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
P53856 UniProt NPD GO	YNX5_YEAST	Hypothetical 16.2 kDa protein in SIN4-BNI4 intergenic region	0.10	-	nuc	1					143
P43537 UniProt NPD GO	YFG7_YEAST	Hypothetical 16.5 kDa protein in COS4 5'region	0.10	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				175
P38730 UniProt NPD GO	YHE1_YEAST	Hypothetical 17.6 kDa protein in CBP2 5'region	0.10	-	mit	1 *					149
P46991 UniProt NPD GO	YJR5_YEAST	Hypothetical 17.7 kDa protein in SWI3-KRE9 intergenic region	0.10	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				170
P38452 UniProt NPD GO	YMF03_MARPO	Hypothetical 19.3 kDa protein in RPS2 3'region (ORF 169)	0.10	-	end	3 *					169
P14759 UniProt NPD GO	YCY6_ASTLO	Hypothetical 20.3 kDa protein in rpl12-rps7 intergenic region (ORF167)	0.10	-	cyt	1	Plastid				167
P53084 UniProt NPD GO	YGW8_YEAST	Hypothetical 24.2 kDa protein in NIF3-CLG1 intergenic region	0.10	-	mit	0					216
P48323 UniProt NPD GO	YCX1_CYAPA	Hypothetical 24.3 kDa protein in hemA-psbN intergenic region (ORF206)	0.10	-	mit	0	Plastid; cyanelle				206
P36069 UniProt NPD GO	YKM8_YEAST	Hypothetical 33.8 kDa protein in MYO3-PGM1 intergenic region	0.10	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			295
P31954 UniProt NPD GO	YCX2_PAVLU	Hypothetical 4.8 kDa protein in secA 3'region	0.10	-	nuc	0	Plastid; chloroplast				42
Q04658 UniProt NPD GO	YMG6_YEAST	Hypothetical 40.9 kDa protein in DAK1-ORC1 intergenic region	0.10	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				369
Q9MUM7 UniProt NPD GO	YCX5_MESVI	Hypothetical 8.0 kDa protein in ndhF-psbD intergenic region	0.10	-	mit	0	Plastid; chloroplast				70
P51344 UniProt NPD GO	YCF40_PORPU	Hypothetical 8.1 kDa protein ycf40 (ORF71)	0.10	-	cyt	0	Plastid; chloroplast				71
P53821 UniProt NPD GO	YN77_YEAST	Hypothetical UPF0320 protein YNL337W	0.10	-	nuc	0					84
P05474 UniProt NPD GO	YKP8_KLULA	Hypothetical killer plasmid pGKl-2 protein 8	0.10	-	nuc	0					95
P92515 UniProt NPD GO	M740_ARATH	Hypothetical mitochondrial protein AtMg00740 (ORF100a)	0.10	-	cyt	0	Mitochondrion (Potential)				100
P92518 UniProt NPD GO	M770_ARATH	Hypothetical mitochondrial protein AtMg00770 (ORF100b)	0.10	-	nuc	0	Mitochondrion (Potential)				100
Q11185 UniProt NPD GO	YPD5_CAEEL	Hypothetical protein C05D11.5 in chromosome III	0.10	-	cyt	0					262
O13725 UniProt NPD GO	YDO5_SCHPO	Hypothetical protein C15A10.05c in chromosome I	0.10	-	nuc	0					242
Q10314 UniProt NPD GO	YD62_SCHPO	Hypothetical protein C17G8.02 in chromosome I	0.10	-	mit	0					330
Q09709 UniProt NPD GO	YA32_SCHPO	Hypothetical protein C18B11.02c in chromosome I	0.10	-	mit	0					394
Q09893 UniProt NPD GO	YAI5_SCHPO	Hypothetical protein C24B11.05 in chromosome I	0.10	-	cyt	0					226
O43018 UniProt NPD GO	YGV4_SCHPO	Hypothetical protein C354.04 in chromosome II	0.10	-	cyt	1					163
O74949 UniProt NPD GO	YJBC_SCHPO	Hypothetical protein C553.12c in chromosome III	0.10	-	end	10	Membrane; multi-pass membrane protein (Potential)				521
Q10255 UniProt NPD GO	YD27_SCHPO	Hypothetical protein C56F8.07 in chromosome I	0.10	-	nuc	3 *	Membrane; multi-pass membrane protein (Potential)				507
