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
P40963 UniProt NPD GO	SAS2_YEAST	Histone acetyltransferase SAS2 (EC 2.3.1.48) (Something about silencing protein 2)	0.28	-	mit	0	Cytoplasm. Nucleus	nuclear chromatin [IDA] nuclear chromosome, telomeric region [IC]			338
Q13547 UniProt NPD GO	HDAC1_HUMAN	Histone deacetylase 1 (HD1)	0.28	-	mit	0	Nucleus	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [IDA]	601241		482
O22781 UniProt NPD GO	SUVH2_ARATH	Histone-lysine N-methyltransferase, H3 lysine-9, H3 lysine-27, H4 lysine-20 and cytosine specific SU ...	0.28	-	cyt	0	Nucleus. Associates with centromeric constitutive heterochromatin				651
Q8SW51 UniProt NPD GO	HD8_ENCCU	Homeobox protein HD-8 (EcHD-8)	0.28	-	cyt	0	Nucleus				125
P38185 UniProt NPD GO	YBH1_YEAST	Hypothetical 11.5 kDa protein in RSP8A-AST1 intergenic region	0.28	-	nuc	0					102
P42939 UniProt NPD GO	YG4G_YEAST	Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region	0.28	-	nuc	0		endosome [IDA]			101
P58150 UniProt NPD GO	YCXB_ASTLO	Hypothetical 12.4 kDa protein in rps4-rps11 intergenic region (ORF104)	0.28	-	nuc	0	Plastid				104
P38253 UniProt NPD GO	YBU0_YEAST	Hypothetical 14.3 kDa protein in POL30-MRS5 intergenic region	0.28	-	nuc	1 *		cytoplasm [IDA] nucleus [IDA]			122
P40461 UniProt NPD GO	YIO1_YEAST	Hypothetical 14.4 kDa protein in CCT2-AXL2 intergenic region	0.28	-	nuc	0					129
P36098 UniProt NPD GO	YKD1_YEAST	Hypothetical 15.6 kDa protein in IXR1-TFA1 intergenic region	0.28	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				137
Q04019 UniProt NPD GO	YM80_YEAST	Hypothetical 23.2 kDa protein in ZRC1-FAA4 intergenic region	0.28	-	end	2 *					206
Q9MUL6 UniProt NPD GO	YCX3_MESVI	Hypothetical 30.4 kDa protein in rpoZ-ycf20 intergenic region	0.28	-	mit	1 *	Plastid; chloroplast				261
P38887 UniProt NPD GO	YH02_YEAST	Hypothetical 69.0 kDa protein in PPX1-RPS4B intergenic region	0.28	-	end	0		soluble fraction [IDA] vacuole (sensu Fungi) [IDA]			602
P48260 UniProt NPD GO	YCF24_CYAPA	Hypothetical UPF0051 protein ycf24	0.28	-	cyt	0	Plastid; cyanelle				486
P51240 UniProt NPD GO	YCF24_PORPU	Hypothetical UPF0051 protein ycf24 (ORF487)	0.28	-	nuc	0	Plastid; chloroplast				487
O42654 UniProt NPD GO	YF9F_SCHPO	Hypothetical UPF0300 protein C10F6.15 in chromosome I	0.28	-	nuc	0					432
P92531 UniProt NPD GO	M970_ARATH	Hypothetical mitochondrial protein AtMg00970 (ORF117)	0.28	-	mit	0	Mitochondrion (Potential)				117
P34258 UniProt NPD GO	YKA7_CAEEL	Hypothetical protein B0303.7	0.28	-	nuc	0					493
Q7Z118 UniProt NPD GO	YMPB_CAEEL	Hypothetical protein B0361.11 in chromosome III	0.28	-	end	10	Membrane; multi-pass membrane protein (Potential)				534
P34279 UniProt NPD GO	YKK2_CAEEL	Hypothetical protein C02F5.2	0.28	-	nuc	0					85
Q65ZC1 UniProt NPD GO	YKO9_CAEEL	Hypothetical protein C05B5.9	0.28	-	nuc	0					139
Q10446 UniProt NPD GO	YDED_SCHPO	Hypothetical protein C12B10.13 in chromosome I	0.28	-	nuc	0					240
O60077 UniProt NPD GO	YQK3_SCHPO	Hypothetical protein C1494.03 in chromosome III	0.28	-	cyt	0					492
Q05036 UniProt NPD GO	YLA4_CAEEL	Hypothetical protein C30C11.4 in chromosome III	0.28	-	nuc	0					776
O13886 UniProt NPD GO	YKB2_SCHPO	Hypothetical protein C823.02 in chromosome I	0.28	-	mit	0					43
Q09321 UniProt NPD GO	YR51_CAEEL	Hypothetical protein F42A8.1	0.28	-	vac	0					370
Q09322 UniProt NPD GO	YR53_CAEEL	Hypothetical protein F42A8.3 precursor	0.28	-	end	1					324
Q23247 UniProt NPD GO	YH82_CAEEL	Hypothetical protein ZC168.2 in chromosome IV	0.28	-	mit	0					108
Q75EG6 UniProt NPD GO	ISN1_ASHGO	IMP-specific 5'-nucleotidase 1 (EC 3.1.3.-)	0.28	-	cyt	0					425
