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
Q9VF30 UniProt NPD GO	MCMR_DROME	DNA replication licensing factor REC (Protein mini chromosome maintenance-related) (Protein recombin ...	0.77	-	mit	0	Nucleus (By similarity)	nucleus [TAS]			885
P16355 UniProt NPD GO	RPA1_TRYBB	DNA-directed RNA polymerase I largest subunit (EC 2.7.7.6)	0.77	-	nuc	0	Nucleus				1744
Q02061 UniProt NPD GO	RPB2_SCHPO	DNA-directed RNA polymerase II 138 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 2)	0.77	-	cyt	0	Nucleus	chromosome, pericentric region [IDA] DNA-directed RNA polymerase II, core complex [IDA]			1210
P20433 UniProt NPD GO	RPB4_YEAST	DNA-directed RNA polymerase II 32 kDa polypeptide (EC 2.7.7.6) (B32)	0.77	-	nuc	0	Nucleus	cytoplasm [IDA] DNA-directed RNA polymerase II, core complex [TAS] nucleus [IDA]		2B8K	221
P35074 UniProt NPD GO	RPB1_CAEBR	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6)	0.77	-	nuc	0	Nucleus				1853
P27999 UniProt NPD GO	RPB9_YEAST	DNA-directed RNA polymerase II subunit 9 (EC 2.7.7.6) (DNA-directed RNA polymerase II 14.2 kDa polyp ...	0.77	-	nuc	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS]		2B8K	122
Q85X54 UniProt NPD GO	RPOB_PINKO	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.77	-	nuc	0	Plastid; chloroplast				1075
Q8MA11 UniProt NPD GO	RPOC1_CHAGL	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.77	-	nuc	0	Plastid; chloroplast				661
Q7YJY0 UniProt NPD GO	RPOC2_CALFE	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.77	+	nuc	0	Plastid; chloroplast				1377
O00411 UniProt NPD GO	RPOM_HUMAN	DNA-directed RNA polymerase, mitochondrial precursor (EC 2.7.7.6) (MtRPOL)	0.77	-	nuc	0	Mitochondrion	mitochondrion [TAS]	601778		1230
Q8VDF3 UniProt NPD GO	DAPK2_MOUSE	Death-associated protein kinase 2 (EC 2.7.11.1) (DAP kinase 2) (DAP-kinase-related protein 1) (DRP-1 ...	0.77	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			370
Q39493 UniProt NPD GO	DSK1_CYLFU	Diatom spindle kinesin 1	0.77	-	nuc	0					624
Q9QYZ8 UniProt NPD GO	DKK2_MOUSE	Dickkopf-related protein 2 precursor (Dkk-2) (Dickkopf-2) (mDkk-2)	0.77	+	nuc	0	Secreted protein				259
Q39214 UniProt NPD GO	RPM1_ARATH	Disease resistance protein RPM1 (Resistance to Pseudomonas syringae protein 3)	0.77	-	cyt	0	Intracytoplasmic membrane; peripheral membrane protein				926
Q29277 UniProt NPD GO	IPPD_PIG	Dopamine- and cAMP-regulated neuronal phosphoprotein (DARPP-32) (Fragment)	0.77	-	nuc	0	Cytoplasm				137
Q8CIY2 UniProt NPD GO	DUOX1_RAT	Dual oxidase 1 precursor (EC 1.6.3.1) (EC 1.11.1.-)	0.77	-	end	6 *	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Localizes to the a ...	apical plasma membrane [ISS]			1551
Q6GQT0 UniProt NPD GO	CC14A_MOUSE	Dual specificity protein phosphatase CDC14A (EC 3.1.3.48) (EC 3.1.3.16) (CDC14 cell division cycle 1 ...	0.77	-	nuc	0	Nucleus (By similarity). Centrosomal during interphase; released into the cytoplasm at the onset of ...				603
Q9NR20 UniProt NPD GO	DYRK4_HUMAN	Dual specificity tyrosine-phosphorylation-regulated kinase 4 (EC 2.7.12.1)	0.77	-	nuc	0			609181		520
Q08427 UniProt NPD GO	EGR2_XENLA	Early growth response protein 2 (EGR-2) (Krox-20 protein)	0.77	-	nuc	0	Nucleus				421
Q5AYR3 UniProt NPD GO	EPL1_EMENI	Enhancer of polycomb-like protein 1	0.77	-	nuc	0	Nucleus (By similarity)				570
O42469 UniProt NPD GO	TLE1_XENLA	Enhancer of split groucho-like protein 1	0.77	-	nuc	0	Nucleus (Probable)				767
P13097 UniProt NPD GO	ESM7_DROME	Enhancer of split m7 protein (E(spl)m7)	0.77	-	nuc	0	Nucleus (Probable)	extracellular matrix (sensu Metazoa) [ISS] extracellular region [ISS]			186
P16058 UniProt NPD GO	ESR1_ONCMY	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.77	-	nuc	0	Nucleus				622
Q99L45 UniProt NPD GO	IF2B_MOUSE	Eukaryotic translation initiation factor 2 subunit 2 (Eukaryotic translation initiation factor 2 sub ...	0.77	+	nuc	0					331
P78344 UniProt NPD GO	IF4G2_HUMAN	Eukaryotic translation initiation factor 4 gamma 2 (eIF-4-gamma 2) (eIF-4G 2) (eIF4G 2) (p97) (Death ...	0.77	-	nuc	0		eukaryotic translation initiation factor 4F... [IDA]	602325		907
