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
Q8SWH3 UniProt NPD GO	Y209_ENCCU	Hypothetical protein ECU02_0090	0.13	-	end	6 *					258
Q09320 UniProt NPD GO	YQZ2_CAEEL	Hypothetical protein F40B5.2	0.13	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				482
Q03599 UniProt NPD GO	YMB1_CAEEL	Hypothetical protein F54G8.1	0.13	-	end	0					397
Q93834 UniProt NPD GO	YYVP_CAEEL	Hypothetical protein F59C6.8	0.13	-	mit	1 *					529
Q10022 UniProt NPD GO	YSX3_CAEEL	Hypothetical protein T28D9.3	0.13	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				341
O14074 UniProt NPD GO	YEA9_SCHPO	Hypothetical protein UNK4.09 in chromosome I	0.13	-	cyt	0					339
Q09340 UniProt NPD GO	YR23_CAEEL	Hypothetical protein W02B3.3	0.13	-	cyt	0					111
Q09366 UniProt NPD GO	YS25_CAEEL	Hypothetical protein ZK1320.5	0.13	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				414
P30647 UniProt NPD GO	YOW1_CAEEL	Hypothetical protein ZK643.1	0.13	-	cyt	0					292
Q6ENB7 UniProt NPD GO	YCF68_ORYNI	Hypothetical protein ycf68 (ORF133)	0.13	-	mit	0	Plastid; chloroplast				133
P12173 UniProt NPD GO	YCF68_ORYSA	Hypothetical protein ycf68 (ORF133)	0.13	-	mit	0	Plastid; chloroplast				133
Q09788 UniProt NPD GO	YA9A_SCHPO	Hypothetical serine-rich protein C13G6.10c precursor	0.13	-	exc	0					530
P49248 UniProt NPD GO	IN21_MAIZE	IN2-1 protein	0.13	-	cyt	0					243
P01869 UniProt NPD GO	IGH1M_MOUSE	Ig gamma-1 chain C region, membrane-bound form	0.13	-	cyt	1		immunoglobulin complex, circulating [IDA]		25C8	393
P01859 UniProt NPD GO	IGHG2_HUMAN	Ig gamma-2 chain C region	0.13	-	nuc	0		membrane fraction [NAS]	147110		326
P01867 UniProt NPD GO	GCBM_MOUSE	Ig gamma-2B chain C region, membrane-bound form	0.13	-	nuc	1		immunoglobulin complex, circulating [IDA]		1CIC	404
P18527 UniProt NPD GO	HV56_MOUSE	Ig heavy chain V region 914	0.13	-	nuc	0					97
P01835 UniProt NPD GO	KACB_RAT	Ig kappa chain C region, B allele	0.13	-	nuc	0					106
P01615 UniProt NPD GO	KV2B_HUMAN	Ig kappa chain V-II region FR	0.13	-	cyt	0		extracellular region [NAS]			113
P06310 UniProt NPD GO	KV2F_HUMAN	Ig kappa chain V-II region RPMI 6410 precursor	0.13	-	exc	0		extracellular region [NAS]			133
P01656 UniProt NPD GO	KV3C_MOUSE	Ig kappa chain V-III region MOPC 70	0.13	-	nuc	0					111
P01654 UniProt NPD GO	KV3A_MOUSE	Ig kappa chain V-III region PC 2880/PC 1229	0.13	-	nuc	0					111
P06312 UniProt NPD GO	KV40_HUMAN	Ig kappa chain V-IV region precursor (Fragment)	0.13	-	exc	0		extracellular region [NAS]			121
P06888 UniProt NPD GO	LV1I_HUMAN	Ig lambda chain V-I region EPS	0.13	-	nuc	0		extracellular region [NAS]			109
P01700 UniProt NPD GO	LV1B_HUMAN	Ig lambda chain V-I region HA	0.13	-	nuc	0		extracellular region [NAS]			112
P06887 UniProt NPD GO	LV1H_HUMAN	Ig lambda chain V-I region MEM	0.13	-	nuc	0		extracellular region [NAS]			112
P01707 UniProt NPD GO	LV2D_HUMAN	Ig lambda chain V-II region TRO	0.13	-	nuc	0		extracellular region [NAS]			111
Q8SPV9 UniProt NPD GO	FCGRN_MACFA	IgG receptor FcRn large subunit p51 precursor (FcRn) (Neonatal Fc receptor) (IgG Fc fragment recepto ...	0.13	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				365
Q6XD66 UniProt NPD GO	HIS7_TORDE	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.13	-	cyt	0					223
