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
P68723 UniProt NPD GO	SIX1C_LEIQH	Insect neurotoxin 1c precursor (Lqh IT1-c) (LqhIT1-c)	0.06	-	end	0	Secreted protein				88
Q26292 UniProt NPD GO	SIX2_LEIQH	Insect toxin 2 precursor (Lqh IT2) (LqhIT2) (LqhIT2-44)	0.06	-	vac	0	Secreted protein				85
P55903 UniProt NPD GO	SIX4_BUTOC	Insect toxin 4 (BotIT4)	0.06	-	cyt	0	Secreted protein				61
P55817 UniProt NPD GO	TXI12_DIGCA	Insecticidal toxin DTX12	0.06	-	cyt	0	Secreted protein				61
P01334 UniProt NPD GO	INS_CROAT	Insulin [Contains: Insulin B chain; Insulin A chain]	0.06	-	nuc	0	Secreted protein				51
P30407 UniProt NPD GO	INS_CERAE	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.06	-	exc	0	Secreted protein				110
Q6YK33 UniProt NPD GO	INS_GORGO	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.06	-	vac	0	Secreted protein				110
P01308 UniProt NPD GO	INS_HUMAN	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.06	-	vac	0	Secreted protein	extracellular region [IC]	176730	5AIY	110
Q62587 UniProt NPD GO	INS_PSAOB	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.06	-	vac	0	Secreted protein				110
P21563 UniProt NPD GO	INS_RODSP	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.06	-	end	0	Secreted protein. Stored in spherulous cells prior to secretion				108
O15503 UniProt NPD GO	INSI1_HUMAN	Insulin-induced gene 1 protein (INSIG-1)	0.06	-	end	5	Membrane; multi-pass membrane protein (Potential)		602055		277
P08833 UniProt NPD GO	IBP1_HUMAN	Insulin-like growth factor-binding protein 1 precursor (IGFBP-1) (IBP-1) (IGF-binding protein 1) (Pl ...	0.06	-	exc	0	Secreted protein	extracellular space [TAS]	146730	1ZT5	259
Q61500 UniProt NPD GO	ITM2A_MOUSE	Integral membrane protein 2A (E25 protein)	0.06	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)				263
Q9ERM2 UniProt NPD GO	ICAM4_MOUSE	Intercellular adhesion molecule 4 precursor (ICAM-4) (CD242 antigen)	0.06	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein				262
P09912 UniProt NPD GO	INI2_HUMAN	Interferon-induced protein 6-16 precursor (Ifi-6-16) (Interferon alpha-inducible protein 6)	0.06	-	end	2 *		mitochondrion [IDA]	147572		130
Q28808 UniProt NPD GO	INI2_PANTR	Interferon-induced protein 6-16 precursor (Ifi-6-16) (Interferon alpha-inducible protein 6)	0.06	-	end	2 *		mitochondrion [ISS]			130
Q9XSQ7 UniProt NPD GO	IL18_HORSE	Interleukin-18 precursor (IL-18) (Interferon-gamma-inducing factor) (IFN-gamma-inducing factor) (Int ...	0.06	-	cyt	0	Secreted protein				193
Q5MBA8 UniProt NPD GO	IL2_MOSBE	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.06	-	exc	0	Secreted protein (By similarity)				155
P30367 UniProt NPD GO	IL4_BOVIN	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.06	-	exc	0	Secreted protein	extracellular space [ISS]			135
P36925 UniProt NPD GO	IL8_SHEEP	Interleukin-8 precursor (IL-8) (CXCL8)	0.06	-	exc	1 *	Secreted protein	extracellular space [ISS]			101
Q7YRB5 UniProt NPD GO	IL8_TURTR	Interleukin-8 precursor (IL-8) (CXCL8)	0.06	-	exc	1 *	Secreted protein				101
P49194 UniProt NPD GO	IRBP_MOUSE	Interphotoreceptor retinoid-binding protein precursor (IRBP) (Interstitial retinol-binding protein)	0.06	-	exc	0	Interphotoreceptor matrix that permeates the space between the retina and the contiguous layer of pi ...				1234
Q9EPL5 UniProt NPD GO	MMP1A_MOUSE	Interstitial collagenase A precursor (EC 3.4.24.7) (Matrix metalloproteinase-1a) (MMP-1a) (Mcol-A)	0.06	-	exc	0					464
Q62559 UniProt NPD GO	IFT52_MOUSE	Intraflagellar transport 52 homolog (Protein NGD5)	0.06	-	cyt	0					426
O94220 UniProt NPD GO	INU2_ASPFI	Inulinase precursor (EC 3.2.1.7) (2,1-beta-D-fructanfructanohydrolase) (Inulase)	0.06	-	vac	0	Secreted protein				516
