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
Q9P8F8 UniProt NPD GO	H1_EMENI	Histone H1	0.30	+	nuc	0	Nucleus (Potential)				200
P02275 UniProt NPD GO	H2A1_WHEAT	Histone H2A.1 (wcH2A-9)	0.30	-	nuc	0	Nucleus				145
Q4PHE4 UniProt NPD GO	H2AZ_USTMA	Histone H2A.Z	0.30	-	nuc	0	Nucleus (By similarity)				135
Q2U5A9 UniProt NPD GO	H2B_ASPOR	Histone H2B	0.30	-	nuc	0	Nucleus (By similarity)				140
O49118 UniProt NPD GO	H2B_CAPAN	Histone H2B (CaH2B)	0.30	+	nuc	0	Nucleus				144
Q9FFC0 UniProt NPD GO	H2B10_ARATH	Histone H2B.10 (HTB2)	0.30	+	nuc	0	Nucleus (By similarity)				144
O65818 UniProt NPD GO	H2B2_LYCES	Histone H2B.2 (LeH2B-2)	0.30	-	nuc	0	Nucleus (By similarity)				139
P83864 UniProt NPD GO	H3_PENVA	Histone H3 (Fragments)	0.30	-	nuc	0	Nucleus (By similarity)	nucleosome [ISS]			43
Q9U7D0 UniProt NPD GO	H4_MASBA	Histone H4	0.30	-	cyt	0	Nucleus (By similarity)				107
Q6WV74 UniProt NPD GO	H4_MYTCH	Histone H4	0.30	-	cyt	0	Nucleus (By similarity)				102
Q75AX1 UniProt NPD GO	H42_ASHGO	Histone H4.2	0.30	-	cyt	0	Nucleus (By similarity)				102
P56517 UniProt NPD GO	HDAC1_CHICK	Histone deacetylase 1 (HD1)	0.30	-	cyt	0	Nucleus (Potential)	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]			480
Q9M4U5 UniProt NPD GO	HD2B_MAIZE	Histone deacetylase 2b (HD2b) (Zm-HD2b)	0.30	-	nuc	0	Nucleus; nucleolus (By similarity)				303
Q9ZUM9 UniProt NPD GO	ASHR2_ARATH	Histone-lysine N-methyltransferase ASHR2 (EC 2.1.1.43) (ASH1-related protein 2) (Protein SET DOMAIN ...	0.30	-	nuc	0	Nucleus (By similarity)				398
Q5PP37 UniProt NPD GO	ATXR2_ARATH	Histone-lysine N-methyltransferase ATXR2 (EC 2.1.1.43) (Trithorax-related protein 2) (TRX-related pr ...	0.30	-	nuc	0	Nucleus (By similarity)				473
P54872 UniProt NPD GO	HMCS_DICDI	Hydroxymethylglutaryl-CoA synthase (EC 2.3.3.10) (HMG-CoA synthase) (3-hydroxy-3-methylglutaryl coen ...	0.30	-	nuc	0					163
Q93WP7 UniProt NPD GO	HSYB_TOBAC	Hydroxyproline-rich systemin B precursor [Contains: HypSysB I (TobHypSysB I); HypSysB II (TobHypSysB ...	0.30	-	exc	0		intracellular [NAS]			164
P53284 UniProt NPD GO	YG3G_YEAST	Hypothetical 13.2 kDa protein in PAS5-CBF2 intergenic region	0.30	-	nuc	0					112
Q03231 UniProt NPD GO	YM46_YEAST	Hypothetical 17.6 kDa protein in CTL1-RGM1 intergenic region	0.30	-	nuc	0					154
O60176 UniProt NPD GO	YG41_SCHPO	Hypothetical RNA-binding protein C23E6.01c in chromosome II	0.30	-	nuc	0					473
O49562 UniProt NPD GO	U085_ARATH	Hypothetical UPF0085 protein At4g21210	0.30	-	nuc	0					403
P91343 UniProt NPD GO	YM3M_CAEEL	Hypothetical WD repeat protein F55F8.5	0.30	+	cyt	0					439
P92559 UniProt NPD GO	M1280_ARATH	Hypothetical mitochondrial protein AtMg01280 (ORF291)	0.30	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				291
P46557 UniProt NPD GO	YKG7_CAEEL	Hypothetical protein B0285.7 precursor	0.30	-	cyt	1 *					781
Q09787 UniProt NPD GO	YA99_SCHPO	Hypothetical protein C13G6.09 in chromosome I	0.30	-	nuc	0					274
Q9P7Q5 UniProt NPD GO	YFVA_SCHPO	Hypothetical protein C1834.10c in chromosome I	0.30	-	nuc	0					178
O42656 UniProt NPD GO	YLD4_SCHPO	Hypothetical protein C1851.04c in chromosome I	0.30	-	nuc	0					1052
Q9Y7I1 UniProt NPD GO	YE1K_SCHPO	Hypothetical protein C1B3.20 in chromosome I	0.30	-	nuc	0					78