Q9GZP8 UniProt NPD GO	IMUP_HUMAN	Immortalization-up-regulated protein (Hepatocyte growth factor activator inhibitor type 2-related sm ...	0.13	+	nuc	0	Nucleus	nucleus [TAS]			106
P13411 UniProt NPD GO	MA5D_SCHJA	Immunogenic miracidial antigen 5D (Fragment)	0.13	-	exc	1 *					120
P13523 UniProt NPD GO	MA8C_SCHJA	Immunogenic miracidial antigen 8C (Fragment)	0.13	-	nuc	0					95
P54233 UniProt NPD GO	NIA1_SOYBN	Inducible nitrate reductase [NADH] 1 (EC 1.7.1.1) (NR)	0.13	-	nuc	0					886
P43031 UniProt NPD GO	INHA_CHICK	Inhibin alpha chain precursor	0.13	-	exc	0	Secreted protein				329
Q759B8 UniProt NPD GO	MRS2_ASHGO	Inner membrane magnesium transporter MRS2, mitochondrial precursor (RNA-splicing protein MRS2)	0.13	-	end	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				423
Q9VAS7 UniProt NPD GO	INX3_DROME	Innexin inx3 (Innexin-3)	0.13	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	gap junction [IEP] integral to membrane [NAS]			395
Q9SYQ1 UniProt NPD GO	PHT18_ARATH	Inorganic phosphate transporter 1-8 (AtPht1;8) (H(+)/Pi cotransporter)	0.13	-	end	12 *	Cell membrane; multi-pass membrane protein (By similarity)				534
P12269 UniProt NPD GO	IMDH2_CRIGR	Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) (IMP dehydrogenase 2) (IMPDH-II) (IMPD 2)	0.13	-	cyt	0				1JR1	514
P24547 UniProt NPD GO	IMDH2_MOUSE	Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) (IMP dehydrogenase 2) (IMPDH-II) (IMPD 2)	0.13	-	cyt	0					514
Q8WN98 UniProt NPD GO	MIOX_PIG	Inositol oxygenase (EC 1.13.99.1) (Myo-inositol oxygenase) (Aldehyde reductase-like 6)	0.13	-	cyt	0	Cytoplasm	inclusion body [IDA]			282
P49441 UniProt NPD GO	INPP_HUMAN	Inositol polyphosphate 1-phosphatase (EC 3.1.3.57) (IPPase) (IPP)	0.13	-	cyt	0			147263		399
Q06667 UniProt NPD GO	IPK1_YEAST	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.13	-	cyt	0	Nucleus	nucleus [IDA]			281
P13190 UniProt NPD GO	INS_CALMI	Insulin [Contains: Insulin B chain; Insulin A chain]	0.13	-	cyt	0	Secreted protein				89
P17715 UniProt NPD GO	INS_OCTDE	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.13	-	cyt	0	Secreted protein				109
Q64716 UniProt NPD GO	INSRR_RAT	Insulin receptor-related protein precursor (EC 2.7.10.1) (IRR) (IR-related receptor) (Fragments)	0.13	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				581
P51461 UniProt NPD GO	INSL3_PIG	Insulin-like 3 precursor (Leydig insulin-like peptide) (Ley-I-L) (Relaxin-like factor) [Contains: In ...	0.13	-	nuc	0	Secreted protein				131
P18254 UniProt NPD GO	IGF1_CHICK	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.13	-	nuc	1 *	Secreted protein				153
P70671 UniProt NPD GO	IRF3_MOUSE	Interferon regulatory factor 3 (IRF-3)	0.13	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Shuttles between cytoplasmic and nuclear compart ...				419
P59822 UniProt NPD GO	IL1AP_MACMU	Interleukin-1 receptor accessory protein precursor (IL-1 receptor accessory protein) (IL-1RAcP)	0.13	-	cyt	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein				570
Q9Z1Y5 UniProt NPD GO	IL10_CAVPO	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.13	-	exc	0	Secreted protein	extracellular region [ISS]			178

You are viewing entries 59851 to 59900 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.