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
O14713 UniProt NPD GO	ITBP1_HUMAN	Integrin beta-1-binding protein 1 (Integrin cytoplasmic domain-associated protein 1) (ICAP-1)	0.30	-	mit	0	Cytoplasm	membrane [NAS]	607153	1K11	200
Q9R000 UniProt NPD GO	ITBP2_MOUSE	Integrin beta-1-binding protein 2 (Melusin)	0.30	-	cyt	0		Z disc [IDA]			350
Q5NKV4 UniProt NPD GO	ICAM1_PANPA	Intercellular adhesion molecule 1 precursor (ICAM-1)	0.30	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				532
Q28806 UniProt NPD GO	ICAM1_PANTR	Intercellular adhesion molecule 1 precursor (ICAM-1)	0.30	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				532
P09235 UniProt NPD GO	IFNA9_MOUSE	Interferon alpha-9 precursor	0.30	-	mit	0	Secreted protein				190
Q28595 UniProt NPD GO	IFNT5_SHEEP	Interferon tau-5 precursor (IFN-tau5) (Trophoblast protein 1) (Trophoblastin) (Antiluteolysin) (Trop ...	0.30	-	mit	1 *	Secreted protein. Secreted into the uterine lumen				195
P46648 UniProt NPD GO	IL1B_CERTO	Interleukin-1 beta precursor (IL-1 beta)	0.30	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				269
P51493 UniProt NPD GO	IL1B_MACNE	Interleukin-1 beta precursor (IL-1 beta)	0.30	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				269
P26889 UniProt NPD GO	IL1B_PIG	Interleukin-1 beta precursor (IL-1 beta)	0.30	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				267
Q9XS77 UniProt NPD GO	IL1B_TRIVU	Interleukin-1 beta precursor (IL-1 beta)	0.30	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				269
Q99MF5 UniProt NPD GO	IL11_RAT	Interleukin-11 precursor (IL-11)	0.30	-	end	0	Secreted protein (By similarity)				199
P43432 UniProt NPD GO	IL12B_MOUSE	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.30	-	nuc	1 *	Secreted protein	extracellular space [ISS]			335
Q8NAC3 UniProt NPD GO	I17RC_HUMAN	Interleukin-17 receptor C precursor (IL-17 receptor C) (IL-17RC) (Interleukin-17 receptor-like prote ...	0.30	-	end	1	Cell membrane; single-pass type I membrane protein. Soluble isoforms may be produced				791
Q687Y7 UniProt NPD GO	IL17_BOVIN	Interleukin-17A precursor (IL-17A) (IL-17)	0.30	-	exc	0	Secreted protein (By similarity)				153
Q9UHD0 UniProt NPD GO	IL19_HUMAN	Interleukin-19 precursor (IL-19) (Melanoma differentiation-associated protein-like protein) (NG.1)	0.30	-	mit	0	Secreted protein	extracellular region [NAS]	605687	1N1F	177
P68291 UniProt NPD GO	IL2_MACMU	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.30	-	exc	0	Secreted protein	extracellular space [ISS]			154
P68290 UniProt NPD GO	IL2_MACNE	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.30	-	exc	0	Secreted protein	extracellular space [ISS]			154
Q9NYY1 UniProt NPD GO	IL20_HUMAN	Interleukin-20 precursor (IL-20) (Four alpha helix cytokine Zcyto10)	0.30	-	nuc	0	Secreted protein	extracellular region [TAS]	605619		176
Q9JI24 UniProt NPD GO	IL24_RAT	Interleukin-24 precursor (Cytokine-like protein Mob-5)	0.30	-	exc	0	Secreted protein				183
Q63257 UniProt NPD GO	IL4RA_RAT	Interleukin-4 receptor alpha chain precursor (IL-4R-alpha) (CD124 antigen)	0.30	-	exc	0	Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein (Probable)				801
P46685 UniProt NPD GO	IL5_CERTO	Interleukin-5 precursor (IL-5) (T-cell replacing factor) (TRF) (Eosinophil differentiation factor)	0.30	-	exc	0	Secreted protein				134
P79341 UniProt NPD GO	IL6_MACFA	Interleukin-6 precursor (IL-6)	0.30	-	exc	1 *	Secreted protein	extracellular region [ISS] extracellular space [ISS]			212
P05231 UniProt NPD GO	IL6_HUMAN	Interleukin-6 precursor (IL-6) (B-cell stimulatory factor 2) (BSF-2) (Interferon beta-2) (Hybridoma ...	0.30	-	exc	0	Secreted protein	extracellular region [NAS] extracellular space [TAS]	147620	2IL6	212
P40189 UniProt NPD GO	IL6RB_HUMAN	Interleukin-6 receptor beta chain precursor (IL-6R-beta) (Interleukin 6 signal transducer) (Membrane ...	0.30	-	nuc	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein	integral to plasma membrane [TAS] plasma membrane [TAS]	600694	1PVH	918