P82025 UniProt NPD GO	IOTA_GONVI	Iota-crystallin (Fragment)	0.06	-	nuc	0					62
P78591 UniProt NPD GO	FET3_CANAL	Iron transport multicopper oxidase FET3 precursor (EC 1.-.-.-)	0.06	-	end	1 *	Cell membrane; single-pass type I membrane protein; extracellular side (Potential)				624
P41734 UniProt NPD GO	IAH1_YEAST	Isoamyl acetate-hydrolyzing esterase (EC 3.1.-.-)	0.06	-	cyt	0					238
O43837 UniProt NPD GO	IDH3B_HUMAN	Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehydr ...	0.06	-	mit	0	Mitochondrion	mitochondrion [TAS]	604526		385
Q28479 UniProt NPD GO	IDH3B_MACFA	Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehydr ...	0.06	-	mit	0	Mitochondrion				385
Q5RBT4 UniProt NPD GO	IDH3B_PONPY	Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehydr ...	0.06	-	mit	0	Mitochondrion (By similarity)				385
P12007 UniProt NPD GO	IVD_RAT	Isovaleryl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.10) (IVD)	0.06	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			424
P82227 UniProt NPD GO	TJT1A_HADVE	Janus-atracotoxin-Hv1a (J-AcTx-Hv1a)	0.06	-	nuc	0	Secreted protein				36
P42764 UniProt NPD GO	JIPH_ATRCA	Jasmonate-induced protein homolog	0.06	-	cyt	0					185
Q2WGK2 UniProt NPD GO	JAM1_FELCA	Junctional adhesion molecule A precursor (JAM-A) (Junctional adhesion molecule 1) (JAM-1) (CD321 ant ...	0.06	-	end	1 *	Cell membrane; cell-cell junction; tight junction; single-pass type I membrane protein (By similarit ...				298
O93422 UniProt NPD GO	TXWK_NAJAT	Kappa-cobrotoxin precursor	0.06	-	vac	1 *	Secreted protein				86
Q3LI61 UniProt NPD GO	KR202_HUMAN	Keratin-associated protein 20-2	0.06	-	cyt	1 *					65
Q6L8G9 UniProt NPD GO	KRA56_HUMAN	Keratin-associated protein 5-6 (Keratin-associated protein 5.6) (Ultrahigh sulfur keratin-associated ...	0.06	-	nuc	0					129
Q6L8G8 UniProt NPD GO	KRA57_HUMAN	Keratin-associated protein 5-7 (Keratin-associated protein 5.7) (Ultrahigh sulfur keratin-associated ...	0.06	-	nuc	0					165
Q8K177 UniProt NPD GO	KCP3_MOUSE	Keratinocytes-associated protein 3 (KCP-3)	0.06	-	end	4 *	Membrane; multi-pass membrane protein				240
Q5RD71 UniProt NPD GO	KHK_PONPY	Ketohexokinase (EC 2.7.1.3) (Hepatic fructokinase)	0.06	-	cyt	0					297
Q969F8 UniProt NPD GO	KISSR_HUMAN	KiSS-1 receptor (KiSS-1R) (Kisspeptins receptor) (Metastin receptor) (G-protein coupled receptor 54) ...	0.06	+	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IEP]	604161		398
P83667 UniProt NPD GO	DRTI_DELRE	Kunitz-type serine protease inhibitor DrTI	0.06	-	cyt	1 *	Secreted protein			1R8N	185
Q6CDM0 UniProt NPD GO	KYNU_YARLI	Kynureninase (EC 3.7.1.3) (L-kynurenine hydrolase)	0.06	-	cyt	0	Cytoplasm (By similarity)				437
P32953 UniProt NPD GO	CYBL_RHOGR	L(+)-mandelate dehydrogenase (EC 1.-.-.-) (S-mandelate dehydrogenase) (Flavocytochrome b) (Fragment) ...	0.06	-	nuc	0	Membrane; peripheral membrane protein				32
P50288 UniProt NPD GO	ASPG_LUPAL	L-asparaginase precursor (EC 3.5.1.1) (L-asparagine amidohydrolase) [Contains: L-asparaginase subuni ...	0.06	-	cyt	0					325
Q12719 UniProt NPD GO	LAC4_TRAVE	Laccase 4 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Diphenol o ...	0.06	-	end	0	Secreted protein				520
Q99055 UniProt NPD GO	LAC4_TRAVI	Laccase 4 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Diphenol o ...	0.06	-	end	0	Secreted protein				520
P17489 UniProt NPD GO	LAC1_EMENI	Laccase-1 precursor (EC 1.10.3.2) (Laccase I) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) ...	0.06	-	vac	0	Secreted protein (Potential)				609
P81018 UniProt NPD GO	LADD_ONCMY	Ladderlectin (Fragment)	0.06	-		0					11

You are viewing entries 72351 to 72400 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.