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
Q5W1J5 UniProt NPD GO	FOXP1_XENLA	Forkhead box protein P1 (xlFoxP1)	0.73	-	nuc	0	Nucleus (Probable)				578
Q99JB6 UniProt NPD GO	FOXP3_MOUSE	Forkhead box protein P3 (Scurfin)	0.73	-	nuc	0	Nucleus (Potential)				429
Q61574 UniProt NPD GO	FREA_MOUSE	Forkhead-related transcription factor 10 (FREAC-10) (Forkhead-like 18 protein) (Transcription factor ...	0.73	-	nuc	0	Nucleus				329
P24869 UniProt NPD GO	CG22_YEAST	G2/mitotic-specific cyclin-2	0.73	-	nuc	0		bud neck [IDA] cytoplasm [IDA] nucleus [IDA] spindle [IDA] spindle pole body [IDA]			491
P48559 UniProt NPD GO	YPT11_YEAST	GTP-binding protein YPT11	0.73	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	bud neck [IDA] bud tip [IDA] incipient bud site [IDA]			355
Q66HC8 UniProt NPD GO	GGN_RAT	Gametogenetin	0.73	-	nuc	0					658
P49115 UniProt NPD GO	GCR_CAVPO	Glucocorticoid receptor (GR)	0.73	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in the absence of ligand; nuclear af ...				771
Q74ZH9 UniProt NPD GO	GDE1_ASHGO	Glycerophosphodiester phosphodiesterase GDE1 (EC 3.1.4.46)	0.73	+	nuc	0	Cytoplasm (By similarity)				1321
P23415 UniProt NPD GO	GLRA1_HUMAN	Glycine receptor alpha-1 chain precursor (Glycine receptor 48 kDa subunit) (Strychnine-binding subun ...	0.73	-	end	3	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	138491	1VRY	449
Q9N181 UniProt NPD GO	NMT2_BOVIN	Glycylpeptide N-tetradecanoyltransferase 2 (EC 2.3.1.97) (Peptide N-myristoyltransferase 2) (Myristo ...	0.73	+	cyt	0	Cytoplasm (By similarity)				498
Q9R1D7 UniProt NPD GO	GBF1_CRIGR	Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 (BFA-resistant GEF 1)	0.73	-	nuc	0					1856
Q1RMW5 UniProt NPD GO	GRB7_BOVIN	Growth factor receptor-bound protein 7 (GRB7 adapter protein) (Epidermal growth factor receptor GRB- ...	0.73	-	nuc	0					532
P23625 UniProt NPD GO	GNAQ_DROME	Guanine nucleotide-binding protein G(q) subunit alpha (Guanine nucleotide-binding protein alpha-q) ( ...	0.73	-	cyt	0		inaD signaling complex [IDA]			353
P87035 UniProt NPD GO	GPA4_USTMA	Guanine nucleotide-binding protein alpha-4 subunit	0.73	-	nuc	0					580
Q64221 UniProt NPD GO	HEN2_MOUSE	Helix-loop-helix protein 2 (HEN2) (Nescient helix loop helix 2) (NSCL-2)	0.73	+	nuc	0					135
Q05041 UniProt NPD GO	HNFAA_XENLA	Hepatocyte nuclear factor 1-alpha A (HNF-1A-A) (HNF-1-alpha A) (LFB1) (XLFB1A)	0.73	+	nuc	0	Nucleus				605
P40286 UniProt NPD GO	H1T_MACMU	Histone H1t (Testicular H1 histone)	0.73	-	nuc	0	Nucleus				207
Q27749 UniProt NPD GO	H2BS1_PSAMI	Histone H2B.1, sperm	0.73	+	nuc	0	Nucleus				136
Q9VAN6 UniProt NPD GO	SLBP_DROME	Histone RNA hairpin-binding protein (Histone stem-loop-binding protein)	0.73	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			276
P09076 UniProt NPD GO	HME30_APIME	Homeobox protein E30 (Fragment)	0.73	+	nuc	0	Nucleus				109
P48031 UniProt NPD GO	GBX2_MOUSE	Homeobox protein GBX-2 (Gastrulation and brain-specific homeobox protein 2) (Homeobox protein STRA7) ...	0.73	+	nuc	0	Nucleus (Probable)				348
P09630 UniProt NPD GO	HXC6_HUMAN	Homeobox protein Hox-C6 (Hox-3C) (HHO.C8) (CP25)	0.73	+	nuc	0	Nucleus		142972		235
P09633 UniProt NPD GO	HXC9_MOUSE	Homeobox protein Hox-C9 (Hox-3.2)	0.73	+	nuc	0	Nucleus				260
P31274 UniProt NPD GO	HXC9_HUMAN	Homeobox protein Hox-C9 (Hox-3B)	0.73	+	nuc	0	Nucleus		142971		260
Q01622 UniProt NPD GO	HLOX2_HELRO	Homeobox protein LOX2 (Fragment)	0.73	+	nuc	0	Nucleus (Probable)				429
P21523 UniProt NPD GO	HLOX2_HIRME	Homeobox protein LOX2 (Fragment)	0.73	+	nuc	0	Nucleus (Probable)				118