Q62448 UniProt NPD GO	IF4G2_MOUSE	Eukaryotic translation initiation factor 4 gamma 2 (eIF-4-gamma 2) (eIF-4G 2) (eIF4G 2) (p97) (Novel ...	0.77	-	nuc	0		cytoplasm [IDA] eukaryotic translation initiation factor 4F... [ISS]			906
P79398 UniProt NPD GO	IF4G2_RABIT	Eukaryotic translation initiation factor 4 gamma 2 (eIF-4-gamma 2) (eIF-4G 2) (eIF4G 2) (p97) (Novel ...	0.77	-	nuc	0		eukaryotic translation initiation factor 4F... [ISS]			907
Q10251 UniProt NPD GO	IF2P_SCHPO	Eukaryotic translation initiation factor 5B (eIF-5B) (Translation initiation factor IF-2)	0.77	+	nuc	0					1079
Q62825 UniProt NPD GO	EXOC3_RAT	Exocyst complex component 3 (Exocyst complex component Sec6) (rSec6)	0.77	-	cyt	0					755
P32525 UniProt NPD GO	ECM25_YEAST	Extracellular matrix protein 25	0.77	-	nuc	0	Cytoplasm	cytoplasm [IDA]			599
Q06673 UniProt NPD GO	ECM30_YEAST	Extracellular matrix protein 30	0.77	-	end	0	Cytoplasm	cytoplasm [IDA]			1274
Q8IRG6 UniProt NPD GO	SPT16_DROME	FACT complex subunit spt16 (Facilitates chromatin transcription complex subunit SPT16) (dSPT16)	0.77	-	nuc	0	Nucleus. Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci	FACT complex [TAS]			1083
P42565 UniProt NPD GO	FARX_LYMST	FMRFamide-related neuropeptides precursor [Contains: EFFPL-amide; GDPFLRF-amide 1; GDPFLRF-amide 2; ...	0.77	+	nuc	0	Secreted protein				360
O70514 UniProt NPD GO	FGFP1_MOUSE	Fibroblast growth factor-binding protein 1 precursor (FGF-binding protein 1) (FGF-BP1) (FGFBP-1) (FG ...	0.77	-	nuc	0	Secreted protein; extracellular space (Probable). Extracellular and plasma membrane-associated (By s ...				251
Q43585 UniProt NPD GO	AG_TOBAC	Floral homeotic protein AGAMOUS (NAG1)	0.77	-	nuc	0	Nucleus				248
Q03416 UniProt NPD GO	GLOB_TOBAC	Floral homeotic protein GLOBOSA	0.77	-	nuc	0	Nucleus				209
P70056 UniProt NPD GO	FOXH1_XENLA	Forkhead box protein H1 (Forkhead activin signal transducer 1) (Fast-1) (xFAST-1)	0.77	-	nuc	0	Nucleus				518
Q9BZS1 UniProt NPD GO	FOXP3_HUMAN	Forkhead box protein P3 (Scurfin)	0.77	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	304790		431
P51115 UniProt NPD GO	FXR1A_XENLA	Fragile X mental retardation syndrome-related protein 1 homolog-A (xFxr1p-A)	0.77	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				676
P52168 UniProt NPD GO	PNR_DROME	GATA-binding factor-A (Transcription factor GATA-A) (dGATA-A) (Protein pannier)	0.77	-	nuc	0	Nucleus				540
O00451 UniProt NPD GO	GFRA2_HUMAN	GDNF family receptor alpha-2 precursor (GFR-alpha-2) (Neurturin receptor alpha) (NTNR-alpha) (NRTNR- ...	0.77	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	extrinsic to membrane [TAS]	601956		464
O94380 UniProt NPD GO	GPI16_SCHPO	GPI transamidase component PIG-T homolog precursor	0.77	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				545
P40809 UniProt NPD GO	RG84C_DROME	GTPase-activating protein RacGAP84C (Protein rotund RacGAP)	0.77	-	mit	0					384
O73787 UniProt NPD GO	GCP3_XENLA	Gamma-tubulin complex component 3 homolog (Gamma ring complex protein 109) (Xgrip109) (x109p)	0.77	-	cyt	0	Centrosome				906
P18728 UniProt NPD GO	ZG53_XENLA	Gastrula zinc finger protein XLCGF53.1 (Fragment)	0.77	-	nuc	0	Nucleus (Potential)				516
Q9UHL9 UniProt NPD GO	GT2D1_HUMAN	General transcription factor II-I repeat domain-containing protein 1 (GTF2I repeat domain-containing ...	0.77	-	nuc	0	Nucleus	nucleus [NAS]	604318		959
Q8TCU5 UniProt NPD GO	NMD3A_HUMAN	Glutamate [NMDA] receptor subunit 3A precursor (N-methyl-D-aspartate receptor subtype NR3A) (NMDAR-L ...	0.77	-	end	4	Cell membrane; multi-pass membrane protein (By similarity). Enriched in post-synaptic plasma membran ...		606650		1115
P48506 UniProt NPD GO	GSH1_HUMAN	Glutamate--cysteine ligase catalytic subunit (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) (Gamma ...	0.77	+	nuc	0			606857		636
Q921D9 UniProt NPD GO	GRHL1_MOUSE	Grainyhead-like protein 1 homolog (Transcription factor CP2-like 2) (Transcription factor LBP-32)	0.77	-	nuc	0	Nucleus (By similarity)				618
Q8K5C0 UniProt NPD GO	GRHL2_MOUSE	Grainyhead-like protein 2 homolog (Brother of mammalian grainyhead) (Transcription factor CP2-like 3 ...	0.77	-	nuc	0	Nucleus				625

You are viewing entries 10301 to 10350 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.