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
Q9MTM9 UniProt NPD GO	YCX7_OENHO	Hypothetical 5.4 kDa protein in trnY-trnD intergenic region (ORF50)	0.06	-	nuc	0	Plastid; chloroplast				50
Q9MTN0 UniProt NPD GO	YCX6_OENHO	Hypothetical 6.9 kDa protein in psbD-trnT intergenic region (ORF59a)	0.06	-	mit	1 *	Plastid; chloroplast				59
P38474 UniProt NPD GO	YMF32_MARPO	Hypothetical 7.2 kDa protein in ATPA-COX1 intergenic region (ORF 62)	0.06	-	cyt	0					62
O78445 UniProt NPD GO	YCF20_GUITH	Hypothetical 7.2 kDa protein ycf20	0.06	-	end	2 *	Plastid; chloroplast				64
Q9MUR2 UniProt NPD GO	YCX4_MESVI	Hypothetical 8.1 kDa protein in ndhF-psbD intergenic region	0.06	-	end	2 *	Plastid; chloroplast				71
P40437 UniProt NPD GO	YIR4_YEAST	Hypothetical 8.6 kDa protein in SDL1 5'region	0.06	-	nuc	0					75
P93319 UniProt NPD GO	M670_ARATH	Hypothetical mitochondrial protein AtMg00670 (ORF275)	0.06	-	end	3 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				275
O22288 UniProt NPD GO	Y2979_ARATH	Hypothetical protein At2g39790, mitochondrial precursor	0.06	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				240
P41998 UniProt NPD GO	YKC7_CAEEL	Hypothetical protein B0280.7	0.06	-	mit	0					344
Q10952 UniProt NPD GO	YMP9_CAEEL	Hypothetical protein B0361.9 precursor	0.06	-	vac	0					194
P34272 UniProt NPD GO	YKH4_CAEEL	Hypothetical protein C02C2.4 in chromosome III	0.06	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				568
P34306 UniProt NPD GO	YKQA_CAEEL	Hypothetical protein C06E1.11	0.06	-	cyt	3					371
Q10082 UniProt NPD GO	YAO3_SCHPO	Hypothetical protein C11D3.03c in chromosome I	0.06	-	cyt	0					302
Q09902 UniProt NPD GO	YAJ2_SCHPO	Hypothetical protein C30D11.02c in chromosome I	0.06	-	nuc	0					85
P87173 UniProt NPD GO	YB18_SCHPO	Hypothetical protein C3D6.08c in chromosome II	0.06	-	cyt	0	Nucleus (Potential)				140
Q10079 UniProt NPD GO	YANE_SCHPO	Hypothetical protein C3H1.14 in chromosome I	0.06	-	mit	0					195
Q09503 UniProt NPD GO	YQI1_CAEEL	Hypothetical protein C45G9.1	0.06	-	cyt	0					290
Q8ST35 UniProt NPD GO	Y202_ENCCU	Hypothetical protein ECU02_0020/ECU04_1700	0.06	-	end	7 *					261
Q20256 UniProt NPD GO	YPX2_CAEEL	Hypothetical protein F40H6.2	0.06	-	cyt	0					997
Q21018 UniProt NPD GO	YMI3_CAEEL	Hypothetical protein F59A2.3, mitochondrial precursor	0.06	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				236
Q09419 UniProt NPD GO	YRN5_CAEEL	Hypothetical protein R07B1.5 precursor	0.06	-	mit	0					160
Q09609 UniProt NPD GO	YRN9_CAEEL	Hypothetical protein R07B1.9	0.06	-	end	15 *					770
P82635 UniProt NPD GO	SCR16_ARATH	Hypothetical protein SCRL16 precursor	0.06	-	nuc	1 *					87
Q09360 UniProt NPD GO	YS12_CAEEL	Hypothetical protein ZK1307.2	0.06	-	end	0					127
P30653 UniProt NPD GO	YOW7_CAEEL	Hypothetical protein ZK643.7	0.06	-	cyt	0					109
P03935 UniProt NPD GO	Y122_CAEEL	Hypothetical protein from transposable element Tc1	0.06	-	mit	0					112
Q9Y7N5 UniProt NPD GO	WTF16_SCHPO	Hypothetical protein wtf16	0.06	-	end	6	Membrane; multi-pass membrane protein (Potential)				349
