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
Q09953 UniProt NPD GO	YSR5_CAEEL	Hypothetical protein F59B10.5 precursor	0.08	-	vac	0					96
Q9HDW4 UniProt NPD GO	YFW7_SCHPO	Hypothetical protein PB2B4.07 in chromosome I	0.08	-	nuc	0					239
P34583 UniProt NPD GO	YN24_CAEEL	Hypothetical protein T26G10.4	0.08	-	cyt	0					347
P34590 UniProt NPD GO	YN56_CAEEL	Hypothetical protein ZC21.6	0.08	-	end	6 *					306
Q09338 UniProt NPD GO	YOFB_CAEEL	Hypothetical protein ZK1290.11	0.08	-	cyt	0					141
P30639 UniProt NPD GO	YOU3_CAEEL	Hypothetical protein ZK637.3	0.08	-	end	1					599
Q8I0G4 UniProt NPD GO	YO44_CAEEL	Hypothetical protein ZK757.4	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				403
P25600 UniProt NPD GO	YCH4_YEAST	Hypothetical transposon Ty5-1 protein YCL074W	0.08	-	cyt	0					308
Q9US12 UniProt NPD GO	YK66_SCHPO	Hypothetical zinc metalloproteinase C607.06c (EC 3.4.24.-)	0.08	-	cyt	0					612
Q7Z097 UniProt NPD GO	CXI18_CONRA	I-superfamily conotoxin R11.18 precursor (Fragment)	0.08	-	nuc	0	Secreted protein				46
P54969 UniProt NPD GO	ILL1_ARATH	IAA-amino acid hydrolase ILR1-like 1 precursor (EC 3.5.1.-)	0.08	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				438
O75144 UniProt NPD GO	ICOSL_HUMAN	ICOS ligand precursor (B7 homolog 2) (B7-H2) (B7-like protein Gl50) (B7-related protein 1) (B7RP-1) ...	0.08	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	integral to membrane [NAS]	605717		302
P11920 UniProt NPD GO	ANP7_ELEGR	Ice-structuring glycoprotein 7R (ISGP 7R) (Antifreeze glycoprotein 7R)	0.08	-		0					19
P11921 UniProt NPD GO	ANP8_ELEGR	Ice-structuring glycoprotein 8R (ISGP 8R) (Antifreeze glycoprotein 8R)	0.08	-		0					16
P24856 UniProt NPD GO	ANP_NOTCO	Ice-structuring glycoprotein precursor (ISGP) (Antifreeze glycopeptide polyprotein) (AFGP polyprotei ...	0.08	-	mit	22 *	Secreted protein				790
P20759 UniProt NPD GO	GC1_RAT	Ig gamma-1 chain C region	0.08	-	nuc	0				2FRT	326
P01865 UniProt NPD GO	GCAM_MOUSE	Ig gamma-2A chain C region, membrane-bound form	0.08	-	mit	1		immunoglobulin complex, circulating [IDA] multivesicular body [IDA]		1YEE	398
P84751 UniProt NPD GO	HVCM5_MOUSE	Ig heavy chain Mem5 (Fragment)	0.08	-	nuc	0	Secreted protein			1ZAN	237
P18528 UniProt NPD GO	HV57_MOUSE	Ig heavy chain V region 6.96	0.08	-	cyt	0					98
P01820 UniProt NPD GO	HV44_MOUSE	Ig heavy chain V region PJ14 precursor	0.08	-	exc	0				43CA	115
P01809 UniProt NPD GO	HV39_MOUSE	Ig heavy chain V region X24	0.08	-	cyt	0					118
P01817 UniProt NPD GO	HV2D_HUMAN	Ig heavy chain V-II region MCE	0.08	-	mit	0		extracellular region [NAS]			125
P01627 UniProt NPD GO	KV2B_MOUSE	Ig kappa chain V-II region VKappa167 precursor	0.08	-	exc	0					120
P01634 UniProt NPD GO	KV5B_MOUSE	Ig kappa chain V-V region MOPC 21 precursor	0.08	-	vac	1 *				1IGC	136
P01701 UniProt NPD GO	LV1C_HUMAN	Ig lambda chain V-I region NEW	0.08	-	nuc	0		extracellular region [NAS]			111
P01718 UniProt NPD GO	LV4D_HUMAN	Ig lambda chain V-IV region Kern	0.08	-	nuc	0		extracellular region [NAS]			106
P11272 UniProt NPD GO	KAC_RANCA	Ig light chain C region	0.08	-	nuc	0					108
P55899 UniProt NPD GO	FCGRN_HUMAN	IgG receptor FcRn large subunit p51 precursor (FcRn) (Neonatal Fc receptor) (IgG Fc fragment recepto ...	0.08	-	end	1	Membrane; single-pass type I membrane protein (By similarity)		601437	1EXU	365
