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
P01746 UniProt NPD GO	HV02_MOUSE	Ig heavy chain V region 93G7 precursor	0.04	-	vac	0					140
P01812 UniProt NPD GO	HV42_MOUSE	Ig heavy chain V region MOPC 173	0.04	-	nuc	0					117
P01828 UniProt NPD GO	HV2B_RABIT	Ig heavy chain V-A2 region K-25	0.04	-	mit	0					117
P01744 UniProt NPD GO	HV1C_HUMAN	Ig heavy chain V-I region ND precursor (Fragments)	0.04	-	cyt	0		extracellular region [NAS]			147
P01814 UniProt NPD GO	HV2A_HUMAN	Ig heavy chain V-II region OU	0.04	-	mit	0		extracellular region [NAS]			126
P01693 UniProt NPD GO	KV12_RABIT	Ig kappa chain V region 3368	0.04	-	cyt	0					111
P01695 UniProt NPD GO	KV14_RABIT	Ig kappa chain V region K16-167	0.04	-	mit	0					109
P01633 UniProt NPD GO	KV5A_MOUSE	Ig kappa chain V-V region MPC11 precursor	0.04	-	exc	0					149
P01840 UniProt NPD GO	KAC4_RABIT	Ig kappa-b4 chain C region	0.04	-	cyt	0					103
P01841 UniProt NPD GO	KAC5_RABIT	Ig kappa-b5 chain C region	0.04	-	exc	0					103
P01846 UniProt NPD GO	LAC_PIG	Ig lambda chain C region	0.04	-	nuc	0					105
P04211 UniProt NPD GO	LV0A_HUMAN	Ig lambda chain V region 4A precursor	0.04	-	exc	0		extracellular region [NAS]			117
P01728 UniProt NPD GO	LV2A_MOUSE	Ig lambda-2 chain V region precursor	0.04	-	vac	0					117
Q12578 UniProt NPD GO	HIS7_CANGA	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.04	-	cyt	0					210
Q6CLR6 UniProt NPD GO	HIS7_KLULA	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.04	-	cyt	0					221
Q6JV40 UniProt NPD GO	HIS7_KLUMA	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.04	-	cyt	0					221
O42621 UniProt NPD GO	HIS7_MAGGR	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.04	-	nuc	0					227
O94153 UniProt NPD GO	HIS7_PHARH	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.04	-	mit	0					205
P83869 UniProt NPD GO	IM14_DROME	Immune-induced peptide 14 precursor (DIM-14)	0.04	-	vac	1 *	Secreted protein				46
P40936 UniProt NPD GO	INMT_MOUSE	Indolethylamine N-methyltransferase (EC 2.1.1.49) (Aromatic alkylamine N-methyltransferase) (Indolam ...	0.04	-	cyt	0	Cytoplasm (By similarity)				264
P97287 UniProt NPD GO	MCL1_MOUSE	Induced myeloid leukemia cell differentiation protein Mcl-1 homolog (Bcl-2-related protein EAT/mcl1) ...	0.04	-	nuc	1	Membrane; single-pass membrane protein (By similarity). Cytoplasm (By similarity). Mitochondrion (By ...			1WSX	331
P21327 UniProt NPD GO	INPP_BOVIN	Inositol polyphosphate 1-phosphatase (EC 3.1.3.57) (IPPase) (IPP)	0.04	-	cyt	0				1INP	400
O65195 UniProt NPD GO	INO1_HORVU	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.04	-	cyt	0	Cytoplasm (By similarity)				510
Q9FPK7 UniProt NPD GO	INO1_MAIZE	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.04	-	cyt	0	Cytoplasm (By similarity)				510
Q40271 UniProt NPD GO	INO1_MESCR	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.04	-	nuc	0	Cytoplasm (By similarity)				512
Q9FYV1 UniProt NPD GO	INO1_SESIN	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.04	-	cyt	0	Cytoplasm (By similarity)				510
Q9LW96 UniProt NPD GO	INO1_TOBAC	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.04	-	cyt	0	Cytoplasm (By similarity)				510
P82813 UniProt NPD GO	SIX3_BUTSI	Insect toxin 3 (BsIT3) (Bs-dprIT3)	0.04	-	nuc	0	Secreted protein				61
P81504 UniProt NPD GO	SIX5_ANDAU	Insect toxin 5 (AaH IT5) (AaHIT5) (AaIT5)	0.04	-	nuc	0	Secreted protein				61
P55816 UniProt NPD GO	TXI11_DIGCA	Insecticidal toxin DTX11	0.04	-	cyt	0	Secreted protein				58
