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
P01757 UniProt NPD GO	HV13_MOUSE	Ig heavy chain V region J558	0.01	-	nuc	0					117
P01795 UniProt NPD GO	HV26_MOUSE	Ig heavy chain V region M167 precursor	0.01	-	exc	0					144
P01790 UniProt NPD GO	HV21_MOUSE	Ig heavy chain V region M511	0.01	-	cyt	0					122
P01785 UniProt NPD GO	HV02_CANFA	Ig heavy chain V region MOO	0.01	-	cyt	0					117
P01756 UniProt NPD GO	HV12_MOUSE	Ig heavy chain V region MOPC 104E	0.01	-	cyt	0					117
P01786 UniProt NPD GO	HV17_MOUSE	Ig heavy chain V region MOPC 47A	0.01	-	cyt	0					117
P18524 UniProt NPD GO	HV53_MOUSE	Ig heavy chain V region RF precursor	0.01	-	vac	0					117
P03980 UniProt NPD GO	HV48_MOUSE	Ig heavy chain V region TEPC 1017 precursor	0.01	-	vac	0					138
P20957 UniProt NPD GO	HV02_XENLA	Ig heavy chain V region XIG14 precursor (Fragment)	0.01	-	mit	0					135
P01826 UniProt NPD GO	HV1A_RABIT	Ig heavy chain V-A1 region BS-5	0.01	-	mit	0					116
P01827 UniProt NPD GO	HV2A_RABIT	Ig heavy chain V-A2 region BS-1	0.01	-	mit	0					114
P01796 UniProt NPD GO	HV27_MOUSE	Ig heavy chain V-III region A4	0.01	-	cyt	0					113
P01799 UniProt NPD GO	HV30_MOUSE	Ig heavy chain V-III region ABE-47N	0.01	-	cyt	0					113
P01766 UniProt NPD GO	HV3E_HUMAN	Ig heavy chain V-III region BRO	0.01	-	cyt	0		extracellular region [NAS]			120
P01782 UniProt NPD GO	HV3U_HUMAN	Ig heavy chain V-III region DOB	0.01	-	cyt	0		extracellular region [NAS]			120
P01798 UniProt NPD GO	HV29_MOUSE	Ig heavy chain V-III region E109	0.01	-	cyt	0					113
P01769 UniProt NPD GO	HV3H_HUMAN	Ig heavy chain V-III region GA	0.01	-	cyt	0		extracellular region [NAS]			122
P01781 UniProt NPD GO	HV3T_HUMAN	Ig heavy chain V-III region GAL	0.01	-	cyt	0		extracellular region [NAS]			116
P01801 UniProt NPD GO	HV32_MOUSE	Ig heavy chain V-III region J606	0.01	-	cyt	0					115
P01800 UniProt NPD GO	HV31_MOUSE	Ig heavy chain V-III region T957	0.01	-	cyt	0					113
P01765 UniProt NPD GO	HV3D_HUMAN	Ig heavy chain V-III region TIL	0.01	-	cyt	0		extracellular region [NAS]			115
P01797 UniProt NPD GO	HV28_MOUSE	Ig heavy chain V-III region U61	0.01	-	cyt	0					113
P01689 UniProt NPD GO	KV08_RABIT	Ig kappa chain V region 120	0.01	-	cyt	0					108
P01682 UniProt NPD GO	KV01_RABIT	Ig kappa chain V region 2717	0.01	-	mit	0					110
P01698 UniProt NPD GO	KV17_RABIT	Ig kappa chain V region XP-1 (Fragment)	0.01	-	cyt	0					104
P80748 UniProt NPD GO	LV3B_HUMAN	Ig lambda chain V-III region LOI	0.01	-	cyt	0		extracellular region [NAS]		2LOI	111
P01719 UniProt NPD GO	LV5A_HUMAN	Ig lambda chain V-V region DEL	0.01	-	cyt	0		extracellular region [NAS]			108
P01720 UniProt NPD GO	LV7A_HUMAN	Ig lambda chain V-VII region MOT	0.01	-	cyt	0		extracellular region [NAS]			111
P01726 UniProt NPD GO	LV1D_MOUSE	Ig lambda-1 chain V region H2020 precursor	0.01	-	vac	0					129
P01725 UniProt NPD GO	LV1C_MOUSE	Ig lambda-1 chain V region S178	0.01	-	cyt	0					110
P01729 UniProt NPD GO	LV2B_MOUSE	Ig lambda-2 chain V region MOPC 315 precursor	0.01	-	vac	0					129
P40374 UniProt NPD GO	HIS7_SCHPO	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.01	-	mit	0					216
P06633 UniProt NPD GO	HIS7_YEAST	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.01	-	cyt	0		intracellular [TAS]			220
Q96UK2 UniProt NPD GO	HIS7_ZYGBA	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.01	-	cyt	0					223
P82706 UniProt NPD GO	IM01_DROME	Immune-induced peptide 1 precursor (DIM-1)	0.01	-	exc	1 *	Secreted protein	extracellular region [IDA]			45
O77150 UniProt NPD GO	IM02_DROME	Immune-induced peptide 2 precursor (DIM-2)	0.01	-	exc	1 *	Secreted protein	extracellular region [IDA]			45
P80412 UniProt NPD GO	FVE_FLAVE	Immunomodulatory protein FIP-Fve	0.01	-	cyt	0				1OSY	114
P79693 UniProt NPD GO	IHH_CARAU	Indian hedgehog protein (IHH) (Fragment)	0.01	-	nuc	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				58
O13240 UniProt NPD GO	IHH_DANAT	Indian hedgehog protein (IHH) (Fragment)	0.01	-	nuc	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				58
P79711 UniProt NPD GO	IHH_DANKE	Indian hedgehog protein (IHH) (Fragment)	0.01	-	nuc	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				58
P79719 UniProt NPD GO	IHH_DANPU	Indian hedgehog protein (IHH) (Fragment)	0.01	-	nuc	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				58
O13243 UniProt NPD GO	IHH_DEVDE	Indian hedgehog protein (IHH) (Fragment)	0.01	-	nuc	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				58
O13215 UniProt NPD GO	IHH_DEVMA	Indian hedgehog protein (IHH) (Fragment)	0.01	-	nuc	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				58
O13220 UniProt NPD GO	IHH_DEVPA	Indian hedgehog protein (IHH) (Fragment)	0.01	-	nuc	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				58
P79852 UniProt NPD GO	IHH_PUNTE	Indian hedgehog protein (IHH) (Fragment)	0.01	-	nuc	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				58
P79860 UniProt NPD GO	IHH_RASEL	Indian hedgehog protein (IHH) (Fragment)	0.01	-	nuc	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				58
P79866 UniProt NPD GO	IHH_RASHE	Indian hedgehog protein (IHH) (Fragment)	0.01	-	nuc	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				58
P79871 UniProt NPD GO	IHH_RASPA	Indian hedgehog protein (IHH) (Fragment)	0.01	-	nuc	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				58
Q41819 UniProt NPD GO	IAAG_MAIZE	Indole-3-acetate beta-glucosyltransferase (EC 2.4.1.121) (IAA-Glu synthetase) ((Uridine 5'-diphospha ...	0.01	-	mit	0					471
P32292 UniProt NPD GO	ARG2_PHAAU	Indole-3-acetic acid-induced protein ARG2	0.01	-	mit	0					99

You are viewing entries 89151 to 89200 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.