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
Q8NHY5 UniProt NPD GO	HUS1B_HUMAN	Checkpoint protein HUS1B (hHUS1B)	0.29	-	cyt	0			609713		278
P30601 UniProt NPD GO	CHS2_EXODE	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2) (Class-I chitin synth ...	0.29	-	end	9	Cell membrane; multi-pass membrane protein				928
P46876 UniProt NPD GO	CHI1_CANAL	Chitinase 1 precursor (EC 3.2.1.14)	0.29	-	exc	1 *	Secreted protein (Probable)				462
P51790 UniProt NPD GO	CLCN3_HUMAN	Chloride channel protein 3 (ClC-3)	0.29	-	end	11	Membrane; multi-pass membrane protein. Isoform 1 is localized mainly in early and late endosomes. Is ...	cell surface [NAS] early endosome [IDA] Golgi apparatus [IDA] integral to membrane [TAS] late endosome [IDA] vesicle membrane [IDA]	600580		762
O18894 UniProt NPD GO	CLCN3_RABIT	Chloride channel protein 3 (ClC-3)	0.29	-	end	11	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein (By similarity). End ...	cell surface [ISS] early endosome [ISS] Golgi apparatus [ISS] integral to membrane [ISS] late endosome [ISS] vesicle membrane [ISS]			760
P51795 UniProt NPD GO	CLCN5_HUMAN	Chloride channel protein 5 (ClC-5)	0.29	-	end	10	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	310468		746
Q9WVD4 UniProt NPD GO	CLCN5_MOUSE	Chloride channel protein 5 (ClC-5)	0.29	-	end	12	Membrane; multi-pass membrane protein				746
P51796 UniProt NPD GO	CLCN5_RAT	Chloride channel protein 5 (ClC-5)	0.29	-	end	12	Membrane; multi-pass membrane protein				746
Q8WQA4 UniProt NPD GO	EXC4_CAEEL	Chloride intracellular channel exc-4 (Excretory canal abnormal protein 4)	0.29	-	cyt	0	Cytoplasm. Membrane. Can be translocated to membranes, possibly as integral membrane proteins, with ...				290
P69655 UniProt NPD GO	RR11_ATRBE	Chloroplast 30S ribosomal protein S11	0.29	-	mit	0	Plastid; chloroplast				138
P27419 UniProt NPD GO	RR11_EUGGR	Chloroplast 30S ribosomal protein S11	0.29	+	nuc	0	Plastid; chloroplast				129
Q2MI68 UniProt NPD GO	RR11_LYCES	Chloroplast 30S ribosomal protein S11	0.29	-	nuc	0	Plastid; chloroplast				138
Q3C1M2 UniProt NPD GO	RR11_NICSY	Chloroplast 30S ribosomal protein S11	0.29	-	mit	0	Plastid; chloroplast				138
Q85WZ9 UniProt NPD GO	RR11_PINKO	Chloroplast 30S ribosomal protein S11	0.29	-	mit	0	Plastid; chloroplast				130
Q2MIF5 UniProt NPD GO	RR11_SOLBU	Chloroplast 30S ribosomal protein S11	0.29	-	nuc	0	Plastid; chloroplast				138
Q2VEE7 UniProt NPD GO	RR11_SOLTU	Chloroplast 30S ribosomal protein S11	0.29	-	nuc	0	Plastid; chloroplast				138
P69656 UniProt NPD GO	RR11_TOBAC	Chloroplast 30S ribosomal protein S11	0.29	-	mit	0	Plastid; chloroplast				138
Q85BW6 UniProt NPD GO	RR12_ANTFO	Chloroplast 30S ribosomal protein S12	0.29	-	mit	0	Plastid; chloroplast				123
Q9B133 UniProt NPD GO	RR12_LOTJA	Chloroplast 30S ribosomal protein S12	0.29	-	mit	0	Plastid; chloroplast				123
Q6YXM6 UniProt NPD GO	RR12_PHYPA	Chloroplast 30S ribosomal protein S12	0.29	-	nuc	0	Plastid; chloroplast				123
P30390 UniProt NPD GO	RR18_EUGGR	Chloroplast 30S ribosomal protein S18	0.29	-	nuc	0	Plastid; chloroplast				64
P08242 UniProt NPD GO	RR2_SPIOL	Chloroplast 30S ribosomal protein S2	0.29	-	cyt	0	Plastid; chloroplast				236
Q3V4Z5 UniProt NPD GO	RR3_ACOCL	Chloroplast 30S ribosomal protein S3	0.29	-	nuc	0	Plastid; chloroplast				218
Q70XX2 UniProt NPD GO	RR3_AMBTC	Chloroplast 30S ribosomal protein S3	0.29	-	mit	0	Plastid; chloroplast				218