Q8ST40 UniProt NPD GO	Y704_ENCCU	Hypothetical protein ECU07_0040/ECU09_2030	0.10	-	end	7 *					268
Q09308 UniProt NPD GO	YQR5_CAEEL	Hypothetical protein F19C6.5	0.10	-	end	5	Membrane; multi-pass membrane protein (Potential)				251
Q21985 UniProt NPD GO	YNQ2_CAEEL	Hypothetical protein R13F6.2	0.10	-	exc	0					207
P82638 UniProt NPD GO	SCR19_ARATH	Hypothetical protein SCRL19 precursor	0.10	-	nuc	1 *					98
Q10012 UniProt NPD GO	YSV6_CAEEL	Hypothetical protein T19C3.6	0.10	-	cyt	0					201
Q09652 UniProt NPD GO	YS21_CAEEL	Hypothetical protein ZK1320.1	0.10	-	pox	0					226
P30638 UniProt NPD GO	YOU1_CAEEL	Hypothetical protein ZK637.1 in chromosome III	0.10	-	end	10	Membrane; multi-pass membrane protein (Probable)				520
P30160 UniProt NPD GO	YCF43_DICDH	Hypothetical tatC-like protein ycf43 (Fragment)	0.10	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				78
Q9P6S0 UniProt NPD GO	YJP1_SCHPO	Hypothetical threonine-rich protein C1742.01 precursor	0.10	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				1563
Q04301 UniProt NPD GO	YMX8_YEAST	Hypothetical transport protein YMR088C	0.10	-	end	12 *	Membrane; multi-pass membrane protein (Potential)	vacuolar membrane (sensu Fungi) [IDA]			562
P01877 UniProt NPD GO	IGHA2_HUMAN	Ig alpha-2 chain C region	0.10	-	nuc	0		membrane fraction [NAS]	147000		340
P20761 UniProt NPD GO	GCB_RAT	Ig gamma-2B chain C region	0.10	-	nuc	0					333
P06315 UniProt NPD GO	KV5A_HUMAN	Ig kappa chain V region EV15 precursor	0.10	-	vac	0		extracellular region [NAS]			115
P01597 UniProt NPD GO	KV1E_HUMAN	Ig kappa chain V-I region DEE	0.10	-	nuc	0		extracellular region [NAS]			108
P01631 UniProt NPD GO	KV2G_MOUSE	Ig kappa chain V-II region 26-10	0.10	-	nuc	0					113
P01616 UniProt NPD GO	KV2C_HUMAN	Ig kappa chain V-II region MIL	0.10	-	cyt	0					112
P06313 UniProt NPD GO	KV4B_HUMAN	Ig kappa chain V-IV region JI precursor	0.10	-	exc	0		extracellular region [NAS]			133
P01699 UniProt NPD GO	LV1A_HUMAN	Ig lambda chain V-I region VOR	0.10	-	nuc	0		extracellular region [NAS]			111
P01710 UniProt NPD GO	LV2G_HUMAN	Ig lambda chain V-II region BO	0.10	-	nuc	0		extracellular region [NAS]			111
P01711 UniProt NPD GO	LV2H_HUMAN	Ig lambda chain V-II region VIL	0.10	-	exc	0		extracellular region [NAS]			111
P06319 UniProt NPD GO	LV6E_HUMAN	Ig lambda chain V-VI region EB4 precursor	0.10	-	exc	0		extracellular region [NAS]			131
Q9P4P9 UniProt NPD GO	HIS5_EMENI	Imidazole glycerol phosphate synthase hisHF (IGP synthase) (ImGP synthase) (IGPS) [Includes: Glutami ...	0.10	-	cyt	0					553
P40919 UniProt NPD GO	HIS7_CRYNE	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.10	-	cyt	0				1RHY	202
P52297 UniProt NPD GO	IMB_XENLA	Importin subunit beta (Karyopherin subunit beta) (P97) (Importin 90) (Fragments)	0.10	-	cyt	0	Cytoplasm (By similarity). Nucleus; nuclear envelope (By similarity)				260
Q9U3K5 UniProt NPD GO	INX2_CAEEL	Innexin-2	0.10	-	end	4 *	Membrane; multi-pass membrane protein				419

You are viewing entries 64501 to 64550 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.