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
P0C1B8 UniProt NPD GO	IKIT_PARTR	Ikitoxin	0.00	-	cyt	0	Secreted protein				58
Q60414 UniProt NPD GO	NTCP2_CRIGR	Ileal sodium/bile acid cotransporter (Ileal Na(+)/bile acid cotransporter) (Na(+)-dependent ileal bi ...	0.00	-	end	8 *	Membrane; multi-pass membrane protein				348
Q12908 UniProt NPD GO	NTCP2_HUMAN	Ileal sodium/bile acid cotransporter (Ileal Na(+)/bile acid cotransporter) (Na(+)-dependent ileal bi ...	0.00	-	end	8 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	601295		348
P70172 UniProt NPD GO	NTCP2_MOUSE	Ileal sodium/bile acid cotransporter (Ileal Na(+)/bile acid cotransporter) (Na(+)-dependent ileal bi ...	0.00	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				348
Q28727 UniProt NPD GO	NTCP2_RABIT	Ileal sodium/bile acid cotransporter (Ileal Na(+)/bile acid cotransporter) (Na(+)-dependent ileal bi ...	0.00	-	end	8 *	Membrane; multi-pass membrane protein				347
Q62633 UniProt NPD GO	NTCP2_RAT	Ileal sodium/bile acid cotransporter (Ileal Na(+)/bile acid cotransporter) (Na(+)-dependent ileal bi ...	0.00	-	end	8 *	Membrane; multi-pass membrane protein	nucleus [IDA]			348
Q9TLQ8 UniProt NPD GO	HIS5_CYACA	Imidazole glycerol phosphate synthase subunit hisH (EC 2.4.2.-) (IGP synthase glutamine amidotransfe ...	0.00	-	mit	0	Plastid; chloroplast				214
Q85FY4 UniProt NPD GO	HIS5_CYAME	Imidazole glycerol phosphate synthase subunit hisH (EC 2.4.2.-) (IGP synthase glutamine amidotransfe ...	0.00	-	cyt	0	Plastid; chloroplast				206
P14945 UniProt NPD GO	LZ8_GANLU	Immunomodulatory protein Ling Zhi-8 (LZ-8)	0.00	-	cyt	0					110
Q38954 UniProt NPD GO	PHT21_ARATH	Inorganic phosphate transporter 2-1, chloroplast precursor (H(+)/Pi cotransporter) (AtPht2;1)	0.00	-	end	12	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (Probable)				587
Q757J8 UniProt NPD GO	IPYR_ASHGO	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.00	-	cyt	0	Cytoplasm (By similarity)				287
P37980 UniProt NPD GO	IPYR_BOVIN	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.00	-	cyt	0	Cytoplasm				289
Q9D819 UniProt NPD GO	IPYR_MOUSE	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.00	-	cyt	0	Cytoplasm (By similarity)				289
Q27546 UniProt NPD GO	IUNH_CRIFA	Inosine-uridine preferring nucleoside hydrolase (EC 3.2.2.1) (IU-nucleoside hydrolase) (IU-NH) (Puri ...	0.00	-	mit	0				2MAS	314
P29219 UniProt NPD GO	IMPA1_XENLA	Inositol monophosphatase (EC 3.1.3.25) (IMPase) (IMP) (Inositol-1(or 4)-monophosphatase)	0.00	-	cyt	0	Cytoplasm				285
P20456 UniProt NPD GO	IMPA1_BOVIN	Inositol monophosphatase (EC 3.1.3.25) (IMPase) (IMP) (Inositol-1(or 4)-monophosphatase) (Lithium-se ...	0.00	-	cyt	0	Cytoplasm			2BJI	277
P97697 UniProt NPD GO	IMPA1_RAT	Inositol monophosphatase (EC 3.1.3.25) (IMPase) (IMP) (Inositol-1(or 4)-monophosphatase) (Lithium-se ...	0.00	-	cyt	0	Cytoplasm				277
P54926 UniProt NPD GO	IMP1_LYCES	Inositol monophosphatase 1 (EC 3.1.3.25) (IMPase 1) (IMP 1) (Inositol-1(or 4)-monophosphatase 1)	0.00	-	cyt	0					273
P54928 UniProt NPD GO	IMP3_LYCES	Inositol monophosphatase 3 (EC 3.1.3.25) (IMPase 3) (IMP 3) (Inositol-1(or 4)-monophosphatase 3)	0.00	-	cyt	0					268
Q8H1S0 UniProt NPD GO	MIOX4_ARATH	Inositol oxygenase 4 (EC 1.13.99.1) (Myo-inositol oxygenase 4) (AtMIOX4)	0.00	-	cyt	0	Cytoplasm (Probable)				317
P17728 UniProt NPD GO	SCXA_LEIQH	Insect toxin alpha precursor (Alpha-IT) (Lqh-alpha-IT) (LqhaIT)	0.00	-	exc	0	Secreted protein			1LQI	85
P00305 UniProt NPD GO	ICYA_MANSE	Insecticyanin A form (Blue biliprotein) (INS-a)	0.00	-	cyt	0	Secreted protein			1Z24	189
Q00630 UniProt NPD GO	ICYB_MANSE	Insecticyanin B form precursor (Blue biliprotein) (INS-b)	0.00	-	vac	0	Secreted protein				206
P81423 UniProt NPD GO	INS_ACIGU	Insulin [Contains: Insulin B chain; Insulin A chain]	0.00	-	cyt	0	Secreted protein				52
P29335 UniProt NPD GO	INS_AMICA	Insulin [Contains: Insulin B chain; Insulin A chain]	0.00	-	cyt	0	Secreted protein				52
P42633 UniProt NPD GO	INS_ANGRO	Insulin [Contains: Insulin B chain; Insulin A chain]	0.00	-	mit	0	Secreted protein				51
