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
Q6FRN1 UniProt NPD GO	IPK1_CANGA	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.10	-	cyt	0	Nucleus (By similarity)				278
P01313 UniProt NPD GO	INS_CRILO	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.10	-	exc	0	Secreted protein				110
P01315 UniProt NPD GO	INS_PIG	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.10	-	vac	0	Secreted protein			9INS	108
Q91XI3 UniProt NPD GO	INS_SPETR	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.10	-	vac	0	Secreted protein				110
P01322 UniProt NPD GO	INS1_RAT	Insulin-1 precursor [Contains: Insulin-1 B chain; Insulin-1 A chain]	0.10	-	vac	0	Secreted protein				110
P12706 UniProt NPD GO	INS1_XENLA	Insulin-1 precursor [Contains: Insulin-1 B chain; Insulin-1 A chain]	0.10	-	vac	0	Secreted protein				106
Q28933 UniProt NPD GO	IGF1_SUNMU	Insulin-like growth factor I precursor (IGF-I) (Somatomedin) (Fragment)	0.10	-	nuc	0	Secreted protein				81
P62756 UniProt NPD GO	IATR_CAPHI	Inter-alpha-trypsin inhibitor (ITI) (GIK-14) (Inhibitory fragment of ITI) (Fragment)	0.10	-	cyt	0	Secreted protein				123
P62757 UniProt NPD GO	IATR_SHEEP	Inter-alpha-trypsin inhibitor (ITI) (Inhibitory fragment of ITI) (Fragment)	0.10	-	cyt	0					123
Q14773 UniProt NPD GO	ICAM4_HUMAN	Intercellular adhesion molecule 4 precursor (ICAM-4) (Landsteiner-Wiener blood group glycoprotein) ( ...	0.10	-	exc	1 *	Isoform Long: Cell membrane; single-pass type I membrane protein. Isoform Short: Secreted protein	integral to membrane [TAS] plasma membrane [TAS]	111250		271
P15260 UniProt NPD GO	INGR1_HUMAN	Interferon-gamma receptor alpha chain precursor (IFN-gamma-R1) (CD119 antigen) (CDw119)	0.10	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	107470	1JRH	489
P05161 UniProt NPD GO	UCRP_HUMAN	Interferon-induced 17 kDa protein precursor [Contains: Ubiquitin cross-reactive protein (hUCRP) (Int ...	0.10	-	cyt	0	Cytoplasm. UCRP conjugates seem to be noncovalently associated with the intermediate filaments and d ...	cytoplasm [NAS] extracellular space [NAS]	147571	1Z2M	164
Q8WNR2 UniProt NPD GO	IL1B_DELLE	Interleukin-1 beta precursor (IL-1 beta)	0.10	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				266
Q8WWZ1 UniProt NPD GO	IL1FA_HUMAN	Interleukin-1 family member 10 (IL-1F10) (Interleukin-1 receptor antagonist-like FIL1 theta) (Interl ...	0.10	-	mit	0	Secreted protein				152
P55029 UniProt NPD GO	IL10_FELCA	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.10	-	exc	0	Secreted protein	extracellular region [ISS]			178
Q29055 UniProt NPD GO	IL10_PIG	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.10	-	end	0	Secreted protein	extracellular region [ISS]			175
P29456 UniProt NPD GO	IL10_RAT	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.10	-	end	0	Secreted protein	extracellular region [ISS]			178
Q14627 UniProt NPD GO	I13R2_HUMAN	Interleukin-13 receptor alpha-2 chain precursor (Interleukin-13-binding protein) (CD213a2 antigen)	0.10	-	end	1	Membrane; single-pass type I membrane protein	extracellular space [TAS] soluble fraction [TAS]	300130		380
Q9XSJ6 UniProt NPD GO	IL15_SHEEP	Interleukin-15 precursor (IL-15)	0.10	-	exc	0	Secreted protein				162
P36835 UniProt NPD GO	IL2_CAPHI	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.10	-	exc	0	Secreted protein				155
Q925S4 UniProt NPD GO	IL24_MOUSE	Interleukin-24 precursor (Melanoma differentiation-associated gene 7 protein) (MDA-7) (IL-4-induced ...	0.10	-	mit	0	Secreted protein (Potential)	extracellular region [IDA]			181
Q6UWB1 UniProt NPD GO	I27RA_HUMAN	Interleukin-27 receptor alpha chain precursor (IL-27R-alpha) (WSX-1) (Type I T-cell cytokine recepto ...	0.10	-	end	1	Membrane; single-pass type I membrane protein		605350		636
Q8IU54 UniProt NPD GO	IL29_HUMAN	Interleukin-29 precursor (IL-29) (Interferon lambda-1) (IFN-lambda-1) (Cytokine ZCYTO21)	0.10	-	mit	1 *	Secreted protein	extracellular region [IDA] interleukin-28 receptor complex [IDA]	607403		200
O02699 UniProt NPD GO	IL5_HORSE	Interleukin-5 precursor (IL-5) (T-cell replacing factor) (TRF) (Eosinophil differentiation factor)	0.10	-	mit	0	Secreted protein				134
