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
Q6IMX7 UniProt NPD GO	HPBP1_RAT	Hsp70-binding protein 1 (HspBP1) (Heat shock protein-binding protein 1) (Hsp70-interacting protein 1 ...	0.36	-	nuc	0					357
P23613 UniProt NPD GO	HYALP_CAVPO	Hyaluronidase PH-20 precursor (EC 3.2.1.35) (Hyal-PH20) (Sperm surface protein PH-20) (Sperm adhesio ...	0.36	-	end	0	Cell membrane; lipid-anchor; GPI-anchor				529
Q14526 UniProt NPD GO	HIC1_HUMAN	Hypermethylated in cancer 1 protein (Hic-1) (Zinc finger and BTB domain-containing protein 29)	0.36	-	nuc	0	Nucleus	nucleus [NAS]	603825		733
P38296 UniProt NPD GO	YB28_YEAST	Hypothetical 14.4 kDa protein in SMY2-RPS6B intergenic region	0.36	-	cyt	0					124
Q03233 UniProt NPD GO	YM47_YEAST	Hypothetical 22.1 kDa protein in SSO2-HSC82 intergenic region	0.36	-	nuc	0		cytoplasm [IDA]			198
P49957 UniProt NPD GO	YMB4_YEAST	Hypothetical 32.4 kDa protein in TAF40-ERV25 intergenic region	0.36	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			279
P53171 UniProt NPD GO	YGF7_YEAST	Hypothetical 33.0 kDa protein in UBC2-OLE1 intergenic region	0.36	-	nuc	0		mitochondrion [IDA]			287
P47122 UniProt NPD GO	YJ42_YEAST	Hypothetical 43.2 kDa protein in HAM1-PEM2 intergenic region	0.36	-	nuc	0		cytoplasm [IDA]			385
P46982 UniProt NPD GO	YJS6_YEAST	Hypothetical 67.3 kDa protein in SWE1-ATP12 intergenic region	0.36	-	mit	1 *		Golgi apparatus [IDA]			586
P32034 UniProt NPD GO	YCF15_CUSRE	Hypothetical 9.1 kDa protein ycf15 (ORF 77)	0.36	-	cyt	0	Plastid				77
P34312 UniProt NPD GO	YKT1_CAEEL	Hypothetical C-type lectin protein C07A9.1 precursor	0.36	-	nuc	0					313
P93282 UniProt NPD GO	M130_ARATH	Hypothetical mitochondrial protein AtMg00130 (ORF121a)	0.36	-	mit	0	Mitochondrion (Potential)				121
P93283 UniProt NPD GO	M140_ARATH	Hypothetical mitochondrial protein AtMg00140 (ORF167)	0.36	-	nuc	1 *	Mitochondrion (Potential)				167
P92548 UniProt NPD GO	M1180_ARATH	Hypothetical mitochondrial protein AtMg01180 (ORF111b)	0.36	-	nuc	0	Mitochondrion (Potential)				111
P92552 UniProt NPD GO	M1220_ARATH	Hypothetical mitochondrial protein AtMg01220 (ORF113)	0.36	-	nuc	0	Mitochondrion (Potential)				113
Q09746 UniProt NPD GO	YB65_SCHPO	Hypothetical protein C12C2.05c in chromosome II	0.36	-	nuc	0					642
Q09245 UniProt NPD GO	YP97_CAEEL	Hypothetical protein C28H8.7	0.36	-	exc	1 *					283
P34375 UniProt NPD GO	YLM1_CAEEL	Hypothetical protein D2007.1	0.36	-	exc	1 *					111
Q8ST80 UniProt NPD GO	Y101_ENCCU	Hypothetical protein ECU01_0010/ECU01_1600/ECU04_0010	0.36	-	nuc	0					158
Q10035 UniProt NPD GO	YSI3_CAEEL	Hypothetical protein F15G9.3	0.36	-	nuc	0					162
Q09563 UniProt NPD GO	YR47_CAEEL	Hypothetical protein F47D12.7 in chromosome III	0.36	-	cyt	0					579
P45965 UniProt NPD GO	YNZ5_CAEEL	Hypothetical protein T09A5.5	0.36	-	mit	0					163
P45969 UniProt NPD GO	YNZ9_CAEEL	Hypothetical protein T09A5.9	0.36	-	nuc	0					326
P34592 UniProt NPD GO	YN58_CAEEL	Hypothetical protein ZC21.8	0.36	-	nuc	1 *					145
Q03000 UniProt NPD GO	YHS3_SACKL	Hypothetical protein in HIS3 3'region (Fragment)	0.36	-	nuc	0					341
Q9MUM0 UniProt NPD GO	YCF1_MESVI	Hypothetical protein ycf1 (RF1)	0.36	-	end	6 *	Plastid; chloroplast				410
P08746 UniProt NPD GO	YMF19_OENBE	Hypothetical protein ymf19	0.36	-	cyt	1 *	Mitochondrion (Potential)				159
P01604 UniProt NPD GO	KV1L_HUMAN	Ig kappa chain V-I region Kue	0.36	-	nuc	0		extracellular region [NAS]			108
P01645 UniProt NPD GO	KV5L_MOUSE	Ig kappa chain V-V region HP 93G7	0.36	-	nuc	0				1A14	108
