunit epsilon 2 precursor (N-methyl D-aspartate receptor subtype 2B) (NR ...	0.68	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	138252	1S2S	1484
P19468 UniProt NPD GO	GSH1_RAT	Glutamate--cysteine ligase catalytic subunit (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) (Gamma ...	0.68	+	nuc	0					636
O08522 UniProt NPD GO	GOSR1_CRIGR	Golgi SNAP receptor complex member 1 (28 kDa Golgi SNARE protein) (28 kDa cis-Golgi SNARE p28) (GOS- ...	0.68	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein. Enriched on vesicular compone ...	Golgi trans cisterna [IDA]			250
O88630 UniProt NPD GO	GOSR1_MOUSE	Golgi SNAP receptor complex member 1 (28 kDa Golgi SNARE protein) (28 kDa cis-Golgi SNARE p28) (GOS- ...	0.68	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity). Enriched on v ...	Golgi membrane [IDA]			250
Q62931 UniProt NPD GO	GOSR1_RAT	Golgi SNAP receptor complex member 1 (28 kDa Golgi SNARE protein) (28 kDa cis-Golgi SNARE p28) (GOS- ...	0.68	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein. Enriched on vesicular compone ...	Golgi cis-face [IDA]			250
Q9HFW7 UniProt NPD GO	GPA3_NEUCR	Guanine nucleotide-binding protein alpha-3 subunit (GP3-alpha)	0.68	-	cyt	0					356
P63132 UniProt NPD GO	POK5_HUMAN	HERV-K_19p13.11 provirus ancestral Pol protein (HERV-K113 Pol protein) [Includes: Reverse transcript ...	0.68	-	nuc	0					956
Q9YNA8 UniProt NPD GO	GAK3_HUMAN	HERV-K_19q12 provirus ancestral Gag polyprotein (Gag polyprotein) (HERV-K(C19) Gag protein) [Contain ...	0.68	-	nuc	0	Cell membrane. Cytoplasmic membrane (in a transfection system) (By similarity)				665
Q7LDI9 UniProt NPD GO	GAK2_HUMAN	HERV-K_7p22.1 provirus ancestral Gag polyprotein (Gag polyprotein) (HERV-K(HML-2.HOM) Gag protein) ( ...	0.68	-	nuc	0	Cell membrane. Cytoplasmic membrane (in a transfection system) (By similarity)				665
P62685 UniProt NPD GO	GAK6_HUMAN	HERV-K_8p23.1 provirus ancestral Gag polyprotein (Gag polyprotein) (HERV-K115 Gag protein) [Contains ...	0.68	-	nuc	0	Cell membrane. Cytoplasmic membrane (in a transfection system) (By similarity)				646
Q9R0L1 UniProt NPD GO	HSF4_MOUSE	Heat shock factor protein 4 (HSF 4) (Heat shock transcription factor 4) (HSTF 4) (mHSF4)	0.68	-	nuc	0					492
Q9QYK4 UniProt NPD GO	H6ST3_MOUSE	Heparan-sulfate 6-O-sulfotransferase 3 (EC 2.8.2.-) (HS6ST-3) (mHS6ST-3)	0.68	+	nuc	1 *	Membrane; single-pass type II membrane protein (Potential)				470
Q08048 UniProt NPD GO	HGF_MOUSE	Hepatocyte growth factor precursor (Scatter factor) (SF) (Hepatopoeitin A) [Contains: Hepatocyte gro ...	0.68	+	exc	1 *					728
P23738 UniProt NPD GO	DCHS_MOUSE	Histidine decarboxylase (EC 4.1.1.22) (HDC)	0.68	-	mit	0					662
P06348 UniProt NPD GO	H1T_PIG	Histone H1t	0.68	-	nuc	0	Nucleus				211
P06349 UniProt NPD GO	H1T_RAT	Histone H1t	0.68	-	nuc	0	Nucleus				207
Q64475 UniProt NPD GO	H2B1B_MOUSE	Histone H2B type 1-B (h2B-143)	0.68	+	nuc	0	Nucleus				125
Q92831 UniProt NPD GO	PCAF_HUMAN	Histone acetyltransferase PCAF (EC 2.3.1.48) (P300/CBP-associated factor) (P/CAF) (Histone acetylase ...	0.68	-	nuc	0	Nucleus (By similarity)	nucleus [TAS]	602303	1ZS5	832
P53772 UniProt NPD GO	DLLH_BRAFL	Homeobox protein DLL homolog	0.68	+	nuc	0	Nucleus (Potential)				321
P09075 UniProt NPD GO	HME60_APIME	Homeobox protein E60 (Fragment)	0.68	+	nuc	0	Nucleus				109
O42230 UniProt NPD GO	GBX2_CHICK	Homeobox protein GBX-2 (Gastrulation and brain-specific homeobox protein 2)	0.68	+	nuc	0	Nucleus (Probable)				340
P15860 UniProt NPD GO	HM90_APIME	Homeobox protein H90 (Fragment)	0.68	+	nuc	0	Nucleus (Potential)				74
P28356 UniProt NPD GO	HXD9_HUMAN	Homeobox protein Hox-D9 (Hox-4C) (Hox-5.2)	0.68	+	nuc	0	Nucleus		142982		342
P97503 UniProt NPD GO	NKX32_MOUSE	Homeobox protein Nkx-3.2 (Bagpipe homeobox protein homolog 1)	0.68	+	nuc	0	Nucleus (Probable)				333
P09636 UniProt NPD GO	HMSA_SALSA	Homeobox protein S12-A (Fragment)	0.68	+	nuc	0	Nucleus (Probable)				75
Q22909 UniProt NPD GO	HM30_CAEEL	Homeobox protein ceh-30	0.68	+	mit	0	Nucleus (Probable)				299
Q9GLL9 UniProt NPD GO	PROP1_PIG	Homeobox protein prophet of Pit-1 (PROP-1) (Pituitary-specific homeodomain factor)	0.68	+	nuc	0	Nucleus (By similarity)				226
P53139 UniProt NPD GO	YGK8_YEAST	Hypothetical 16.0 kDa protein in TAF60-MLC1 intergenic region	0.68	+	nuc	0					140
P40455 UniProt NPD GO	YIP2_YEAST	Hypothetical 27.2 kDa protein in IMP2-DNA43 intergenic region	0.68	-	mit	0					235
P53122 UniProt NPD GO	YGN8_YEAST	Hypothetical 40.8 kDa protein in HUL5-SEC27 intergenic region	0.68	-	nuc	0					345
Q85BK9 UniProt NPD GO	YCF1A_ANTFO	Hypothetical 58 kDa protein ycf1 (ORF473)	0.68	-	mit	0	Plastid; chloroplast				473

You are viewing entries 14701 to 14750 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.