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
Q9LEY9 UniProt NPD GO	NOLA2_ARATH	H/ACA ribonucleoprotein complex subunit 2-like protein (Nhp2-like protein)	0.19	-	cyt	0	Nucleus; nucleolus (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			156
P01916 UniProt NPD GO	HB2S_HUMAN	HLA class II histocompatibility antigen, SB beta chain (Fragment)	0.19	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				224
P11143 UniProt NPD GO	HSP70_MAIZE	Heat shock 70 kDa protein	0.19	-	cyt	0					645
P04792 UniProt NPD GO	HSPB1_HUMAN	Heat-shock protein beta-1 (HspB1) (Heat shock 27 kDa protein) (HSP 27) (Stress-responsive protein 27 ...	0.19	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic in interphase cells. Colocalizes with mitotic spindles in mitotic ce ...	cell surface [IEP] cytoplasm [TAS] cytoskeleton [TAS]	608634		205
P30519 UniProt NPD GO	HMOX2_HUMAN	Heme oxygenase 2 (EC 1.14.99.3) (HO-2)	0.19	-	nuc	1	Microsome		141251		316
P12659 UniProt NPD GO	HCYA_OCTDO	Hemocyanin A-type, units Ode to Odg (Fragment)	0.19	-	cyt	0					1233
Q9NFL6 UniProt NPD GO	HCYC_EURCA	Hemocyanin C chain (HcC)	0.19	-	cyt	0	Secreted protein; extracellular space	extracellular space [ISS]			628
P49182 UniProt NPD GO	HEP2_MOUSE	Heparin cofactor 2 precursor (Heparin cofactor II) (HC-II) (Protease inhibitor leuserpin 2)	0.19	-	nuc	0					478
Q17127 UniProt NPD GO	HEXA_BLADI	Hexamerin precursor	0.19	-	vac	0	Secreted protein; extracellular space (By similarity)				733
Q6Z398 UniProt NPD GO	HXK4_ORYSA	Hexokinase-4, chloroplast precursor (EC 2.7.1.1) (Hexokinase II)	0.19	-	nuc	0	Plastid; chloroplast; chloroplast stroma (Probable)				509
P26151 UniProt NPD GO	FCGR1_MOUSE	High affinity immunoglobulin gamma Fc receptor I precursor (Fc-gamma RI) (FcRI) (IgG Fc receptor I)	0.19	-	nuc	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			404
P31580 UniProt NPD GO	HCE23_ORYLA	High choriolytic enzyme 1 precursor (EC 3.4.24.67) (Hatching enzyme zinc-protease HCE 1 subunit) (Ch ...	0.19	-	exc	0	Stored as proenzymes in the zymogen granules				270
Q96MC6 UniProt NPD GO	HIAT1_HUMAN	Hippocampus abundant transcript 1 protein (Putative tetracycline transporter-like protein)	0.19	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				490
Q9JI35 UniProt NPD GO	HRH3_CAVPO	Histamine H3 receptor (HH3R)	0.19	-	end	7 *	Membrane; multi-pass membrane protein				445
Q9QYN8 UniProt NPD GO	HRH3_RAT	Histamine H3 receptor (HH3R)	0.19	-	end	7 *	Membrane; multi-pass membrane protein				445
P06350 UniProt NPD GO	H1_ONCMY	Histone H1 [Contains: Oncorhyncin II]	0.19	+	nuc	0	Nucleus. Oncorhyncin II is secreted	extracellular region [NAS]			206
P40264 UniProt NPD GO	H12_GLYBA	Histone H1-II	0.19	-	nuc	0	Nucleus				232
P16403 UniProt NPD GO	H12_HUMAN	Histone H1.2 (Histone H1d)	0.19	+	nuc	0	Nucleus	nucleosome [NAS]	142710		212
Q875B8 UniProt NPD GO	H2A_PODAN	Histone H2A	0.19	-	nuc	0	Nucleus (By similarity)				134
P02270 UniProt NPD GO	H2A_SIPNU	Histone H2A	0.19	-	nuc	0	Nucleus				123
P59890 UniProt NPD GO	H2A_HIPHI	Histone H2A [Contains: Hipposin] (Fragment)	0.19	-	mit	0	Nucleus. Hipposin: Secreted protein				51
Q96KK5 UniProt NPD GO	H2A1H_HUMAN	Histone H2A type 1-H	0.19	-	nuc	0	Nucleus				127
Q99878 UniProt NPD GO	H2A1J_HUMAN	Histone H2A type 1-J	0.19	-	nuc	0	Nucleus	nucleosome [NAS]	602791		127
Q16777 UniProt NPD GO	H2A2C_HUMAN	Histone H2A type 2-C (H2A-GL101) (H2A/r)	0.19	-	nuc	0	Nucleus	nucleosome [NAS]	602797		128
