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
O78500 UniProt NPD GO	YCF47_GUITH	Hypothetical 7.8 kDa protein ycf47	0.02	-	nuc	2 *	Plastid; chloroplast				68
P51274 UniProt NPD GO	YCF47_PORPU	Hypothetical 8.2 kDa protein ycf47 (ORF71)	0.02	-	end	2 *	Plastid; chloroplast				71
Q9W1K0 UniProt NPD GO	U136_DROME	Hypothetical UPF0136 protein CG5532	0.02	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				112
P87304 UniProt NPD GO	YB22_SCHPO	Hypothetical UPF0152 protein C31F10.02 in chromosome II	0.02	-	cyt	0					161
Q9HFF0 UniProt NPD GO	YLS3_SCHPO	Hypothetical UPF0327 protein PJ691.03	0.02	-	mit	1 *					86
P05471 UniProt NPD GO	YKP5_KLULA	Hypothetical killer plasmid pGKl-2 protein 5	0.02	-	cyt	0					158
P02900 UniProt NPD GO	YKM1_TRYBB	Hypothetical kinetoplast minicircle 201 polypeptide	0.02	-	cyt	1 *					53
P93304 UniProt NPD GO	M490_ARATH	Hypothetical mitochondrial protein AtMg00490 (ORF107c)	0.02	-	nuc	0	Mitochondrion				107
P92512 UniProt NPD GO	M710_ARATH	Hypothetical mitochondrial protein AtMg00710 (ORF120)	0.02	-	nuc	0	Mitochondrion (Potential)				120
P92523 UniProt NPD GO	M860_ARATH	Hypothetical mitochondrial protein AtMg00860 (ORF158)	0.02	-	cyt	0	Mitochondrion (Potential)				158
P92530 UniProt NPD GO	M940_ARATH	Hypothetical mitochondrial protein AtMg00940 (ORF164)	0.02	-	cyt	0	Mitochondrion (Potential)				164
Q11073 UniProt NPD GO	YT45_CAEEL	Hypothetical protein B0416.5	0.02	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				507
Q11074 UniProt NPD GO	YT47_CAEEL	Hypothetical protein B0416.7	0.02	-	mit	0					132
Q09745 UniProt NPD GO	YB64_SCHPO	Hypothetical protein C12C2.04 in chromosome II	0.02	-	cyt	0					384
Q10224 UniProt NPD GO	YAZ3_SCHPO	Hypothetical protein C13D6.03c in chromosome I	0.02	-	cyt	0					228
O13767 UniProt NPD GO	YE95_SCHPO	Hypothetical protein C17A5.05c in chromosome I	0.02	-	mit	0					247
Q09714 UniProt NPD GO	YA38_SCHPO	Hypothetical protein C18B11.08c in chromosome I	0.02	-	cyt	2 *					95
Q10112 UniProt NPD GO	YAQD_SCHPO	Hypothetical protein C18G6.13 in chromosome I	0.02	-	cyt	0					114
Q10352 UniProt NPD GO	YDAA_SCHPO	Hypothetical protein C1F12.10c in chromosome I	0.02	-	nuc	0					147
Q09921 UniProt NPD GO	YAKA_SCHPO	Hypothetical protein C1F7.10 in chromosome I	0.02	-	cyt	0					238
Q10163 UniProt NPD GO	YAU8_SCHPO	Hypothetical protein C26A3.08 in chromosome I	0.02	-	cyt	0					147
Q8J1M7 UniProt NPD GO	YJ8J_SCHPO	Hypothetical protein C330.19c in chromosome III	0.02	-	cyt	1 *					90
Q03567 UniProt NPD GO	YLD2_CAEEL	Hypothetical protein C38C10.2 in chromosome III	0.02	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				493
P34361 UniProt NPD GO	YLH7_CAEEL	Hypothetical protein C48B4.7	0.02	-	end	4 *					159
Q10244 UniProt NPD GO	YD1E_SCHPO	Hypothetical protein C4G9.14 in chromosome I	0.02	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				221
P87054 UniProt NPD GO	YDJ6_SCHPO	Hypothetical protein C57A10.06 in chromosome I	0.02	-	nuc	0					133
Q9P7Z3 UniProt NPD GO	YHRE_SCHPO	Hypothetical protein C839.14c in chromosome II	0.02	-	nuc	0					238
Q9UT21 UniProt NPD GO	YFY7_SCHPO	Hypothetical protein C9.07c in chromosome I	0.02	-	mit	0					366
Q8ST79 UniProt NPD GO	Y106_ENCCU	Hypothetical protein ECU01_0060/ECU01_1550/ECU02_1580/ECU04_0070/ ECU08_2110	0.02	-	nuc	0					101
Q8SW19 UniProt NPD GO	Y3B4_ENCCU	Hypothetical protein ECU03_1140	0.02	-	mit	0					117
Q8SV56 UniProt NPD GO	Y702_ENCCU	Hypothetical protein ECU07_0020	0.02	-	nuc	0					101
Q8SV55 UniProt NPD GO	Y706_ENCCU	Hypothetical protein ECU07_0060	0.02	-	end	7 *					258
Q8STD6 UniProt NPD GO	Y7I8_ENCCU	Hypothetical protein ECU07_1880/ECU10_0020	0.02	-	cyt	0					211
Q09944 UniProt NPD GO	YSH2_CAEEL	Hypothetical protein F12A10.2	0.02	-	cyt	0					160
P34406 UniProt NPD GO	YLW3_CAEEL	Hypothetical protein F22B7.3	0.02	-	cyt	0					99
Q09318 UniProt NPD GO	YQY2_CAEEL	Hypothetical protein F36G3.2	0.02	-	cyt	0					313
Q9GQ63 UniProt NPD GO	YL59_CAEEL	Hypothetical protein F44E2.9	0.02	-	mit	0					122
P34444 UniProt NPD GO	YL86_CAEEL	Hypothetical protein F54C8.6	0.02	-	end	2					265
Q09411 UniProt NPD GO	YRJ5_CAEEL	Hypothetical protein K10D2.5	0.02	-	nuc	1 *					118
Q09412 UniProt NPD GO	YRJ7_CAEEL	Hypothetical protein K10D2.7	0.02	-	mit	0					84
O45686 UniProt NPD GO	YEC2_CAEEL	Hypothetical protein K11D2.2 precursor	0.02	-	end	0					393
Q09420 UniProt NPD GO	YRN6_CAEEL	Hypothetical protein R07B1.6	0.02	-	mit	0					136
Q21984 UniProt NPD GO	YNQ8_CAEEL	Hypothetical protein R13F6.8 precursor	0.02	-	exc	0					211
Q10000 UniProt NPD GO	YRR6_CAEEL	Hypothetical protein R144.6	0.02	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				345
P82634 UniProt NPD GO	SCR15_ARATH	Hypothetical protein SCRL15 precursor	0.02	-	mit	0					101
P82628 UniProt NPD GO	SCRL9_ARATH	Hypothetical protein SCRL9 precursor	0.02	-	exc	0					90
Q10011 UniProt NPD GO	YSV5_CAEEL	Hypothetical protein T19C3.5 precursor	0.02	-	vac	0					489
O14082 UniProt NPD GO	YEAH_SCHPO	Hypothetical protein UNK4.17 in chromosome I	0.02	-	nuc	0					405
Q09342 UniProt NPD GO	YR25_CAEEL	Hypothetical protein W02B3.5	0.02	-	mit	0					181
Q02334 UniProt NPD GO	YOL7_CAEEL	Hypothetical protein ZK370.7 in chromosome III	0.02	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				355

You are viewing entries 83951 to 84000 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.