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
Q7ZTY4 UniProt NPD GO	RBBP7_BRARE	Histone-binding protein RBBP7 (Retinoblastoma-binding protein 7) (RBBP-7)	0.07	-	cyt	0					426
Q6P315 UniProt NPD GO	RBBP7_XENTR	Histone-binding protein RBBP7 (Retinoblastoma-binding protein 7) (RBBP-7)	0.07	-	cyt	0	Nucleus (By similarity)				425
Q9I8G9 UniProt NPD GO	RBBP7_CHICK	Histone-binding protein RBBP7 (Retinoblastoma-binding protein 7) (RBBP-7) (Retinoblastoma-binding pr ...	0.07	-	cyt	0	Nucleus (By similarity)	nucleus [ISS] NuRD complex [ISS]			424
Q8JHU0 UniProt NPD GO	HOP_CHICK	Homeodomain-only protein (Odd homeobox protein 1)	0.07	-	nuc	0	Nucleus (By similarity)				73
Q12449 UniProt NPD GO	AHA1_YEAST	Hsp90 co-chaperone AHA1 (Activator of Hsp90 ATPase protein 1)	0.07	-	cyt	0	Cytoplasm	cytoplasm [IPI]		1USV	350
Q29448 UniProt NPD GO	HMGCL_BOVIN	Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) (HMG-CoA lyase) (HL) (3-hydroxy-3-methylglutarate-CoA l ...	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix				140
Q8HXZ6 UniProt NPD GO	HMGCL_MACFA	Hydroxymethylglutaryl-CoA lyase, mitochondrial precursor (EC 4.1.3.4) (HMG-CoA lyase) (HL) (3-hydrox ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				325
O78424 UniProt NPD GO	YCF19_GUITH	Hypothetical 10.4 kDa protein ycf19	0.07	-	exc	2 *	Plastid; chloroplast				91
P39982 UniProt NPD GO	YEG9_YEAST	Hypothetical 11.3 kDa protein in SOM1-PCM1 intergenic region	0.07	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				102
P36153 UniProt NPD GO	YK53_YEAST	Hypothetical 12.0 kDa protein in SIS2-MTD1 intergenic region	0.07	-	end	2 *					106
P39977 UniProt NPD GO	YEH8_YEAST	Hypothetical 12.9 kDa protein in HXT13-CAN1 intergenic region	0.07	-	cyt	0					110
P38726 UniProt NPD GO	YHE5_YEAST	Hypothetical 13.3 kDa protein in CBP2 5'region	0.07	-	nuc	1 *					115
O96805 UniProt NPD GO	YCF35_SKECO	Hypothetical 15.1 kDa protein ycf35	0.07	-	nuc	0	Plastid; chloroplast				130
P53842 UniProt NPD GO	YN06_YEAST	Hypothetical 15.5 kDa protein in PIK1-POL2 intergenic region	0.07	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				139
P36128 UniProt NPD GO	YK13_YEAST	Hypothetical 15.7 kDa protein in SPO14-DAL80 intergenic region	0.07	-	end	1 *					141
P38322 UniProt NPD GO	YB76_YEAST	Hypothetical 15.8 kDa protein in FAT2-MCX1 intergenic region	0.07	-	cyt	0					136
P49829 UniProt NPD GO	YCF88_ODOSI	Hypothetical 17.4 kDa protein ycf88 (ORF148)	0.07	-	cyt	0	Plastid; chloroplast				148
P48327 UniProt NPD GO	YCF51_CYAPA	Hypothetical 18.2 kDa protein ycf51 (ORF163)	0.07	-	end	2 *	Plastid; cyanelle				163
O78458 UniProt NPD GO	YCF37_GUITH	Hypothetical 20.9 kDa protein ycf37	0.07	-	exc	1 *	Plastid; chloroplast				178
P15617 UniProt NPD GO	YM16_PARTE	Hypothetical 22.4 kDa protein (ORF16)	0.07	-	cyt	2					189
P36099 UniProt NPD GO	YKD0_YEAST	Hypothetical 23.0 kDa protein in IXR1-TFA1 intergenic region	0.07	-	end	3 *					201
Q9TLS5 UniProt NPD GO	YCF43_CYACA	Hypothetical 27.3 kDa protein ycf43	0.07	-	end	6 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				239
P10580 UniProt NPD GO	YMS4_MAIZE	Hypothetical 29 kDa protein in mitochondrial S-1 DNA (URF 4)	0.07	-	nuc	2					256
