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
P51353 UniProt NPD GO	YCF19_PORPU	Hypothetical 10.8 kDa protein ycf19 (ORF95)	0.01	-	exc	2 *	Plastid; chloroplast				95
P34813 UniProt NPD GO	YCF20_AGLNE	Hypothetical 11.4 kDa protein ycf20	0.01	-	mit	3 *	Plastid; chloroplast				100
Q9TM18 UniProt NPD GO	YCF49_CYACA	Hypothetical 11.6 kDa protein ycf49	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				97
P40524 UniProt NPD GO	YIF4_YEAST	Hypothetical 12.0 kDa protein in SNP1-GPP1 intergenic region	0.01	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				105
P53161 UniProt NPD GO	YGH2_YEAST	Hypothetical 13.4 kDa protein in HSF1-AFT1 intergenic region	0.01	-	mit	2 *					119
P22371 UniProt NPD GO	YPC3_CLAPU	Hypothetical 13.8 kDa protein (ORF3)	0.01	-	exc	2 *	Membrane; peripheral membrane protein (Potential)				122
P15608 UniProt NPD GO	YM07_PARTE	Hypothetical 14.9 kDa protein (ORF7)	0.01	-	cyt	0					125
P38475 UniProt NPD GO	YMF33_MARPO	Hypothetical 15.6 kDa protein in ATPA-COX1 intergenic region (ORF 136)	0.01	-	cyt	0					136
P38240 UniProt NPD GO	YBR4_YEAST	Hypothetical 16.0 kDa protein in ORC2-TIP1 intergenic region	0.01	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				142
P53071 UniProt NPD GO	YGY5_YEAST	Hypothetical 19.3 kDa protein in HAP2-ADE5,6 intergenic region	0.01	-	cyt	0					178
P51192 UniProt NPD GO	YCF52_PORPU	Hypothetical 20.1 kDa protein ycf52 (ORF174)	0.01	-	cyt	0	Plastid; chloroplast				174
P51360 UniProt NPD GO	YCXM_PORPU	Hypothetical 23.3 kDa protein in rps6-thiG intergenic region (ORF203)	0.01	-	end	5 *	Plastid; chloroplast				203
P40103 UniProt NPD GO	YE18_YEAST	Hypothetical 27.3 kDa protein in ISC10 3'region	0.01	-	cyt	0					239
P49830 UniProt NPD GO	YCX4_ODOSI	Hypothetical 3.5 kDa protein in ycf33-trnY intergenic region (ORF29A)	0.01	-	vac	0	Plastid; chloroplast				29
P49838 UniProt NPD GO	YCXC_ODOSI	Hypothetical 3.7 kDa protein in psbV-trnM intergenic region (ORF29B)	0.01	-	cyt	0	Plastid; chloroplast				29
P47141 UniProt NPD GO	YJ71_YEAST	Hypothetical 30.2 kDa protein in YUH1-URA8 intergenic region	0.01	-	nuc	0		mitochondrial small ribosomal subunit [IDA]			266
P36151 UniProt NPD GO	YK50_YEAST	Hypothetical 39.4 kDa protein in MET1-SIS2 intergenic region	0.01	-	mit	0		mitochondrion [IDA]			352
P28625 UniProt NPD GO	YM27_YEAST	Hypothetical 41.6 kDa protein in IMP1-HLJ1 intergenic region (RF1095)	0.01	-	cyt	0		cytoplasm [IDA] lipid particle [IDA] mitochondrion [IDA]			365
Q32063 UniProt NPD GO	YCX8_CHLRE	Hypothetical 6.2 kDa protein in psaC-petL intergenic region (ORF58)	0.01	-	mit	0	Plastid; chloroplast				58
O78425 UniProt NPD GO	YCF17_GUITH	Hypothetical 6.2 kDa protein ycf17	0.01	-	mit	1 *	Plastid; chloroplast				53
Q32618 UniProt NPD GO	YCX1_MARPO	Hypothetical 6.4 kDa protein in atpA-psbA intergenic region (ORF50)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				50
O78517 UniProt NPD GO	YCF33_GUITH	Hypothetical 7.4 kDa protein ycf33	0.01	-	end	2 *	Plastid; chloroplast				65
P48273 UniProt NPD GO	YCF33_CYAPA	Hypothetical 7.6 kDa protein ycf33	0.01	-	end	2 *	Plastid; cyanelle				65
