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
P06798 UniProt NPD GO	HXA4_MOUSE	Homeobox protein Hox-A4 (Hox-1.4) (MH-3)	0.61	+	nuc	0	Nucleus				285
P50208 UniProt NPD GO	HXA5_AMBME	Homeobox protein Hox-A5 (Fragment)	0.61	+	nuc	0	Nucleus				148
P09631 UniProt NPD GO	HXA9_MOUSE	Homeobox protein Hox-A9 (Hox-1.7)	0.61	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]		1PUF	271
P31269 UniProt NPD GO	HXA9_HUMAN	Homeobox protein Hox-A9 (Hox-1G)	0.61	+	nuc	0	Nucleus		142956		272
P09027 UniProt NPD GO	HXD3_MOUSE	Homeobox protein Hox-D3 (Hox-4.1) (MH-19)	0.61	+	nuc	0	Nucleus				417
P09016 UniProt NPD GO	HXD4_HUMAN	Homeobox protein Hox-D4 (Hox-4B) (Hox-5.1) (HHO.C13)	0.61	+	nuc	0	Nucleus	nucleus [NAS]	142981		255
Q01703 UniProt NPD GO	MSXC_BRARE	Homeobox protein MSH-C	0.61	+	nuc	0	Nucleus				273
P32242 UniProt NPD GO	OTX1_HUMAN	Homeobox protein OTX1	0.61	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	600036		354
Q62233 UniProt NPD GO	SIX3_MOUSE	Homeobox protein SIX3 (Sine oculis homeobox homolog 3)	0.61	-	exc	0	Nucleus	nucleus [IDA]			333
P29552 UniProt NPD GO	ABDA_AEDAE	Homeobox protein abdominal-A homolog (Fragment)	0.61	+	nuc	0	Nucleus (Probable)				74
P26797 UniProt NPD GO	HM19_CAEEL	Homeobox protein ceh-19	0.61	+	nuc	0	Nucleus (Probable)				199
P56659 UniProt NPD GO	KNOX1_MAIZE	Homeobox protein knotted-1-like 1 (Fragment)	0.61	-	nuc	0	Nucleus (Probable)				88
Q09604 UniProt NPD GO	VAB15_CAEEL	Homeobox protein vab-15	0.61	+	nuc	0	Nucleus (Probable)				225
Q8BNV1 UniProt NPD GO	HTF9C_MOUSE	HpaII tiny fragments locus 9c protein	0.61	-	cyt	0					574
Q9XYD3 UniProt NPD GO	HBL1_CAEEL	Hunchback-like protein	0.61	-	nuc	0	Nucleus (Probable)				982
P47108 UniProt NPD GO	YJ11_YEAST	Hypothetical 135.1 kDa protein in GEF1-NUP85 intergenic region	0.61	-	end	0		nucleolus [IDA]			1174
Q8HUH1 UniProt NPD GO	RR2B_CHLRE	Hypothetical 30S ribosomal S2-like protein	0.61	+	nuc	0	Plastid; chloroplast				208
P36155 UniProt NPD GO	YK55_YEAST	Hypothetical 36.1 kDa protein in SIS2-MTD1 intergenic region	0.61	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			307
O19920 UniProt NPD GO	YCF45_CYACA	Hypothetical 37.9 kDa protein ycf45	0.61	-	nuc	0	Plastid; chloroplast				335
P54005 UniProt NPD GO	YM95_YEAST	Hypothetical 38.8 kDa protein in PRE5-FET4 intergenic region	0.61	-	nuc	0		cytoplasm [IDA]			336
P36157 UniProt NPD GO	YK57_YEAST	Hypothetical 39.9 kDa protein in SIS2-MTD1 intergenic region	0.61	+	mit	0		cytoplasm [IDA] nucleus [IDA]			363
Q05029 UniProt NPD GO	YM76_YEAST	Hypothetical 82.0 kDa protein in RNA1-RNT1 intergenic region	0.61	-	mit	0					724
O14053 UniProt NPD GO	YC47_SCHPO	Hypothetical WD repeat protein C1672.07 in chromosome III	0.61	-	nuc	0					902
Q6B184 UniProt NPD GO	MATA2_YEAST	Hypothetical mating-type protein A2 (MATa2 protein)	0.61	+	nuc	0	Nucleus (Potential)				119
O13852 UniProt NPD GO	YFGD_SCHPO	Hypothetical protein C19G12.13c in chromosome I	0.61	-	nuc	0					249
O42855 UniProt NPD GO	YFHI_SCHPO	Hypothetical protein C23A1.18c in chromosome I	0.61	-	nuc	0					291
P34357 UniProt NPD GO	YLH3_CAEEL	Hypothetical protein C48B4.3	0.61	-	nuc	0					216
Q09296 UniProt NPD GO	YQO6_CAEEL	Hypothetical protein EEED8.6	0.61	-	cyt	0					477
Q21874 UniProt NPD GO	YF1M_CAEEL	Hypothetical protein R09E10.5 precursor	0.61	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				1459