P34041 UniProt NPD GO	HIS7_TRIHA	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.08	-	mit	0					208
Q9Z1P3 UniProt NPD GO	MCL1_RAT	Induced myeloid leukemia cell differentiation protein Mcl-1 homolog	0.08	-	nuc	1	Membrane; single-pass membrane protein (By similarity). Cytoplasm (By similarity). Mitochondrion (By ...				330
Q23593 UniProt NPD GO	INX8_CAEEL	Innexin-8	0.08	-	end	5 *	Membrane; multi-pass membrane protein				382
Q9D892 UniProt NPD GO	ITPA_MOUSE	Inosine triphosphate pyrophosphatase (EC 3.6.1.19) (ITPase) (Inosine triphosphatase)	0.08	-	cyt	0	Cytoplasm (By similarity)				198
P47996 UniProt NPD GO	IMDH1_ARATH	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) (IMP dehydrogenase) (IMPDH) (IMPD)	0.08	-	cyt	0					503
O14344 UniProt NPD GO	IMDH_SCHPO	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) (IMP dehydrogenase) (IMPDH) (IMPD)	0.08	-	cyt	0					524
P38697 UniProt NPD GO	IMDH2_YEAST	Inosine-5'-monophosphate dehydrogenase IMD2 (EC 1.1.1.205) (IMP dehydrogenase) (IMPDH) (IMPD)	0.08	-	mit	0		cytoplasm [IDA]			523
P42803 UniProt NPD GO	INO1_SPIPO	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.08	-	nuc	0	Cytoplasm (Potential)				510
Q17231 UniProt NPD GO	SIX3_MESMA	Insect toxin 3 precursor (Fragment)	0.08	-	nuc	0	Secreted protein				64
P59368 UniProt NPD GO	TX461_PHONI	Insecticidal neurotoxin Tx4(6-1) precursor	0.08	-	exc	0	Secreted protein				82
P60270 UniProt NPD GO	SCXS_BUTEU	Insectotoxin-I5 (BeI5)	0.08	-	nuc	0	Secreted protein				35
P15222 UniProt NPD GO	SCX5_BUTEU	Insectotoxin-I5A	0.08	-	nuc	0	Secreted protein			1SIS	35
P30406 UniProt NPD GO	INS_MACFA	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.08	-	exc	0	Secreted protein				110
P01342 UniProt NPD GO	INS_MYXGL	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.08	-	vac	0	Secreted protein				115
P01311 UniProt NPD GO	INS_RABIT	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.08	-	exc	0	Secreted protein				110
P01326 UniProt NPD GO	INS2_MOUSE	Insulin-2 precursor [Contains: Insulin-2 B chain; Insulin-2 A chain]	0.08	-	exc	0	Secreted protein	nucleus [IDA] small nucleolar ribonucleoprotein complex [IDA]			110
P51458 UniProt NPD GO	IGF1_HORSE	Insulin-like growth factor I precursor (IGF-I) (Somatomedin) (Fragment)	0.08	-	nuc	0	Secreted protein				122
Q90WX8 UniProt NPD GO	IGF3_XENLA	Insulin-like growth factor III precursor (IGF-III) (Insulin-like growth factor 3) (xIGF-3)	0.08	-	mit	0	Secreted protein (By similarity)				127
Q3T0P7 UniProt NPD GO	ITM2B_BOVIN	Integral membrane protein 2B	0.08	-	mit	1	Membrane; single-pass type II membrane protein (Potential)				266
Q8WWU7 UniProt NPD GO	ITLN2_HUMAN	Intelectin-2 precursor (Endothelial lectin HL-2)	0.08	-	exc	1 *	Secreted protein (Potential)		609874		325
P32942 UniProt NPD GO	ICAM3_HUMAN	Intercellular adhesion molecule 3 precursor (ICAM-3) (ICAM-R) (CDw50) (CD50 antigen)	0.08	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [NAS]	146631	1T0P	547
Q9VG73 UniProt NPD GO	ILF2_DROME	Interleukin enhancer-binding factor 2 homolog	0.08	-	mit	0	Nucleus (By similarity)	nucleolus [ISS] nucleus [ISS]			396

You are viewing entries 68251 to 68300 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.