P51329 UniProt NPD GO	YCF33_PORPU	Hypothetical 7.7 kDa protein ycf33 (ORF67)	0.01	-	end	2 *	Plastid; chloroplast				67
P34781 UniProt NPD GO	YCX7_ASTLO	Hypothetical 9.2 kDa protein in rpl23-rpl2 intergenic region (ORF76)	0.01	-	mit	2 *	Plastid				76
P22376 UniProt NPD GO	YPA3_ASCIM	Hypothetical 9.8 kDa protein (ORF3)	0.01	-	mit	0					90
P38455 UniProt NPD GO	YMF07_MARPO	Hypothetical 9.9 kDa protein in ATPA-COX1 intergenic region (ORF 86B)	0.01	-	mit	2 *					86
Q18610 UniProt NPD GO	YYC5_CAEEL	Hypothetical UPF0017 protein C44C1.5 in chromosome X	0.01	-	mit	1 *					375
Q18161 UniProt NPD GO	YBPT_CAEEL	Hypothetical UPF0046 protein C25E10.12 in chromosome V	0.01	-	cyt	0					281
Q9M095 UniProt NPD GO	RC23_ARATH	Hypothetical UPF0057 protein At4g30650	0.01	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				73
Q9SUI0 UniProt NPD GO	RC24_ARATH	Hypothetical UPF0057 protein At4g30660	0.01	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				74
Q22702 UniProt NPD GO	YCU5_CAEEL	Hypothetical UPF0057 protein T23F2.5 in chromosome X	0.01	-	exc	1 *	Membrane; multi-pass membrane protein (Potential)				57
Q09674 UniProt NPD GO	YA01_SCHPO	Hypothetical UPF0317 protein C5H10.01 in chromosome I	0.01	-	nuc	0					301
Q8TGJ1 UniProt NPD GO	YO16A_YEAST	Hypothetical UPF0320 protein YOL166W-A	0.01	-	cyt	1 *					51
Q9URW1 UniProt NPD GO	YI81_SCHPO	Hypothetical UPF0321 protein PJ695.01c precursor	0.01	-	cyt	1 *					117
Q9N4K0 UniProt NPD GO	U327_CAEEL	Hypothetical UPF0327 protein F54A3.5	0.01	-	nuc	0					105
P02899 UniProt NPD GO	YKM2_TRYBB	Hypothetical kinetoplast minicircle 51 polypeptide	0.01	-	cyt	1 *					71
P93296 UniProt NPD GO	M370_ARATH	Hypothetical mitochondrial protein AtMg00370 (ORF199)	0.01	-	mit	4 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				199
O42896 UniProt NPD GO	YBQ3_SCHPO	Hypothetical oxidoreductase C115.03 (EC 1.-.-.-)	0.01	-	cyt	0					368
P0C0B0 UniProt NPD GO	Y1400_ARATH	Hypothetical protein At1g24000	0.01	-	cyt	0				1VJH	122
P41942 UniProt NPD GO	YKB4_CAEEL	Hypothetical protein B0272.4 in chromosome III	0.01	-	end	0	Peroxisome (Potential)				255
Q10942 UniProt NPD GO	YWS6_CAEEL	Hypothetical protein B0310.6	0.01	-	exc	0					95
Q8WZY3 UniProt NPD GO	YBG3_NEUCR	Hypothetical protein B24G3.190 precursor	0.01	-	exc	0					94
Q93169 UniProt NPD GO	YQJQ_CAEEL	Hypothetical protein C01G10.9	0.01	-	mit	0					366
P34282 UniProt NPD GO	YKK5_CAEEL	Hypothetical protein C02F5.5	0.01	-	end	3 *					173
Q11116 UniProt NPD GO	YX0A_CAEEL	Hypothetical protein C03B1.10	0.01	-	cyt	0					52
Q86DA7 UniProt NPD GO	YKO8_CAEEL	Hypothetical protein C05B5.8	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				177
P34296 UniProt NPD GO	YKQ1_CAEEL	Hypothetical protein C06E1.1	0.01	-	mit	2 *					161
Q09688 UniProt NPD GO	YA16_SCHPO	Hypothetical protein C13C5.06c precursor	0.01	-	exc	1 *					177
Q10153 UniProt NPD GO	YAT8_SCHPO	Hypothetical protein C1D4.08 in chromosome I	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				251

You are viewing entries 89051 to 89100 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.