Q10019 UniProt NPD GO	YSW4_CAEEL	Hypothetical protein T25D10.4	0.61	-	nuc	0					246
P34603 UniProt NPD GO	YO63_CAEEL	Hypothetical protein ZK1098.3	0.61	-	nuc	0					784
P34624 UniProt NPD GO	YOJ1_CAEEL	Hypothetical protein ZK353.1 in chromosome III	0.61	-	nuc	0					357
P43650 UniProt NPD GO	YMF19_WHEAT	Hypothetical protein ymf19 (ORF156) (18 kDa membrane-bound protein)	0.61	-	nuc	1 *	Mitochondrion (Potential)				156
P46958 UniProt NPD GO	IDS2_YEAST	IME2-dependent signaling protein	0.61	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			469
O13636 UniProt NPD GO	TIM50_SCHPO	Import inner membrane translocase subunit tim50, mitochondrial precursor	0.61	-	nuc	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				452
O22190 UniProt NPD GO	GH33_ARATH	Indole-3-acetic acid-amido synthetase GH3.3 (EC 6.3.2.-) (Auxin-responsive GH3-like protein 3) (AtGH ...	0.61	-	cyt	0					595
Q60680 UniProt NPD GO	IKKA_MOUSE	Inhibitor of nuclear factor kappa-B kinase alpha subunit (EC 2.7.11.10) (I kappa-B kinase alpha) (Ik ...	0.61	-	nuc	0	Cytoplasm	cytoplasm [TAS]			745
P29995 UniProt NPD GO	ITPR2_RAT	Inositol 1,4,5-trisphosphate receptor type 2 (Type 2 inositol 1,4,5-trisphosphate receptor) (Type 2 ...	0.61	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				2701
Q9R0U1 UniProt NPD GO	IP6K2_RAT	Inositol hexakisphosphate kinase 2 (EC 2.7.4.21) (InsP6 kinase 2) (Inositol hexakisphosphate kinase ...	0.61	+	cyt	0	Nucleus (By similarity)				424
P53407 UniProt NPD GO	ISL3_BRARE	Insulin gene enhancer protein isl-3 (Islet-3)	0.61	+	nuc	0	Nucleus				358
P24592 UniProt NPD GO	IBP6_HUMAN	Insulin-like growth factor-binding protein 6 precursor (IGFBP-6) (IBP-6) (IGF-binding protein 6)	0.61	-	exc	0	Secreted protein		146735	1RMJ	240
P01566 UniProt NPD GO	IFN10_HUMAN	Interferon alpha-10 precursor (Interferon alpha-C) (LeIF C) (Interferon alpha-6L)	0.61	-	mit	0	Secreted protein	extracellular region [NAS]	147577		189
P05009 UniProt NPD GO	IFNAC_BOVIN	Interferon alpha-C precursor	0.61	-	mit	0	Secreted protein				189
P14316 UniProt NPD GO	IRF2_HUMAN	Interferon regulatory factor 2 (IRF-2)	0.61	-	nuc	0	Nucleus		147576		349
O43187 UniProt NPD GO	IRAK2_HUMAN	Interleukin-1 receptor-associated kinase-like 2 (IRAK-2)	0.61	-	nuc	0		cell surface [IEP]	603304		590
Q9QXT6 UniProt NPD GO	IL17B_MOUSE	Interleukin-17B precursor (IL-17B) (Cytokine-like protein ZCYTO7) (Neuronal interleukin-17-related f ...	0.61	-	nuc	0	Secreted protein				180
P78415 UniProt NPD GO	IRX3_HUMAN	Iroquois-class homeodomain protein IRX-3 (Iroquois homeobox protein 3) (Homeodomain protein IRXB1)	0.61	-	nuc	0	Nucleus (Probable)				501
Q9GKY7 UniProt NPD GO	JPH2_RABIT	Junctophilin-2 (Junctophilin type 2) (JP-2)	0.61	+	nuc	1	Cell membrane; peripheral membrane protein (By similarity). Endoplasmic reticulum; endoplasmic retic ...				694
Q96JJ6 UniProt NPD GO	JPH4_HUMAN	Junctophilin-4 (Junctophilin-like 1 protein)	0.61	-	cyt	0	Membrane; single-pass type IV membrane protein (By similarity)				628
Q61097 UniProt NPD GO	KSR1_MOUSE	Kinase suppressor of ras-1 (Kinase suppressor of ras) (mKSR1) (Hb protein)	0.61	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. In unstimulated cells, where the phosphorylated fo ...			1KBF	873

You are viewing entries 18501 to 18550 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.