P10594 UniProt NPD GO	INV1_YEAST	Invertase 1 precursor (EC 3.2.1.26) (Beta-fructofuranosidase 1) (Saccharase)	0.30	-	vac	0					532
Q9DCX8 UniProt NPD GO	IYD1_MOUSE	Iodotyrosine dehalogenase 1 precursor (EC 1.-.-.-) (IYD-1)	0.30	-	mit	1 *	Membrane; single-pass membrane protein (By similarity)				285
P80366 UniProt NPD GO	PPAF_PHAVU	Iron(III)-zinc(II) purple acid phosphatase (EC 3.1.3.2) (PAP)	0.30	-	cyt	0	Secreted protein			4KBP	432
Q9P8Q7 UniProt NPD GO	ACEA_CANAL	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.30	-	cyt	0	Peroxisome (By similarity)				550
P49296 UniProt NPD GO	ACEA_CUCSA	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.30	-	exc	0	Glyoxysome				576
P17069 UniProt NPD GO	ACEA_GOSHI	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.30	-	cyt	0	Glyoxysome				576
P36422 UniProt NPD GO	SYI_TETTH	Isoleucyl-tRNA synthetase (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS)	0.30	-	nuc	0					1081
P50421 UniProt NPD GO	CASK_CAPSW	Kappa-casein precursor	0.30	-	exc	0	Secreted protein				192
Q8IYD2 UniProt NPD GO	KLD8A_HUMAN	Kelch domain-containing protein 8A	0.30	-	cyt	0					350
Q8CE33 UniProt NPD GO	KLH11_MOUSE	Kelch-like protein 11 precursor	0.30	-	cyt	0	Secreted protein (Potential)				709
P19012 UniProt NPD GO	K1C15_HUMAN	Keratin, type I cytoskeletal 15 (Cytokeratin-15) (CK-15) (Keratin-15) (K15)	0.30	-	cyt	0		intermediate filament [TAS]	148030		456
Q9NSB2 UniProt NPD GO	KRHB4_HUMAN	Keratin, type II cuticular Hb4 (Hair keratin, type II Hb4)	0.30	-	mit	0			602766		600
P39731 UniProt NPD GO	MTW1_YEAST	Kinetochore-associated protein MTW1 (Mis12-like protein)	0.30	-	nuc	0	Nucleus. Associated with the kinetochore	MIND complex [IDA] spindle pole [IDA]			289
O21436 UniProt NPD GO	KM11_LEITR	Kinetoplastid membrane protein 11 (KMP-11)	0.30	-	nuc	0	Cytoplasm (By similarity). Associated with microtubules (By similarity)	microtubule cytoskeleton [ISS]			92
P79368 UniProt NPD GO	SCF_SHEEP	Kit ligand precursor (C-kit ligand) (Stem cell factor) (SCF) (Mast cell growth factor) (MGF) (Fragme ...	0.30	-	exc	1 *	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				267
Q9NRN7 UniProt NPD GO	ADPPT_HUMAN	L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase (EC 2.7.8.-) (4'-phosphopa ...	0.30	-	mit	0	Cytoplasm		607756	2CG5	309
P34416 UniProt NPD GO	LASP1_CAEEL	LIM and SH3 domain protein F42H10.3	0.30	-	nuc	0					335
Q25060 UniProt NPD GO	LWA_HYDEC	LWamide neuropeptides precursor [Contains: LWamide I; LWamide II; LWS]	0.30	-	exc	0	Secreted protein				419
Q5AUI1 UniProt NPD GO	LBSA_EMENI	Lactobacillus shifted protein	0.30	-	mit	0					213
O77811 UniProt NPD GO	TRFL_HORSE	Lactotransferrin precursor (EC 3.4.21.-) (Lactoferrin) (Fragment)	0.30	-	nuc	0	Secreted protein			1QJM	695
Q8JZZ7 UniProt NPD GO	LPHN2_MOUSE	Latrophilin-2 (Calcium-independent alpha-latrotoxin receptor 2) (Fragment)	0.30	-	end	7	Membrane; multi-pass membrane protein				891
Q28603 UniProt NPD GO	LEP_SHEEP	Leptin (Obesity factor)	0.30	-	nuc	0	Secreted protein (Probable)				146
Q15334 UniProt NPD GO	L2GL1_HUMAN	Lethal(2) giant larvae protein homolog 1 (LLGL) (Human homolog to the D-lgl gene) (Hugl-1) (DLG4)	0.30	-	mit	0	Cytoplasm. Localized to the lateral membrane during the polarization and formation cell-cell contact ...	cortical actin cytoskeleton [IDA] cytoplasm [IDA] cytoskeleton [TAS]	600966		1062
Q6C3P4 UniProt NPD GO	LCMT2_YARLI	Leucine carboxyl methyltransferase 2 (EC 2.1.1.-)	0.30	+	mit	0					989
Q99PH1 UniProt NPD GO	LRRC4_MOUSE	Leucine-rich repeat-containing 4 protein precursor (Brain tumor-associated protein MBAG1)	0.30	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				652
Q5EAD8 UniProt NPD GO	LRC51_BOVIN	Leucine-rich repeat-containing protein 51	0.30	-	nuc	0					192

You are viewing entries 40451 to 40500 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.