Q10301 UniProt NPD GO	YD48_SCHPO	Hypothetical protein C22H10.08 in chromosome I	0.30	-	cyt	0	Membrane; multi-pass membrane protein (Potential)				492
Q09910 UniProt NPD GO	YAJB_SCHPO	Hypothetical protein C30D11.11 in chromosome I	0.30	-	end	7	Membrane; multi-pass membrane protein (Probable)				442
Q9USS8 UniProt NPD GO	YNB2_SCHPO	Hypothetical protein C4.02c in chromosome II	0.30	-	cyt	0					456
O94665 UniProt NPD GO	YBW7_SCHPO	Hypothetical protein C651.07 in chromosome II	0.30	-	nuc	0					268
P41879 UniProt NPD GO	YPT1_CAEEL	Hypothetical protein F37A4.1	0.30	-	cyt	2 *					482
P01594 UniProt NPD GO	KV1B_HUMAN	Ig kappa chain V-I region AU	0.30	-	nuc	0		extracellular region [NAS]		1JV5	108
P01595 UniProt NPD GO	KV1C_HUMAN	Ig kappa chain V-I region Bi	0.30	-	nuc	0		extracellular region [NAS]			108
P04207 UniProt NPD GO	KV3H_HUMAN	Ig kappa chain V-III region CLL precursor (Rheumatoid factor)	0.30	-	nuc	0		extracellular region [NAS]			129
Q8R0A6 UniProt NPD GO	IGX1_MOUSE	Immunoglobulin-like domain protein MGC33530 precursor	0.30	-	mit	0	Secreted protein (Potential)				235
Q6BVK1 UniProt NPD GO	TIM21_DEBHA	Import inner membrane translocase subunit TIM21, mitochondrial precursor	0.30	-	nuc	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				277
Q9FZ87 UniProt NPD GO	GH317_ARATH	Indole-3-acetic acid-amido synthetase GH3.17 (EC 6.3.2.-) (Auxin-responsive GH3-like protein 17) (At ...	0.30	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			609
Q9UHH9 UniProt NPD GO	IP6K2_HUMAN	Inositol hexakisphosphate kinase 2 (EC 2.7.4.21) (InsP6 kinase 2) (Inositol hexakisphosphate kinase ...	0.30	-	mit	0	Nucleus	nucleus [ISS]	606992		426
Q8NFU5 UniProt NPD GO	IPMK_HUMAN	Inositol polyphosphate multikinase (EC 2.7.1.151) (Inositol 1,3,4,6-tetrakisphosphate 5-kinase)	0.30	-	nuc	0	Nucleus		609851		416
Q6BHL8 UniProt NPD GO	IPK1_DEBHA	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.30	-	nuc	0	Nucleus (By similarity)				377
Q5KI57 UniProt NPD GO	IPPK_CRYNE	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.30	-	cyt	0					414
Q7ZU91 UniProt NPD GO	ITPK1_BRARE	Inositol-tetrakisphosphate 1-kinase (EC 2.7.1.134) (Inositol-triphosphate 5/6-kinase) (EC 2.7.1.-) ( ...	0.30	-	cyt	0					396
Q08279 UniProt NPD GO	IGF2_CAVPO	Insulin-like growth factor II precursor (IGF-II) (Somatomedin A) (Fragment)	0.30	-	exc	0	Secreted protein				128
Q05717 UniProt NPD GO	IBP5_BOVIN	Insulin-like growth factor-binding protein 5 (IGFBP-5) (IBP-5) (IGF-binding protein 5) (Fragment)	0.30	-	nuc	0	Secreted protein				111
Q60QP4 UniProt NPD GO	U359_CAEBR	Integral membrane UPF0359 protein CBG21730	0.30	+	end	7	Membrane; multi-pass membrane protein (By similarity)				454
P80746 UniProt NPD GO	ITAV_BOVIN	Integrin alpha-V precursor (Vitronectin receptor subunit alpha) (CD51 antigen) [Contains: Integrin a ...	0.30	-	nuc	1	Membrane; single-pass type I membrane protein				1047
P53713 UniProt NPD GO	ITB1_FELCA	Integrin beta-1 precursor (Fibronectin receptor subunit beta) (Integrin VLA-4 subunit beta) (CD29 an ...	0.30	-	end	1	Membrane; single-pass type I membrane protein				798
P12606 UniProt NPD GO	ITB1A_XENLA	Integrin beta-1-A precursor	0.30	-	end	1	Membrane; single-pass type I membrane protein				798

You are viewing entries 40401 to 40450 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.