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
Q8MUK3 UniProt NPD GO	CCNE_CAEBR	G1/S-specific cyclin-E	0.81	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			518
O15995 UniProt NPD GO	CCNE_HEMPU	G1/S-specific cyclin-E	0.81	+	mit	0					424
O13839 UniProt NPD GO	FIN1_SCHPO	G2-specific protein kinase fin1 (EC 2.7.11.1)	0.81	-	nuc	0	Spindle pole body	spindle pole body [IDA]			722
Q9SD38 UniProt NPD GO	GATA9_ARATH	GATA transcription factor 9 (AtGATA-9)	0.81	-	nuc	0	Nucleus (Probable)				312
P43695 UniProt NPD GO	GAT5A_XENLA	GATA-binding factor 5-A (Transcription factor xGATA-5A)	0.81	-	nuc	0	Nucleus				390
Q62847 UniProt NPD GO	ADDG_RAT	Gamma-adducin (Adducin-like protein 70) (Protein kinase C-binding protein 35H)	0.81	+	nuc	0		cytoskeleton [IDA]			705
Q9Y3A4 UniProt NPD GO	ZG14_HUMAN	Gastric cancer antigen Zg14	0.81	+	nuc	0					280
Q92990 UniProt NPD GO	GLMN_HUMAN	Glomulin (FKBP-associated protein) (FK506-binding protein-associated protein) (FAP)	0.81	-	cyt	0		intracellular [NAS]	601749		594
Q95267 UniProt NPD GO	GCR_TUPGB	Glucocorticoid receptor (GR)	0.81	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in the absence of ligand; nuclear af ...				776
Q9WTW1 UniProt NPD GO	GRIP2_RAT	Glutamate receptor-interacting protein 2 (GRIP2 protein) (AMPA receptor-interacting protein GRIP2)	0.81	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Isoform 1 and isoform 3 were found in synaptic pla ...	dendrite [IDA] postsynaptic membrane [IDA]			1043
P97564 UniProt NPD GO	PLSB_RAT	Glycerol-3-phosphate acyltransferase, mitochondrial precursor (EC 2.3.1.15) (GPAT)	0.81	-	nuc	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	mitochondrion [TAS]			828
O60551 UniProt NPD GO	NMT2_HUMAN	Glycylpeptide N-tetradecanoyltransferase 2 (EC 2.3.1.97) (Peptide N-myristoyltransferase 2) (Myristo ...	0.81	+	cyt	0	Cytoplasm		603801		498
Q6GL65 UniProt NPD GO	GRHL3_XENTR	Grainyhead-like protein 3 homolog (Transcription factor CP2-like 4)	0.81	-	nuc	0	Nucleus (By similarity)				594
Q13322 UniProt NPD GO	GRB10_HUMAN	Growth factor receptor-bound protein 10 (GRB10 adaptor protein) (Insulin receptor-binding protein GR ...	0.81	-	nuc	0		cytoplasm [TAS] plasma membrane [TAS]	601523	1NRV	594
P43026 UniProt NPD GO	GDF5_HUMAN	Growth/differentiation factor 5 precursor (GDF-5) (Cartilage-derived morphogenetic protein 1) (CDMP- ...	0.81	-	exc	0	Secreted protein		113100	2BHK	501
Q6KF10 UniProt NPD GO	GDF6_HUMAN	Growth/differentiation factor 6 precursor (GDF-6) (Growth/differentiation factor 16)	0.81	+	nuc	0	Secreted protein (Probable)				455
O96722 UniProt NPD GO	GAR1_ENCCU	H/ACA ribonucleoprotein complex subunit 1 (snoRNP protein GAR1)	0.81	-	mit	0	Nucleus; nucleolus (By similarity)				195
Q06623 UniProt NPD GO	HDA3_YEAST	HDA1 complex subunit 3 (Histone deacetylase complex 1 subunit 3)	0.81	+	nuc	0	Nucleus	histone deacetylase complex [IPI] nucleus [IDA]			655
Q9NRZ4 UniProt NPD GO	GAW2_HUMAN	HERV-W_3q26.32 provirus ancestral Gag polyprotein (Gag polyprotein) [Contains: Matrix protein (Gag P ...	0.81	-	nuc	0	Cell membrane (Potential)				362
O96004 UniProt NPD GO	HAND1_HUMAN	Heart- and neural crest derivatives-expressed protein 1 (Extraembryonic tissues, heart, autonomic ne ...	0.81	+	nuc	0			602406		215
Q92355 UniProt NPD GO	SEN1_SCHPO	Helicase sen1 (EC 3.6.1.-) (Endonuclease sen1)	0.81	-	nuc	0	Nucleus (Potential)				1687
Q09390 UniProt NPD GO	HMG12_CAEEL	High mobility group protein 1.2	0.81	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			235
P32103 UniProt NPD GO	H1_EUPEU	Histone H1, macronuclear	0.81	-	mit	0	Nucleus. Macronuclei				134
P02291 UniProt NPD GO	H2BS2_PARAN	Histone H2B.2, sperm	0.81	+	mit	0	Nucleus				143