Q64523 UniProt NPD GO	H2A2C_MOUSE	Histone H2A type 2-C (H2a-613B)	0.19	-	nuc	0	Nucleus				128
Q59VP2 UniProt NPD GO	H2A2_CANAL	Histone H2A.2	0.19	-	nuc	0	Nucleus (By similarity)				130
P02277 UniProt NPD GO	H2A3_WHEAT	Histone H2A.2.2	0.19	-	nuc	0	Nucleus				151
P80739 UniProt NPD GO	H4_EUPCR	Histone H4	0.19	-	cyt	0	Nucleus (By similarity)				106
Q2UA71 UniProt NPD GO	HAT2_ASPOR	Histone acetyltransferase type B subunit 2 (EC 2.3.1.48)	0.19	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				436
Q9FVE6 UniProt NPD GO	HD2A_ARATH	Histone deacetylase 2a (HD-tuins protein 1)	0.19	-	nuc	0	Nucleus; nucleolus				245
Q8R1H0 UniProt NPD GO	HOP_MOUSE	Homeodomain-only protein (Homeobox-only protein) (Odd homeobox protein 1) (mOB1)	0.19	-	nuc	0	Nucleus. Ref.3: Cytoplasm	nucleus [IDA]		1UHS	73
Q78ZR5 UniProt NPD GO	HOP_RAT	Homeodomain-only protein (Odd homeobox protein 1) (Global ischemia-induced protein 15B) (GIIg15b)	0.19	-	nuc	0	Nucleus (By similarity)				73
P05723 UniProt NPD GO	YCX1_CHLRE	Hypothetical 12.2 kDa protein in 16S rRNA region	0.19	-	exc	1 *	Plastid; chloroplast				111
P39534 UniProt NPD GO	YJT9_YEAST	Hypothetical 12.5 kDa protein in PRP21-UBP12 intergenic region	0.19	-	cyt	0					108
P40076 UniProt NPD GO	YEV1_YEAST	Hypothetical 12.9 kDa protein in SCS2-GLO3 intergenic region	0.19	-	nuc	0					114
P03938 UniProt NPD GO	YCF68_MAIZE	Hypothetical 14 kDa protein ycf68 (ORF 134)	0.19	-	mit	0	Plastid; chloroplast				134
P36065 UniProt NPD GO	YKN6_YEAST	Hypothetical 14.3 kDa protein in MRPL31-APL2 intergenic region	0.19	-	nuc	0					132
P40551 UniProt NPD GO	YIB2_YEAST	Hypothetical 15.1 kDa protein in PDR11-FAA3 intergenic region	0.19	-	cyt	0					130
P43625 UniProt NPD GO	YFM7_YEAST	Hypothetical 17.5 kDa protein in HXK1 3'region	0.19	-	nuc	0					151
P40515 UniProt NPD GO	YIG5_YEAST	Hypothetical 17.7 kDa protein in RNR3-ARC15 intergenic region	0.19	-	cyt	1		mitochondrial outer membrane [IDA]		1Y8M	155
Q03798 UniProt NPD GO	YM32_YEAST	Hypothetical 29.1 kDa protein in IMP1-HLJ1 intergenic region	0.19	-	mit	0		mitochondrion [IDA]			255
P47086 UniProt NPD GO	YJY1_YEAST	Hypothetical 30.5 kDa protein in SPC1-ILV3 intergenic region	0.19	-	cyt	0					261
P15562 UniProt NPD GO	YMA6_PODAN	Hypothetical 34.3 kDa protein in ATP6 5'region (ORFC)	0.19	-	end	2 *					296
P36164 UniProt NPD GO	YK68_YEAST	Hypothetical 38.3 kDa protein in PRP16-SRP40 intergenic region	0.19	-	end	5	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA] integral to Golgi membrane [IDA]			337
Q03266 UniProt NPD GO	YM8Q_YEAST	Hypothetical 42.6 kDa protein in MSU1-HAS1 intergenic region	0.19	-	cyt	0		cytoplasm [IDA]			374
P05729 UniProt NPD GO	YCX9_EUGGR	Hypothetical 46.2 kDa protein in 16S rRNA 5'region (ORF406)	0.19	-	end	2	Plastid; chloroplast				406
P39973 UniProt NPD GO	YEI4_YEAST	Hypothetical UPF0320 protein YEL074W	0.19	-	nuc	0					112
P05473 UniProt NPD GO	YKP7_KLULA	Hypothetical killer plasmid pGKl-2 protein 7	0.19	-	nuc	0					132
P92528 UniProt NPD GO	M910_ARATH	Hypothetical mitochondrial protein AtMg00910 (ORF215a)	0.19	-	mit	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				215
P92561 UniProt NPD GO	M1300_ARATH	Hypothetical mitochondrial protein AtMg01300 (ORF136a)	0.19	-	nuc	0	Mitochondrion (Potential)				136

You are viewing entries 51901 to 51950 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.