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
P92565 UniProt NPD GO	M1370_ARATH	Hypothetical mitochondrial protein AtMg01370 (ORF111d)	0.19	-	mit	1	Mitochondrion (Potential)				111
Q09220 UniProt NPD GO	YP71_CAEEL	Hypothetical protein B0228.1	0.19	-	mit	0					196
Q11105 UniProt NPD GO	YPB2_CAEEL	Hypothetical protein C03B8.2	0.19	-	cyt	0					59
Q10436 UniProt NPD GO	YDE2_SCHPO	Hypothetical protein C12B10.02c in chromosome I	0.19	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				235
Q9P782 UniProt NPD GO	YNY8_SCHPO	Hypothetical protein C1711.08 in chromosome II	0.19	-	cyt	0					336
Q9USW9 UniProt NPD GO	YO77_SCHPO	Hypothetical protein C1921.07c in chromosome II	0.19	-	nuc	0					244
Q9UUD4 UniProt NPD GO	YNQ6_SCHPO	Hypothetical protein C19C2.06c in chromosome II	0.19	-	mit	0	Membrane; multi-pass membrane protein (Potential)				145
O14346 UniProt NPD GO	YNQF_SCHPO	Hypothetical protein C19C2.15c in chromosome II	0.19	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				208
P91127 UniProt NPD GO	YBYK_CAEEL	Hypothetical protein C32E8.3 in chromosome I	0.19	-	cyt	0				1PUL	180
P87124 UniProt NPD GO	YDL8_SCHPO	Hypothetical protein C3A12.08 in chromosome I	0.19	-	nuc	1 *					214
Q10139 UniProt NPD GO	YAS3_SCHPO	Hypothetical protein C3H8.03 in chromosome I	0.19	-	mit	0					105
Q09300 UniProt NPD GO	YQOB_CAEEL	Hypothetical protein EEED8.11 precursor	0.19	-	exc	1 *					304
Q09294 UniProt NPD GO	YQO3_CAEEL	Hypothetical protein EEED8.3	0.19	-	cyt	0					194
Q19417 UniProt NPD GO	YSNK_CAEEL	Hypothetical protein F13G3.3	0.19	-	gol	1 *					501
P34412 UniProt NPD GO	YLW9_CAEEL	Hypothetical protein F22B7.9	0.19	-	cyt	0					243
Q8WT51 UniProt NPD GO	YL4M_CAEEL	Hypothetical protein F35H12.5	0.19	-	mit	0					357
P34426 UniProt NPD GO	YL35_CAEEL	Hypothetical protein F44B9.5	0.19	-	nuc	1 *					390
Q9C0X5 UniProt NPD GO	YLNA_SCHPO	Hypothetical protein PB8E5.10 in chromosome I	0.19	-	mit	1 *					73
P34538 UniProt NPD GO	YNC5_CAEEL	Hypothetical protein R05D3.5	0.19	-	nuc	0					179
P82643 UniProt NPD GO	SCR24_ARATH	Hypothetical protein SCRL24 precursor	0.19	-	mit	1 *					89
P49049 UniProt NPD GO	YJ95_CAEEL	Hypothetical protein T05E11.5 in chromosome IV	0.19	-	end	7 *					468
Q09347 UniProt NPD GO	YRS3_CAEEL	Hypothetical protein T05H10.3 precursor	0.19	-	exc	0					158
P41847 UniProt NPD GO	YO97_CAEEL	Hypothetical protein T20B12.7	0.19	-	cyt	0					238
P50581 UniProt NPD GO	YD43_CAEEL	Hypothetical protein T27A8.3 in chromosome X	0.19	-	cyt	0					182
Q09343 UniProt NPD GO	YR27_CAEEL	Hypothetical protein W02B3.7	0.19	-	mit	1 *					162
Q09377 UniProt NPD GO	YS53_CAEEL	Hypothetical protein ZK673.3	0.19	-	nuc	0					322
Q41407 UniProt NPD GO	RBLL_SYMSP	Hypothetical ribulose bisphosphate carboxylase-like protein (RuBisCO-like protein) (Fragment)	0.19	-	nuc	0					537
O42970 UniProt NPD GO	YB95_SCHPO	Hypothetical serine-rich protein C1E8.05 precursor	0.19	-	exc	0					317
Q9HDY9 UniProt NPD GO	YK02_SCHPO	Hypothetical serine/threonine-rich protein P11E10.02c precursor	0.19	-	exc	0					1082
Q7Z0A4 UniProt NPD GO	CXI12_CONRA	I-superfamily conotoxin R11.12 precursor (Fragment)	0.19	-	nuc	0	Secreted protein				45