P01319 UniProt NPD GO	INS_CAPHI	Insulin [Contains: Insulin B chain; Insulin A chain]	0.00	-	cyt	0	Secreted protein				51
P01316 UniProt NPD GO	INS_ELEMA	Insulin [Contains: Insulin B chain; Insulin A chain]	0.00	-	cyt	0	Secreted protein				51
P01340 UniProt NPD GO	INS_KATPE	Insulin [Contains: Insulin B chain; Insulin A chain]	0.00	-	cyt	0	Secreted protein				50
P09476 UniProt NPD GO	INS_LEPSP	Insulin [Contains: Insulin B chain; Insulin A chain]	0.00	-	cyt	0	Secreted protein				52
P68989 UniProt NPD GO	INS_ONCGO	Insulin [Contains: Insulin B chain; Insulin A chain]	0.00	-	cyt	0	Secreted protein				50
P68990 UniProt NPD GO	INS_ONCKI	Insulin [Contains: Insulin B chain; Insulin A chain]	0.00	-	cyt	0	Secreted protein				50
Q9TQY7 UniProt NPD GO	INS_ORNAN	Insulin [Contains: Insulin B chain; Insulin A chain]	0.00	-	cyt	0	Secreted protein				51
P81881 UniProt NPD GO	INS_PIAME	Insulin [Contains: Insulin B chain; Insulin A chain]	0.00	-	cyt	0	Secreted protein				52
P12704 UniProt NPD GO	INS_SQUAC	Insulin [Contains: Insulin B chain; Insulin A chain]	0.00	-	cyt	0	Secreted protein				54
P41522 UniProt NPD GO	INS_ANGAN	Insulin precursor [Contains: Insulin A chain] (Fragment)	0.00	-	cyt	0	Secreted protein				53
Q8CFA6 UniProt NPD GO	INSI1_CRIGR	Insulin-induced gene 1 protein (INSIG-1)	0.00	-	end	5	Membrane; multi-pass membrane protein (Potential)				257
Q8BGI3 UniProt NPD GO	INSI1_MOUSE	Insulin-induced gene 1 protein (INSIG-1)	0.00	-	end	5	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [TAS]			259
Q08755 UniProt NPD GO	INSI1_RAT	Insulin-induced gene 1 protein (INSIG-1) (Insulin-induced growth response protein CL-6) (Immediate-e ...	0.00	-	end	5	Membrane; multi-pass membrane protein (Potential)				259
P83770 UniProt NPD GO	INSL_VIGUN	Insulin-like protein [Contains: Insulin-like protein B chain; Insulin-like protein A chain] (Fragmen ...	0.00	-	cyt	0					51
Q09062 UniProt NPD GO	ITB2_XENLA	Integrin beta-2 (Fragment)	0.00	-	nuc	0	Membrane; single-pass type I membrane protein (Potential)				77
P56651 UniProt NPD GO	ITIH2_BOVIN	Inter-alpha-trypsin inhibitor heavy chain H2 (ITI heavy chain H2) (Inter-alpha-inhibitor heavy chain ...	0.00	-	cyt	0					50
P40305 UniProt NPD GO	INI7_HUMAN	Interferon-alpha-induced 11.5 kDa protein (p27) (ISG12(a) protein)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]	600009		122
Q9UBH0 UniProt NPD GO	IL1F5_HUMAN	Interleukin-1 family member 5 (IL-1F5) (Interleukin-1 delta) (IL-1 delta) (FIL1 delta) (Interleukin- ...	0.00	-	mit	0	Secreted protein		605507		155
P46653 UniProt NPD GO	IL8_CERTO	Interleukin-8 precursor (IL-8) (CXCL8)	0.00	-	exc	0	Secreted protein	extracellular space [ISS]			101
P12666 UniProt NPD GO	IRBP_CAVPO	Interphotoreceptor retinoid-binding protein (IRBP) (Interstitial retinol-binding protein) (Fragment) ...	0.00	-		0	Interphotoreceptor matrix that permeates the space between the retina and the contiguous layer of pi ...				19
P12662 UniProt NPD GO	IRBP_PIG	Interphotoreceptor retinoid-binding protein (IRBP) (Interstitial retinol-binding protein) (Fragment) ...	0.00	-	cyt	0	Interphotoreceptor matrix that permeates the space between the retina and the contiguous layer of pi ...				25
P12664 UniProt NPD GO	IRBP_RABIT	Interphotoreceptor retinoid-binding protein (IRBP) (Interstitial retinol-binding protein) (Fragment) ...	0.00	-	cyt	0	Interphotoreceptor matrix that permeates the space between the retina and the contiguous layer of pi ...				23
P12663 UniProt NPD GO	IRBP_SHEEP	Interphotoreceptor retinoid-binding protein (IRBP) (Interstitial retinol-binding protein) (Fragment) ...	0.00	-	cyt	0	Interphotoreceptor matrix that permeates the space between the retina and the contiguous layer of pi ...				24
P81563 UniProt NPD GO	MMP1_RAT	Interstitial collagenase (EC 3.4.24.7) (Matrix metalloproteinase-1) (MMP-1) (Fibroblast collagenase) ...	0.00	-		0					15

You are viewing entries 95301 to 95350 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.