P24854 UniProt NPD GO	IBP4_PIG	Insulin-like growth factor-binding protein 4 (IGFBP-4) (IBP-4) (IGF-binding protein 4) (Fragment)	0.04	-		0	Secreted protein				16
O89051 UniProt NPD GO	ITM2B_MOUSE	Integral membrane protein 2B (E25B protein)	0.04	-	mit	1	Membrane; single-pass type II membrane protein (Potential)	membrane fraction [TAS]			266
Q99MU1 UniProt NPD GO	GP175_MOUSE	Integral membrane protein GPR175 (Transmembrane domain protein of 40 kDa regulated in adipocytes) (T ...	0.04	-	end	7 *	Membrane; multi-pass membrane protein				369
Q791F6 UniProt NPD GO	GP175_RAT	Integral membrane protein GPR175 (Transmembrane domain protein of 40 kDa regulated in adipocytes) (T ...	0.04	-	end	7 *	Membrane; multi-pass membrane protein				369
Q90615 UniProt NPD GO	ITA1_CHICK	Integrin alpha-1 (Laminin and collagen receptor) (VLA-1) (Fragment)	0.04	-	cyt	0	Membrane; single-pass type I membrane protein				285
Q9ERS7 UniProt NPD GO	ILRL2_MOUSE	Interleukin-1 receptor-like 2 precursor (IL-1Rrp2)	0.04	-	end	3 *	Membrane; single-pass type I membrane protein				574
P20109 UniProt NPD GO	IL13_MOUSE	Interleukin-13 precursor (IL-13) (T-cell activation protein P600)	0.04	-	cyt	1 *	Secreted protein				131
P48346 UniProt NPD GO	IL15_MOUSE	Interleukin-15 precursor (IL-15)	0.04	-	vac	1 *	Secreted protein				162
P05016 UniProt NPD GO	IL2_BOVIN	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.04	-	exc	0	Secreted protein				155
Q9JKV9 UniProt NPD GO	IL20_MOUSE	Interleukin-20 precursor (IL-20) (Four alpha helix cytokine ZCYTO10)	0.04	-	mit	0	Secreted protein				176
P19874 UniProt NPD GO	IL8_RABIT	Interleukin-8 precursor (IL-8) (CXCL8) (Neutrophil attractant/activation protein 1) (NAP-1) (Permeab ...	0.04	-	exc	1 *	Secreted protein	extracellular space [ISS]			101
Q9UTC6 UniProt NPD GO	ISU1_SCHPO	Iron sulfur cluster assembly protein 1, mitochondrial precursor (Iron sulfur cluster scaffold protei ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				192
Q12056 UniProt NPD GO	ISU2_YEAST	Iron sulfur cluster assembly protein 2, mitochondrial precursor (Iron sulfur cluster scaffold protei ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			156
Q6CII3 UniProt NPD GO	FET3_KLULA	Iron transport multicopper oxidase FET3 precursor (EC 1.-.-.-)	0.04	-	end	1	Cell membrane; single-pass type I membrane protein; extracellular side (Potential)				631
P43561 UniProt NPD GO	FET5_YEAST	Iron transport multicopper oxidase FET5 precursor (EC 1.-.-.-)	0.04	-	end	0		vacuolar membrane (sensu Fungi) [IDA]			622
O88844 UniProt NPD GO	IDHC_MOUSE	Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) (Cytosolic NADP-isocitrate dehydrogenase) ...	0.04	-	pox	0	Cytoplasm	cytosol [IDA]			414
Q04467 UniProt NPD GO	IDHP_BOVIN	Isocitrate dehydrogenase [NADP], mitochondrial precursor (EC 1.1.1.42) (Oxalosuccinate decarboxylase ...	0.04	-	mit	0	Mitochondrion				452
P33198 UniProt NPD GO	IDHP_PIG	Isocitrate dehydrogenase [NADP], mitochondrial precursor (EC 1.1.1.42) (Oxalosuccinate decarboxylase ...	0.04	-	nuc	0	Mitochondrion			1LWD	421
O22308 UniProt NPD GO	7OMT6_MEDSA	Isoflavone-7-O-methyltransferase 6 (EC 2.1.1.150) (Isoflavone-O-methyltransferase 6) (7-IOMT-6)	0.04	-	cyt	0					352
P93324 UniProt NPD GO	CHOMT_MEDSA	Isoliquiritigenin 2'-O-methyltransferase (EC 2.1.1.-) (Chalcone O-methyltransferase) (ChOMT)	0.04	-	cyt	0				1FPQ	372

You are viewing entries 77351 to 77400 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.