P79943 UniProt NPD GO	SLBP1_XENLA	Histone RNA hairpin-binding protein (Histone stem-loop-binding protein 1)	0.81	-	nuc	0	Nucleus. Nuclear (coiled bodies). Cytoplasm				254
Q5KM33 UniProt NPD GO	ESA1_CRYNE	Histone acetyltransferase ESA1 (EC 2.3.1.48)	0.81	-	nuc	0	Nucleus (By similarity)				564
Q01448 UniProt NPD GO	HPC2_YEAST	Histone promoter control 2 protein	0.81	+	nuc	0		nucleus [IC]			623
P16909 UniProt NPD GO	18C_DROME	Histone-like protein 18C	0.81	-	nuc	0					215
Q8W595 UniProt NPD GO	SUVR4_ARATH	Histone-lysine N-methyltransferase SUVR4 (EC 2.1.1.43) (Suppressor of variegation 3-9-related protei ...	0.81	+	exc	0	Nucleus (By similarity). Associates with euchromatic regions (By similarity)				492
Q9EQQ0 UniProt NPD GO	SUV92_MOUSE	Histone-lysine N-methyltransferase, H3 lysine-9 specific 2 (EC 2.1.1.43) (Histone H3-K9 methyltransf ...	0.81	-	nuc	0	Nucleus. Associates with constitutive heterochromatin during most stages of spermato- and spermiogen ...	chromatin [ISS] nuclear heterochromatin [IDA]			477
Q8AWY2 UniProt NPD GO	HXAAB_BRARE	Homeobox protein Hox-A10b (Hox-A10)	0.81	+	nuc	0	Nucleus (By similarity)				330
Q9DDU2 UniProt NPD GO	HXABB_DANAE	Homeobox protein Hox-A11b	0.81	+	nuc	0	Nucleus (By similarity)				283
Q9DDU1 UniProt NPD GO	HXABB_BRARE	Homeobox protein Hox-A11b (Hox-A11)	0.81	+	nuc	0	Nucleus (By similarity)				283
P09071 UniProt NPD GO	HXA7_XENLA	Homeobox protein Hox-A7 (XlHbox-3) (Xhox-36)	0.81	+	nuc	0	Nucleus				209
P10284 UniProt NPD GO	HXB4_MOUSE	Homeobox protein Hox-B4 (Hox-2.6)	0.81	+	nuc	0	Nucleus				250
P04476 UniProt NPD GO	HXB7B_XENLA	Homeobox protein Hox-B7 B (XlHbox-2 B) (P52)	0.81	+	nuc	0	Nucleus				220
P18863 UniProt NPD GO	HXB8_RAT	Homeobox protein Hox-B8 (R1A) (Fragment)	0.81	+	nuc	0	Nucleus				92
Q43484 UniProt NPD GO	KNOX3_HORVU	Homeobox protein KNOX3 (Hooded protein)	0.81	-	nuc	0	Nucleus (Probable)				364
Q62231 UniProt NPD GO	SIX1_MOUSE	Homeobox protein SIX1 (Sine oculis homeobox homolog 1)	0.81	-	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			284
Q06453 UniProt NPD GO	AL_DROME	Homeobox protein aristaless	0.81	+	nuc	0	Nucleus (By similarity)				408
O22299 UniProt NPD GO	LET6_LYCES	Homeobox protein knotted-1-like LET6	0.81	+	nuc	0	Nucleus (Probable)				355
Q41853 UniProt NPD GO	RSH1_MAIZE	Homeobox protein rough sheath 1	0.81	-	nuc	0	Nucleus (Probable)				351
Q9H422 UniProt NPD GO	HIPK3_HUMAN	Homeodomain-interacting protein kinase 3 (EC 2.7.11.1) (Homolog of protein kinase YAK1) (Fas-interac ...	0.81	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA] PML body [IDA]	604424		1215
Q24740 UniProt NPD GO	CDC37_DROVI	Hsp90 co-chaperone Cdc37 (Hsp90 chaperone protein kinase-targeting subunit)	0.81	+	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			399
P51111 UniProt NPD GO	HD_RAT	Huntingtin (Huntington disease protein homolog) (HD protein)	0.81	+	end	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [TAS]			3110
P53952 UniProt NPD GO	YNF0_YEAST	Hypothetical 31.4 kDa protein in COX5A-ALG11 intergenic region	0.81	+	nuc	0					270
P38961 UniProt NPD GO	YD083_YEAST	Hypothetical 47.2 kDa protein in STN1-AFR1 intergenic region	0.81	+	nuc	0		nucleolus [IDA]			402
Q03508 UniProt NPD GO	YM8F_YEAST	Hypothetical 54.1 kDa protein in TPS3-IPP2 intergenic region	0.81	+	nuc	0					461
P49541 UniProt NPD GO	YCF46_ODOSI	Hypothetical 56.9 kDa protein ycf46 (ORF497)	0.81	+	cyt	0	Plastid; chloroplast				497
P46945 UniProt NPD GO	YGS6_YEAST	Hypothetical 63.3 kDa protein in MPT5-SAE2 intergenic region	0.81	-	nuc	0					554

You are viewing entries 8351 to 8400 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.