Q33BZ3 UniProt NPD GO	RR3_NICTO	Chloroplast 30S ribosomal protein S3	0.29	-	cyt	0	Plastid; chloroplast				218
P16633 UniProt NPD GO	RK16_GRATE	Chloroplast 50S ribosomal protein L16	0.29	-	mit	0	Plastid; chloroplast				135
Q6B8W0 UniProt NPD GO	RK16_GRATL	Chloroplast 50S ribosomal protein L16	0.29	-	mit	0	Plastid; chloroplast				135
P06388 UniProt NPD GO	RK22_MARPO	Chloroplast 50S ribosomal protein L22	0.29	-	mit	0	Plastid; chloroplast				119
Q9MUU1 UniProt NPD GO	RK22_MESVI	Chloroplast 50S ribosomal protein L22	0.29	-	nuc	0	Plastid; chloroplast				119
O46902 UniProt NPD GO	RK29_GUITH	Chloroplast 50S ribosomal protein L29	0.29	-	nuc	0	Plastid; chloroplast				65
P31558 UniProt NPD GO	RK32_EUGGR	Chloroplast 50S ribosomal protein L32	0.29	-	nuc	0	Plastid; chloroplast				53
P15820 UniProt NPD GO	RK32_VICFA	Chloroplast 50S ribosomal protein L32	0.29	-	nuc	0	Plastid; chloroplast				48
Q5RJI2 UniProt NPD GO	CTL5_MOUSE	Choline transporter-like protein 5 (Solute carrier family 44 member 5)	0.29	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				710
P81908 UniProt NPD GO	CHLE_HORSE	Cholinesterase (EC 3.1.1.8) (Acylcholine acylhydrolase) (Choline esterase II) (Butyrylcholine estera ...	0.29	+	cyt	1 *					574
Q8BJQ9 UniProt NPD GO	CGAT1_MOUSE	Chondroitin beta-1,4-N-acetylgalactosaminyltransferase 1 (EC 2.4.1.174) (beta4GalNAcT-1)	0.29	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)	integral to Golgi membrane [ISS] intracellular [ISS] soluble fraction [ISS]			530
P34207 UniProt NPD GO	CSHV_RAT	Chorionic somatomammotropin hormone 1 variant precursor (Placental lactogen I variant) (PL-IV)	0.29	-	cyt	0	Secreted protein				223
Q6FJ46 UniProt NPD GO	EAF6_CANGA	Chromatin modification-related protein EAF6	0.29	-	nuc	0	Nucleus (By similarity)				91
P83516 UniProt NPD GO	IXCI_BOOMI	Chymotrypsin-elastase inhibitor ixodidin	0.29	-	mit	0					65
Q9N9X3 UniProt NPD GO	CTX80_EUPOC	Ciliary WD repeat-containing protein ctxp80	0.29	-	cyt	0					716
P26441 UniProt NPD GO	CNTF_HUMAN	Ciliary neurotrophic factor (CNTF)	0.29	-	cyt	0	Cytoplasm		118945	1CNT	200
Q28GR1 UniProt NPD GO	CCD72_XENTR	Coiled-coil domain-containing protein 72	0.29	-	nuc	0					64
P17139 UniProt NPD GO	CO4A1_CAEEL	Collagen alpha-1(IV) chain precursor	0.29	-	mit	0		basement membrane [IDA]			1759
P70560 UniProt NPD GO	COCA1_RAT	Collagen alpha-1(XII) chain (Fragment)	0.29	-	nuc	0		collagen type XII [IDA]			317
O42350 UniProt NPD GO	CO1A2_RANCA	Collagen alpha-2(I) chain precursor	0.29	-	nuc	0					1355
Q28084 UniProt NPD GO	CO4A3_BOVIN	Collagen alpha-3(IV) chain (Fragment)	0.29	-	nuc	0	Cell surface (Potential)	collagen type IV [ISS]			471
Q28247 UniProt NPD GO	CO4A5_CANFA	Collagen alpha-5(IV) chain precursor	0.29	-	exc	0	Cell surface (Potential)				1691
Q8R066 UniProt NPD GO	C1QT4_MOUSE	Complement C1q tumor necrosis factor-related protein 4 precursor	0.29	-	end	0	Secreted protein (Potential)				326
Q3MHN2 UniProt NPD GO	CO9_BOVIN	Complement component C9 precursor	0.29	-	exc	0	Secreted protein				548
Q5R4W6 UniProt NPD GO	CPNE6_PONPY	Copine-6 (Copine VI)	0.29	-	cyt	0					557
Q02874 UniProt NPD GO	H2AY_RAT	Core histone macro-H2A.1 (Histone macroH2A1) (mH2A1) (H2A.y) (H2A/y)	0.29	+	mit	0	Nucleus. Enriched in inactive X chromosome chromatin and in senescence-associated heterochromatin (B ...	nucleosome [IDA]		1YD9	370

You are viewing entries 41101 to 41150 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.