P03983 UniProt NPD GO	HV01_HETFR	Ig heavy chain V region precursor	0.19	-	exc	0					116
P01617 UniProt NPD GO	KV2D_HUMAN	Ig kappa chain V-II region TEW	0.19	-	nuc	0		extracellular region [NAS]			113
P01722 UniProt NPD GO	LV6B_HUMAN	Ig lambda chain V-VI region NIG-48	0.19	-	nuc	0		extracellular region [NAS]			112
P06317 UniProt NPD GO	LV6C_HUMAN	Ig lambda chain V-VI region SUT	0.19	-	nuc	0				1CD0	111
Q9C1D4 UniProt NPD GO	HIS7_PICST	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.19	-	cyt	0					222
Q75CX4 UniProt NPD GO	TIM21_ASHGO	Import inner membrane translocase subunit TIM21, mitochondrial precursor	0.19	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				234
P82176 UniProt NPD GO	IMPI_GALME	Inducible metalloproteinase inhibitor protein precursor [Contains: IMPI alpha]	0.19	-	exc	0		extracellular space [IDA]			170
P55103 UniProt NPD GO	INHBC_HUMAN	Inhibin beta C chain precursor (Activin beta-C chain)	0.19	-	exc	0	Secreted protein (By similarity)	extracellular region [TAS]	601233		352
Q75A69 UniProt NPD GO	LPE10_ASHGO	Inner membrane magnesium transporter LPE10, mitochondrial precursor	0.19	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				330
Q6B9Z1 UniProt NPD GO	IGFL4_HUMAN	Insulin growth factor-like family member 4 precursor	0.19	-	exc	0	Secreted protein (Potential)				124
P08025 UniProt NPD GO	IGF1_RAT	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.19	-	nuc	0	Secreted protein				153
Q29400 UniProt NPD GO	IBP2_SHEEP	Insulin-like growth factor-binding protein 2 precursor (IGFBP-2) (IBP-2) (IGF-binding protein 2)	0.19	-	exc	1 *	Secreted protein				317
Q27977 UniProt NPD GO	ITA5_BOVIN	Integrin alpha-5 (Fibronectin receptor subunit alpha) (Integrin alpha-F) (VLA-5) (CD49e antigen) (Fr ...	0.19	-	cyt	1	Membrane; single-pass type I membrane protein				385
Q13797 UniProt NPD GO	ITA9_HUMAN	Integrin alpha-9 precursor (Integrin alpha-RLC)	0.19	-	end	2 *	Membrane; single-pass type I membrane protein	integrin complex [TAS]	603963		1035
Q9V7A4 UniProt NPD GO	ITA4_DROME	Integrin alpha-PS4 precursor (Position-specific antigen 4 alpha chain)	0.19	-	nuc	1	Membrane; single-pass type I membrane protein	integrin complex [NAS]			1015
P43406 UniProt NPD GO	ITAV_MOUSE	Integrin alpha-V precursor (Vitronectin receptor subunit alpha) (CD51 antigen) [Contains: Integrin a ...	0.19	-	end	1	Membrane; single-pass type I membrane protein				1044
Q27874 UniProt NPD GO	PAT3_CAEEL	Integrin beta pat-3 precursor	0.19	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				809
P05106 UniProt NPD GO	ITB3_HUMAN	Integrin beta-3 precursor (Platelet membrane glycoprotein IIIa) (GPIIIa) (CD61 antigen)	0.19	-	end	1 *	Membrane; single-pass type I membrane protein	integrin complex [TAS]	173470	1U8C	788
P57044 UniProt NPD GO	ILK_CAVPO	Integrin-linked protein kinase (EC 2.7.11.1) (Beta-integrin-linked kinase)	0.19	-	cyt	0	Cytoplasm (By similarity)				451
P97280 UniProt NPD GO	ITIH3_MESAU	Inter-alpha-trypsin inhibitor heavy chain H3 precursor (ITI heavy chain H3) (Inter-alpha-inhibitor h ...	0.19	-	exc	0					886

You are viewing entries 51951 to 52000 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.