Q7Z091 UniProt NPD GO	CXI8_CONRA	I-superfamily conotoxin R11.8 (r11d)	0.06	-	nuc	0	Secreted protein				41
Q7YZS9 UniProt NPD GO	CXI_CONVR	I-superfamily conotoxin ViTx precursor	0.06	-	vac	1 *	Secreted protein				67
P69500 UniProt NPD GO	CXI1_CONVX	I-superfamily conotoxin-1 precursor	0.06	-	exc	1 *	Secreted protein (By similarity)				67
P54968 UniProt NPD GO	ILR1_ARATH	IAA-amino acid hydrolase ILR1 precursor (EC 3.5.1.-)	0.06	-	cyt	0					442
P02734 UniProt NPD GO	ANP4_PSEAM	Ice-structuring protein 4 precursor (ISP 4) (Antifreeze peptide 4)	0.06	-	cyt	0					85
P20760 UniProt NPD GO	GCA_RAT	Ig gamma-2A chain C region	0.06	-	nuc	0				1I1C	322
P01822 UniProt NPD GO	HV46_MOUSE	Ig heavy chain V region MOPC 315 precursor	0.06	-	vac	0					137
P01755 UniProt NPD GO	HV11_MOUSE	Ig heavy chain V region S43 precursor	0.06	-	vac	0					137
P01771 UniProt NPD GO	HV3J_HUMAN	Ig heavy chain V-III region HIL	0.06	-	cyt	0		extracellular region [NAS]			121
P01684 UniProt NPD GO	KV03_RABIT	Ig kappa chain V region 3374	0.06	-	cyt	0					109
P01685 UniProt NPD GO	KV04_RABIT	Ig kappa chain V region 4135	0.06	-	cyt	0					107
P01688 UniProt NPD GO	KV07_RABIT	Ig kappa chain V region K-25	0.06	-	cyt	0					108
Q9SZ30 UniProt NPD GO	HIS5_ARATH	Imidazole glycerol phosphate synthase hisHF, chloroplast precursor (IGP synthase) (ImGP synthase) (I ...	0.06	-	mit	0	Plastid; chloroplast				592
P32295 UniProt NPD GO	ARG7_PHAAU	Indole-3-acetic acid-induced protein ARG7	0.06	-	mit	0					92
P49572 UniProt NPD GO	TRPC_ARATH	Indole-3-glycerol phosphate synthase, chloroplast precursor (EC 4.1.1.48) (IGPS)	0.06	-	nuc	0	Plastid; chloroplast (Probable)				402
P81905 UniProt NPD GO	ISP1_GALME	Inducible serine protease inhibitor 1 (ISPI-1) (Fragment)	0.06	-	nuc	0					50
Q9XYN0 UniProt NPD GO	INX1_SCHAM	Innexin inx1 (Innexin-1) (G-Inx1)	0.06	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				361
Q9V3W6 UniProt NPD GO	INX7_DROME	Innexin inx7 (Innexin-7) (Gap junction protein prp7) (Pas-related protein 7)	0.06	-	nuc	4 *	Membrane; multi-pass membrane protein (Potential)	gap junction [IEP] integral to membrane [NAS]			438
Q96303 UniProt NPD GO	PHT14_ARATH	Inorganic phosphate transporter 1-4 (AtPht1;4) (H(+)/Pi cotransporter)	0.06	-	end	11 *	Cell membrane; multi-pass membrane protein (Probable)				534
Q8GYF4 UniProt NPD GO	PHT15_ARATH	Inorganic phosphate transporter 1-5 (AtPht1;5) (H(+)/Pi cotransporter)	0.06	-	end	10 *	Membrane; multi-pass membrane protein (By similarity)				542
O14732 UniProt NPD GO	IMPA2_HUMAN	Inositol monophosphatase 2 (EC 3.1.3.25) (IMPase 2) (IMP 2) (Inositol-1(or 4)-monophosphatase 2) (My ...	0.06	-	cyt	0			605922	2FVZ	288
Q6FQI1 UniProt NPD GO	INO1_CANGA	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.06	-	nuc	0	Cytoplasm (By similarity)				538
Q75EW5 UniProt NPD GO	IPK1_ASHGO	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.06	-	cyt	0	Nucleus (By similarity)				278

You are viewing entries 72301 to 72350 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.