P22272 UniProt NPD GO	IL6RA_MOUSE	Interleukin-6 receptor alpha chain precursor (IL-6R-alpha) (IL-6R 1) (CD126 antigen)	0.10	-	end	1 *	Membrane; single-pass type I membrane protein				460
P10745 UniProt NPD GO	IRBP_HUMAN	Interphotoreceptor retinoid-binding protein precursor (IRBP) (Interstitial retinol-binding protein)	0.10	-	mit	0	Interphotoreceptor matrix that permeates the space between the retina and the contiguous layer of pi ...		180290		1247
P24822 UniProt NPD GO	PPBI_MOUSE	Intestinal alkaline phosphatase precursor (EC 3.1.3.1) (IAP)	0.10	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				559
P00724 UniProt NPD GO	INV2_YEAST	Invertase 2 precursor (EC 3.2.1.26) (Beta-fructofuranosidase 2) (Saccharase)	0.10	-	exc	0		cytoplasm [IDA] extracellular region [IDA] mitochondrion [IDA]			532
O70617 UniProt NPD GO	IRK13_RAT	Inward rectifier potassium channel 13 (Potassium channel, inwardly rectifying subfamily J member 13) ...	0.10	-	mit	2	Membrane; multi-pass membrane protein				360
Q6BGU0 UniProt NPD GO	ISU1_DEBHA	Iron sulfur cluster assembly protein 1, mitochondrial precursor (Iron sulfur cluster scaffold protei ...	0.10	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				179
Q8LBM4 UniProt NPD GO	ISAM1_ARATH	Iron-sulfur assembly protein IscA-like 1, mitochondrial precursor	0.10	-	mit	0	Mitochondrion (Potential)				137
Q8LCY2 UniProt NPD GO	ISAM2_ARATH	Iron-sulfur assembly protein IscA-like 2, mitochondrial precursor	0.10	-	mit	0	Mitochondrion (Potential)				158
Q07334 UniProt NPD GO	IAPP_RABIT	Islet amyloid polypeptide precursor (Amylin) (Fragment)	0.10	-	vac	0	Secreted protein				67
O13439 UniProt NPD GO	ACEA_COPCI	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.10	-	pox	0	Peroxisome (By similarity)				537
O42641 UniProt NPD GO	IDI1_PHARH	Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) (IPP isomerase) (Isopentenyl pyrophosphate isom ...	0.10	-	cyt	0					251
P15496 UniProt NPD GO	IDI1_YEAST	Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) (IPP isomerase) (Isopentenyl pyrophosphate isom ...	0.10	-	cyt	0	Cytoplasm				287
Q39471 UniProt NPD GO	IDI2_CLABR	Isopentenyl-diphosphate delta-isomerase II (EC 5.3.3.2) (IPP isomerase II) (Isopentenyl pyrophosphat ...	0.10	-	mit	0					286
Q91166 UniProt NPD GO	NEU1_ONCKE	Isoticin-neurophysin IT 1 precursor [Contains: Isotocin (IT); Neurophysin IT 1]	0.10	-	exc	1 *	Secreted protein				157
Q9D8B7 UniProt NPD GO	JAM3_MOUSE	Junctional adhesion molecule C precursor (JAM-C) (Junctional adhesion molecule 3) (JAM-3) (JAM-2)	0.10	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				310
Q92876 UniProt NPD GO	KLK6_HUMAN	Kallikrein-6 precursor (EC 3.4.21.-) (Protease M) (Neurosin) (Zyme) (SP59)	0.10	-	exc	0	Secreted protein	cytoplasm [IDA] extracellular region [IDA]	602652	1LO6	244
O12961 UniProt NPD GO	NXL4_BUNMU	Kappa-4-bungarotoxin precursor	0.10	-	nuc	0	Secreted protein				87
Q5E9V5 UniProt NPD GO	KLD8B_BOVIN	Kelch domain-containing protein 8B	0.10	-	cyt	0					354
Q8IXV7 UniProt NPD GO	KLD8B_HUMAN	Kelch domain-containing protein 8B	0.10	-	cyt	0					354
Q9D2D9 UniProt NPD GO	KLD8B_MOUSE	Kelch domain-containing protein 8B	0.10	-	cyt	0					354
Q5RCW7 UniProt NPD GO	KLD8B_PONPY	Kelch domain-containing protein 8B	0.10	-	cyt	0					354
Q9N010 UniProt NPD GO	KBTB4_MACFA	Kelch repeat and BTB domain-containing protein 4	0.10	-	cyt	0					543
Q8JZP3 UniProt NPD GO	KLHL2_MOUSE	Kelch-like protein 2	0.10	-	cyt	0					593
Q6L8H4 UniProt NPD GO	KRA51_HUMAN	Keratin-associated protein 5-1 (Keratin-associated protein 5.1) (Ultrahigh sulfur keratin-associated ...	0.10	-	nuc	0					278
Q6L8G4 UniProt NPD GO	KR511_HUMAN	Keratin-associated protein 5-11 (Keratin-associated protein 5.11) (Ultrahigh sulfur keratin-associat ...	0.10	-	nuc	0					156
O82043 UniProt NPD GO	ILV5_PEA	Ketol-acid reductoisomerase, chloroplast precursor (EC 1.1.1.86) (Acetohydroxy-acid reductoisomerase ...	0.10	-	mit	0	Plastid; chloroplast				581

You are viewing entries 64551 to 64600 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.