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
P36089 UniProt NPD GO	YKG6_YEAST	Hypothetical 16.7 kDa protein in NDK1-MNR2 intergenic region	0.00	-	cyt	0					147
Q04767 UniProt NPD GO	YMW1_YEAST	Hypothetical 18.7 kDa protein in HMS1-ABF2 intergenic region	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	integral to Golgi membrane [IDA]			167
P15605 UniProt NPD GO	YM04_PARTE	Hypothetical 18.8 kDa protein (ORF4)	0.00	-	end	5 *					156
P38464 UniProt NPD GO	YMF21_MARPO	Hypothetical 20.3 kDa protein in NAD3-NAD7 intergenic region (ORF 180)	0.00	-	cyt	0					180
P53058 UniProt NPD GO	YGZC_YEAST	Hypothetical 22.2 kDa protein in ADH4 5'region	0.00	-	mit	0		soluble fraction [IDA]			206
P03883 UniProt NPD GO	YMCC_EMENI	Hypothetical 25.4 kDa protein in COX3 5'region (URF-C)	0.00	-	end	5 *	Mitochondrion				228
Q85BU5 UniProt NPD GO	YCX2_ANTFO	Hypothetical 3.0 kDa protein in psbT-psbN intergenic region (ORF27)	0.00	-	cyt	0	Plastid; chloroplast				27
P49834 UniProt NPD GO	YCX8_ODOSI	Hypothetical 3.1 kDa protein in psbJ-trnE intergenic region (ORF25)	0.00	-	cyt	0	Plastid; chloroplast				25
P49839 UniProt NPD GO	YCXD_ODOSI	Hypothetical 3.2 kDa protein in rpoC2-rps2 intergenic region (ORF26B)	0.00	-	cyt	0	Plastid; chloroplast				26
P48328 UniProt NPD GO	YCX7_CYAPA	Hypothetical 3.4 kDa protein in atpE-petA intergenic region (ORF27)	0.00	-	nuc	0	Plastid; cyanelle				27
P03884 UniProt NPD GO	YMCD_EMENI	Hypothetical 3.5 kDa protein in COX1 5'region (URF-D)	0.00	-	cyt	0					27
P38843 UniProt NPD GO	YHU2_YEAST	Hypothetical 34.9 kDa protein in RPL44B-RPC10 intergenic region	0.00	-	end	7	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum membrane [IDA]			316
Q04869 UniProt NPD GO	YM94_YEAST	Hypothetical 38.2 kDa protein in PRE5-FET4 intergenic region	0.00	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			349
P49831 UniProt NPD GO	YCX5_ODOSI	Hypothetical 4.7 kDa protein in ycf33-trnY intergenic region (ORF41)	0.00	-	cyt	0	Plastid; chloroplast				41
Q03102 UniProt NPD GO	YMN1_YEAST	Hypothetical 40.0 kDa protein in COX14-COS3 intergenic region	0.00	-	cyt	2	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA]			365
P51355 UniProt NPD GO	YCF17_PORPU	Hypothetical 5.5 kDa protein ycf17 (ORF48)	0.00	-	nuc	1 *	Plastid; chloroplast				48
Q85BV1 UniProt NPD GO	YCX1_ANTFO	Hypothetical 5.9 kDa protein in rps16-psbA intergenic region (ORF51)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				51
O78452 UniProt NPD GO	YCX4_GUITH	Hypothetical 6.1 kDa protein (ORF53)	0.00	-	cyt	0	Plastid; chloroplast				53
P38473 UniProt NPD GO	YMF31_MARPO	Hypothetical 6.8 kDa protein in COX3-NAD1 intergenic region (ORF 61)	0.00	-	cyt	0					61
P49532 UniProt NPD GO	YCF33_ODOSI	Hypothetical 7.6 kDa protein ycf33 (ORF64)	0.00	-	end	2 *	Plastid; chloroplast				64
P52807 UniProt NPD GO	YCF68_PINTH	Hypothetical 8.1 kDa protein ycf68 (ORF 75A)	0.00	-	cyt	0	Plastid; chloroplast				75
P51336 UniProt NPD GO	YCXI_PORPU	Hypothetical 8.3 kDa protein in rpl9-rpl11 intergenic region (ORF75)	0.00	-	cyt	0	Plastid; chloroplast				75
P38476 UniProt NPD GO	YMF34_MARPO	Hypothetical 8.5 kDa protein in ATPA-COX1 intergenic region (ORF 74)	0.00	-	nuc	0					74