P58149 UniProt NPD GO	YCY4_ASTLO	Hypothetical 30.8 kDa protein in rpl12-rps7 intergenic region (ORF253)	0.07	-	vac	0	Plastid				253
P38690 UniProt NPD GO	YHJ3_YEAST	Hypothetical 46.9 kDa protein in SLT2-PUT2 intergenic region	0.07	-	nuc	0		cytoplasm [IDA]			423
P53098 UniProt NPD GO	YGT8_YEAST	Hypothetical 7.0 kDa protein in RPS26A-COX4 intergenic region	0.07	-	cyt	1 *					57
O14209 UniProt NPD GO	YDT4_SCHPO	Hypothetical aminotransferase C6B12.04c (EC 2.6.1.-)	0.07	-	mit	0	Cytoplasm (By similarity)				421
P93281 UniProt NPD GO	M120_ARATH	Hypothetical mitochondrial protein AtMg00120 (ORF143)	0.07	-	mit	0	Mitochondrion (Potential)				143
P92564 UniProt NPD GO	M1350_ARATH	Hypothetical mitochondrial protein AtMg01350 (ORF145c)	0.07	-	mit	1 *	Mitochondrion (Potential)				145
P34254 UniProt NPD GO	YKA2_CAEEL	Hypothetical protein B0303.2 in chromosome III	0.07	-	cyt	0					273
Q11095 UniProt NPD GO	YWZ5_CAEEL	Hypothetical protein C02B8.5	0.07	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				453
Q8IG57 UniProt NPD GO	YX0F_CAEEL	Hypothetical protein C03B1.15	0.07	-	cyt	0					137
Q10448 UniProt NPD GO	YDEF_SCHPO	Hypothetical protein C12B10.15c in chromosome I	0.07	-	nuc	0					147
Q10343 UniProt NPD GO	YL28_SCHPO	Hypothetical protein C1556.08c in chromosome I	0.07	-	nuc	0					334
Q09839 UniProt NPD GO	YAC1_SCHPO	Hypothetical protein C16C9.01c in chromosome I	0.07	-	cyt	0					361
Q09816 UniProt NPD GO	YAC2_SCHPO	Hypothetical protein C16C9.02c in chromosome I	0.07	-	cyt	0					307
O59681 UniProt NPD GO	YBS1_SCHPO	Hypothetical protein C18E5.01 in chromosome II	0.07	-	cyt	0					342
O42965 UniProt NPD GO	YGMH_SCHPO	Hypothetical protein C19G7.17 in chromosome II	0.07	-	end	9 *					475
Q10058 UniProt NPD GO	YAM3_SCHPO	Hypothetical protein C1F5.03c in chromosome I	0.07	-	mit	1 *	Membrane; multi-pass membrane protein (Potential)				382
Q9P7J0 UniProt NPD GO	YJNG_SCHPO	Hypothetical protein C24B10.16c in chromosome III	0.07	-	nuc	0					110
P90756 UniProt NPD GO	YE1J_CAEEL	Hypothetical protein C27A7.2	0.07	-	cyt	0					362
Q9VAF0 UniProt NPD GO	Y816_DROME	Hypothetical protein CG7816	0.07	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				355
P34377 UniProt NPD GO	YLM3_CAEEL	Hypothetical protein D2007.3	0.07	-	nuc	0					52
P34380 UniProt NPD GO	YLPA_CAEEL	Hypothetical protein F02A9.1 precursor	0.07	-	end	2 *					200
P34393 UniProt NPD GO	YLS8_CAEEL	Hypothetical protein F09G8.8 precursor	0.07	-	end	0					639
P46499 UniProt NPD GO	YLX3_CAEEL	Hypothetical protein F23F12.3	0.07	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				522
Q19978 UniProt NPD GO	YV6L_CAEEL	Hypothetical protein F32G8.4 in chromosome V	0.07	-	nuc	4 *	Membrane; multi-pass membrane protein (Potential)				405
P34493 UniProt NPD GO	YMQ2_CAEEL	Hypothetical protein K02D10.2	0.07	-	nuc	0					124
Q09606 UniProt NPD GO	YRN3_CAEEL	Hypothetical protein R07B1.3 in chromosome X	0.07	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				536
P82630 UniProt NPD GO	SCR11_ARATH	Hypothetical protein SCRL11 precursor	0.07	-	exc	0					86

You are viewing entries 70201 to 70250 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.