P15814 UniProt NPD GO	IGLL1_HUMAN	Immunoglobulin lambda-like polypeptide 1 precursor (Immunoglobulin-related protein 14.1) (Immunoglob ...	0.36	-	nuc	0	Secreted protein (Potential)	membrane [NAS]	146770		213
Q14974 UniProt NPD GO	IMB1_HUMAN	Importin beta-1 subunit (Karyopherin beta-1 subunit) (Nuclear factor P97) (Importin 90)	0.36	-	cyt	0	Cytoplasm. Nucleus; nuclear envelope	cytoplasm [TAS] nuclear pore [TAS]	602738	1QGR	876
P70168 UniProt NPD GO	IMB1_MOUSE	Importin beta-1 subunit (Karyopherin beta-1 subunit) (Nuclear factor P97) (Pore targeting complex 97 ...	0.36	-	cyt	0	Cytoplasm (By similarity). Nucleus; nuclear envelope (By similarity)			1UKL	876
O13671 UniProt NPD GO	CSE1_SCHPO	Importin-alpha re-exporter (Cellular apoptosis susceptibility protein homolog)	0.36	-	end	0	Cytoplasm (By similarity). Nucleus (By similarity)				967
Q9LQ68 UniProt NPD GO	GH34_ARATH	Indole-3-acetic acid-amido synthetase GH3.4 (EC 6.3.2.-) (Auxin-responsive GH3-like protein 4) (AtGH ...	0.36	-	nuc	0					597
P87149 UniProt NPD GO	MRS2_SCHPO	Inner membrane magnesium transporter mrs2, mitochondrial precursor (RNA-splicing protein mrs2)	0.36	-	end	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				422
Q9U3N4 UniProt NPD GO	INX6_CAEEL	Innexin-6 (Protein opu-6)	0.36	-	end	4 *	Membrane; multi-pass membrane protein				389
Q6CNG8 UniProt NPD GO	IPK1_KLULA	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.36	-	cyt	0	Nucleus (By similarity)				266
Q61581 UniProt NPD GO	IBP7_MOUSE	Insulin-like growth factor-binding protein 7 precursor (IGFBP-7) (IBP-7) (IGF-binding protein 7) (MA ...	0.36	-	exc	0	Secreted protein				281
P05556 UniProt NPD GO	ITB1_HUMAN	Integrin beta-1 precursor (Fibronectin receptor subunit beta) (Integrin VLA-4 subunit beta) (CD29 an ...	0.36	-	end	1	Cell membrane; single-pass type I membrane protein. Isoform beta-1B does not localize to focal adhes ...	integrin complex [NAS] ruffle [TAS]	135630	1LHA	798
Q3ZBM4 UniProt NPD GO	ITBP1_BOVIN	Integrin beta-1-binding protein 1	0.36	-	mit	0	Cytoplasm (By similarity)				200
Q9Z0T9 UniProt NPD GO	ITB6_MOUSE	Integrin beta-6 precursor	0.36	-	nuc	1	Membrane; single-pass type I membrane protein				787
P19827 UniProt NPD GO	ITIH1_HUMAN	Inter-alpha-trypsin inhibitor heavy chain H1 precursor (ITI heavy chain H1) (Inter-alpha-inhibitor h ...	0.36	-	cyt	1 *		extracellular region [NAS]	147270		911
P01563 UniProt NPD GO	IFNA2_HUMAN	Interferon alpha-2 precursor (Interferon alpha-A) (LeIF A)	0.36	-	exc	0	Secreted protein		147562	2HIE	188
P05005 UniProt NPD GO	IFNA3_HORSE	Interferon alpha-3 precursor	0.36	-	exc	0	Secreted protein				184
P07349 UniProt NPD GO	IFNA5_MOUSE	Interferon alpha-5 precursor	0.36	-	end	0	Secreted protein				189
P05002 UniProt NPD GO	IFNW2_HORSE	Interferon omega-2 precursor (Interferon alpha-II-2)	0.36	-	cyt	0	Secreted protein				195
Q95141 UniProt NPD GO	INAR2_BOVIN	Interferon-alpha/beta receptor beta chain precursor (IFN-alpha-REC) (Type I interferon receptor) (IF ...	0.36	-	end	2 *	Membrane; single-pass type I membrane protein				530
P27931 UniProt NPD GO	IL1R2_MOUSE	Interleukin-1 receptor type II precursor (IL-1R-2) (IL-1R-beta) (CD121b antigen)	0.36	-	end	1	Membrane; single-pass type I membrane protein				410
Q80XG2 UniProt NPD GO	IL21_PERMA	Interleukin-21 precursor (IL-21) (Fragment)	0.36	-	nuc	0	Secreted protein (By similarity)				123
Q9H293 UniProt NPD GO	IL25_HUMAN	Interleukin-25 precursor (IL-25) (Interleukin-17E) (IL-17E)	0.36	-	nuc	1 *	Secreted protein	membrane [NAS]	605658		177

You are viewing entries 35051 to 35100 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.