P18136 UniProt NPD GO	KV3M_HUMAN	Ig kappa chain V-III region HIC precursor	0.28	-	nuc	0		extracellular region [NAS]			129
P12018 UniProt NPD GO	VPREB_HUMAN	Immunoglobulin iota chain precursor (V(pre)B protein) (VpreB protein) (CD179a antigen)	0.28	-	exc	0		extracellular region [NAS]	605141		145
Q4X1I8 UniProt NPD GO	TIM21_ASPFU	Import inner membrane translocase subunit tim21, mitochondrial precursor	0.28	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				237
O13864 UniProt NPD GO	IMB1_SCHPO	Importin beta-1 subunit (Karyopherin beta-1 subunit) (Importin 95)	0.28	-	cyt	0	Cytoplasm (By similarity). Nucleus; nuclear envelope (By similarity)				863
Q8S339 UniProt NPD GO	ALB31_CHLRE	Inner membrane ALBINO3-like protein 1, chloroplast precursor	0.28	+	end	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				495
O61788 UniProt NPD GO	INX17_CAEEL	Innexin-17 (Gap junction innexin)	0.28	-	end	4 *	Membrane; multi-pass membrane protein	gap junction [ISS] integral to membrane [ISS]			362
Q9SUG3 UniProt NPD GO	ITPK2_ARATH	Inositol-tetrakisphosphate 1-kinase 2 (EC 2.7.1.134) (Inositol-triphosphate 5/6-kinase 2) (EC 2.7.1. ...	0.28	-	cyt	0					353
P18065 UniProt NPD GO	IBP2_HUMAN	Insulin-like growth factor-binding protein 2 precursor (IGFBP-2) (IBP-2) (IGF-binding protein 2)	0.28	-	exc	0	Secreted protein		146731		328
P22692 UniProt NPD GO	IBP4_HUMAN	Insulin-like growth factor-binding protein 4 precursor (IGFBP-4) (IBP-4) (IGF-binding protein 4)	0.28	-	exc	0	Secreted protein		146733	1WQJ	258
P21744 UniProt NPD GO	IBP4_RAT	Insulin-like growth factor-binding protein 4 precursor (IGFBP-4) (IBP-4) (IGF-binding protein 4)	0.28	-	exc	0	Secreted protein				254
Q5NVC3 UniProt NPD GO	ITM2C_PONPY	Integral membrane protein 2C [Contains: CT-BRI3]	0.28	-	mit	1	Membrane; single-pass type II membrane protein (Potential)				267
Q5PQL7 UniProt NPD GO	ITM2C_RAT	Integral membrane protein 2C [Contains: CT-BRI3]	0.28	-	cyt	1	Membrane; single-pass type II membrane protein (Potential)				269
P18614 UniProt NPD GO	ITA1_RAT	Integrin alpha-1 precursor (Laminin and collagen receptor) (VLA-1) (CD49a antigen)	0.28	-	end	2 *	Membrane; single-pass type I membrane protein			2B2X	1180
Q9UKX5 UniProt NPD GO	ITA11_HUMAN	Integrin alpha-11 precursor	0.28	-	end	1	Membrane; single-pass type I membrane protein	integrin complex [TAS]	604789		1189
P26011 UniProt NPD GO	ITB7_MOUSE	Integrin beta-7 precursor (Integrin beta-P) (M290 IEL antigen)	0.28	-	nuc	1	Membrane; single-pass type I membrane protein				806
Q06033 UniProt NPD GO	ITIH3_HUMAN	Inter-alpha-trypsin inhibitor heavy chain H3 precursor (ITI heavy chain H3) (Inter-alpha-inhibitor h ...	0.28	-	mit	0		extracellular region [NAS]	146650		885
Q9D8C4 UniProt NPD GO	IN35_MOUSE	Interferon-induced 35 kDa protein homolog (IFP 35)	0.28	-	cyt	0	Nucleus (By similarity). Nuclear following IFN treatment (By similarity)				285
Q8TCB0 UniProt NPD GO	IFI44_HUMAN	Interferon-induced protein 44 (p44)	0.28	-	cyt	0	Cytoplasm (Potential)				444
Q8R4K2 UniProt NPD GO	IRAK4_MOUSE	Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) (IRAK-4)	0.28	-	nuc	0				2A9I	459
P70380 UniProt NPD GO	IL18_MOUSE	Interleukin-18 precursor (IL-18) (Interferon-gamma-inducing factor) (IFN-gamma-inducing factor) (Int ...	0.28	-	nuc	0	Secreted protein	extracellular region [ISS]			192
P37997 UniProt NPD GO	IL2_HORSE	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.28	-	exc	0	Secreted protein				149

You are viewing entries 42351 to 42400 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.