O35767 UniProt NPD GO	NKX25_RAT	Homeobox protein Nkx-2.5 (Homeobox protein NK-2 homolog E) (rNKx-2.5)	0.73	+	nuc	0	Nucleus (Probable)				318
P78367 UniProt NPD GO	NKX32_HUMAN	Homeobox protein Nkx-3.2 (Bagpipe homeobox protein homolog 1)	0.73	+	nuc	0	Nucleus (Probable)		602183		333
P32243 UniProt NPD GO	OTX2_HUMAN	Homeobox protein OTX2	0.73	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	600037		289
Q91813 UniProt NPD GO	OTX2_XENLA	Homeobox protein OTX2 (XOTX2) (Orthodenticle 2) (Orthodenticle-A-like protein)	0.73	-	nuc	0	Nucleus (Probable)				288
P55347 UniProt NPD GO	PKNX1_HUMAN	Homeobox protein PKNOX1 (PBX/knotted homeobox 1) (Homeobox protein PREP-1)	0.73	-	nuc	0	Nucleus (Probable)		602100	1X2N	435
Q8MIB8 UniProt NPD GO	TF2LX_PONPY	Homeobox protein TGIF2LX (TGFB-induced factor 2-like protein, X-linked) (TGF(beta)induced transcript ...	0.73	-	nuc	0	Nucleus (By similarity)				241
P29556 UniProt NPD GO	ABDA_SCHGR	Homeobox protein abdominal-A homolog (Fragment)	0.73	+	mit	0	Nucleus (Probable)				157
P34663 UniProt NPD GO	HM23_CAEEL	Homeobox protein ceh-23	0.73	+	nuc	0	Nucleus (Probable)				305
Q05466 UniProt NPD GO	HAT4_ARATH	Homeobox-leucine zipper protein HAT4 (HD-ZIP protein 4) (HD-ZIP protein ATHB-2)	0.73	+	nuc	0	Nucleus				284
Q9NS37 UniProt NPD GO	ZHANG_HUMAN	Host cell factor-binding transcription factor Zhangfei (HCF-binding transcription factor Zhangfei)	0.73	-	nuc	0	Nucleus. Colocalizes at punctate nuclear structures with CREB3 and HCFC1	nucleus [IDA]	606444		272
Q91ZR3 UniProt NPD GO	ZHANG_MOUSE	Host cell factor-binding transcription factor Zhangfei (HCF-binding transcription factor Zhangfei) ( ...	0.73	-	nuc	0	Nucleus (By similarity). Colocalizes at punctate nuclear structures with CREB3 and HCFC1 (By similar ...				273
Q63692 UniProt NPD GO	CDC37_RAT	Hsp90 co-chaperone Cdc37 (Hsp90 chaperone protein kinase-targeting subunit) (p50Cdc37)	0.73	-	cyt	0	Cytoplasm (By similarity)				379
P53876 UniProt NPD GO	YNS4_YEAST	Hypothetical 12.5 kDa protein in UBP10-NPR1 intergenic region	0.73	-	nuc	0					108
P53287 UniProt NPD GO	YG3N_YEAST	Hypothetical 13.1 kDa protein in RPL24B-RSR1 intergenic region	0.73	+	nuc	0					111
P56370 UniProt NPD GO	YCXA_CHLVU	Hypothetical 94.7 kDa protein in cysT-rpoB intergenic region (ORF819)	0.73	-	vac	7 *	Membrane; multi-pass membrane protein (Potential)				819
Q09731 UniProt NPD GO	YA4E_SCHPO	Hypothetical WD repeat protein C31A2.14 in chromosome I	0.73	-	nuc	0		barrier septum [IDA] cell cortex of cell tip [IDA]			962
O13693 UniProt NPD GO	YDYE_SCHPO	Hypothetical protein C11E3.14 in chromosome I	0.73	+	nuc	0					588
O74415 UniProt NPD GO	YJL2_SCHPO	Hypothetical protein C14G10.02 in chromosome III	0.73	-	end	0					1568
O74501 UniProt NPD GO	YCRE_SCHPO	Hypothetical protein CC285.14	0.73	-	nuc	0					1150
P34397 UniProt NPD GO	YLU3_CAEEL	Hypothetical protein F10E9.3	0.73	-	nuc	0					362
P54073 UniProt NPD GO	YUY1_CAEEL	Hypothetical protein F44G4.1 in chromosome II	0.73	+	nuc	0					384
Q6NWD4 UniProt NPD GO	TIM50_BRARE	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.73	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)	mitochondrial inner membrane presequence tr... [ISS]			387
Q70EK8 UniProt NPD GO	UBP53_HUMAN	Inactive ubiquitin carboxyl-terminal hydrolase 53 (Ubiquitin-specific peptidase 53)	0.73	-	nuc	0					1073
Q8WYH8 UniProt NPD GO	ING5_HUMAN	Inhibitor of growth protein 5 (p28ING5)	0.73	-	nuc	0			608525		240

You are viewing entries 12301 to 12350 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.