Q04909 UniProt NPD GO	YM9B_YEAST	Hypothetical 9.0 kDa protein in ERR1 3'region	0.00	-	nuc	0					80
Q9FE70 UniProt NPD GO	RC21_ARATH	Hypothetical UPF0057 protein At1g57550	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				52
O82232 UniProt NPD GO	RC22_ARATH	Hypothetical UPF0057 protein At2g24040	0.00	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				75
Q17638 UniProt NPD GO	YAM5_CAEEL	Hypothetical UPF0057 protein C04G6.5 in chromosome II	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				59
Q20516 UniProt NPD GO	YV31_CAEEL	Hypothetical UPF0057 protein F47B7.1 in chromosome X	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				59
Q22700 UniProt NPD GO	YCU3_CAEEL	Hypothetical UPF0057 protein T23F2.3 in chromosome X	0.00	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				57
Q22701 UniProt NPD GO	YCU4_CAEEL	Hypothetical UPF0057 protein T23F2.4 in chromosome X	0.00	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				57
P34655 UniProt NPD GO	YOT0_CAEEL	Hypothetical UPF0057 protein ZK632.10 in chromosome III	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				80
Q9FG71 UniProt NPD GO	U172_ARATH	Hypothetical UPF0172 protein At5g55940	0.00	-	cyt	0					208
Q9Y7S1 UniProt NPD GO	YQO2_SCHPO	Hypothetical UPF0321 protein C569.02c precursor	0.00	-	vac	0					113
Q9HDT7 UniProt NPD GO	YJ52_SCHPO	Hypothetical UPF0321 protein P20C8.02c precursor	0.00	-	vac	0					111
P47145 UniProt NPD GO	YJ77_YEAST	Hypothetical lipase in SOD1-CPA2 intergenic region (EC 3.1.1.-)	0.00	-	cyt	0					328
P93316 UniProt NPD GO	M610_ARATH	Hypothetical mitochondrial protein AtMg00610 (ORF161)	0.00	-	end	5 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				161
Q22230 UniProt NPD GO	YVX3_CAEEL	Hypothetical oxidoreductase T05C12.3 (EC 1.-.-.-)	0.00	-	mit	0					309
Q23116 UniProt NPD GO	YWC4_CAEEL	Hypothetical oxidoreductase W01C9.4 (EC 1.-.-.-)	0.00	-	mit	0					309
O04658 UniProt NPD GO	Y5712_ARATH	Hypothetical protein At5g27120	0.00	-	cyt	0					439
Q11080 UniProt NPD GO	YT64_CAEEL	Hypothetical protein B0563.4 in chromosome X	0.00	-	end	6	Membrane; multi-pass membrane protein (Potential)				276
P61228 UniProt NPD GO	YKKB_CAEEL	Hypothetical protein C02F5.13	0.00	-	end	2					210
Q11104 UniProt NPD GO	YPB1_CAEEL	Hypothetical protein C03B8.1 precursor	0.00	-	cyt	1 *	Membrane; single-pass membrane protein (Potential)				105
Q11175 UniProt NPD GO	YOK2_CAEEL	Hypothetical protein C04F6.2	0.00	-	cyt	1					87
P34300 UniProt NPD GO	YKQ5_CAEEL	Hypothetical protein C06E1.5	0.00	-	mit	1 *					50
P34301 UniProt NPD GO	YKQ6_CAEEL	Hypothetical protein C06E1.6	0.00	-	cyt	1 *					49
Q9US42 UniProt NPD GO	YIZI_SCHPO	Hypothetical protein C1002.18 in chromosome I	0.00	-	cyt	0					399
O13732 UniProt NPD GO	YDOC_SCHPO	Hypothetical protein C15A10.12c in chromosome I	0.00	-	cyt	0					117
O13825 UniProt NPD GO	YEE9_SCHPO	Hypothetical protein C19A8.09 in chromosome I	0.00	-	exc	2 *	Membrane; multi-pass membrane protein (Potential)				81
Q09918 UniProt NPD GO	YAK6_SCHPO	Hypothetical protein C1F7.06 in chromosome I	0.00	-	cyt	0					251
Q10356 UniProt NPD GO	YDB3_SCHPO	Hypothetical protein C22E12.03c in chromosome I	0.00	-	nuc	0					191

You are viewing entries 95201 to 95250 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.