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
Q75ZP3 UniProt NPD GO	IBP1_PIG	Insulin-like growth factor-binding protein 1 precursor (IGFBP-1) (IBP-1) (IGF-binding protein 1)	0.31	-	nuc	0	Secreted protein (By similarity)				262
P13612 UniProt NPD GO	ITA4_HUMAN	Integrin alpha-4 precursor (Integrin alpha-IV) (VLA-4) (CD49d antigen)	0.31	-	nuc	1	Membrane; single-pass type I membrane protein		192975		1038
P12607 UniProt NPD GO	ITB1B_XENLA	Integrin beta-1-B precursor (Integrin beta-1*)	0.31	-	end	1	Membrane; single-pass type I membrane protein				798
O35671 UniProt NPD GO	ITBP1_MOUSE	Integrin beta-1-binding protein 1 (Bodenin)	0.31	-	mit	0					200
P05362 UniProt NPD GO	ICAM1_HUMAN	Intercellular adhesion molecule 1 precursor (ICAM-1) (Major group rhinovirus receptor) (CD54 antigen ...	0.31	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [NAS]	147840	1P53	532
P56829 UniProt NPD GO	IFNT2_SHEEP	Interferon tau-2 precursor (IFN-tau2) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin ...	0.31	-	mit	1 *	Secreted protein. Secreted into the uterine lumen				195
Q08070 UniProt NPD GO	IFNT9_SHEEP	Interferon tau-9 precursor (IFN-tau9) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin ...	0.31	-	cyt	1 *	Secreted protein. Secreted into the uterine lumen				195
Q04790 UniProt NPD GO	INAR1_BOVIN	Interferon-alpha/beta receptor alpha chain precursor (IFN-alpha-REC)	0.31	-	end	1	Membrane; single-pass type I membrane protein				560
P48090 UniProt NPD GO	IL1B_MACMU	Interleukin-1 beta precursor (IL-1 beta)	0.31	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				269
Q9NZH7 UniProt NPD GO	IL1F8_HUMAN	Interleukin-1 family member 8 (IL-1F8) (Interleukin-1 eta) (IL-1 eta) (FIL1 eta) (Interleukin-1 homo ...	0.31	-	nuc	0	Secreted protein (Potential)	extracellular region [TAS]	605508		164
Q29612 UniProt NPD GO	IL1R2_CERAE	Interleukin-1 receptor type II precursor (IL-1R-2) (IL-1R-beta) (CD121b antigen)	0.31	+	nuc	1	Isoform Long: Cell membrane; single-pass type I membrane protein. Isoform short: Cytoplasm; cytosol. ...				393
P47965 UniProt NPD GO	IL10_MERUN	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.31	-	nuc	0	Secreted protein				178
Q61727 UniProt NPD GO	I10R1_MOUSE	Interleukin-10 receptor alpha chain precursor (IL-10R-A) (IL-10R1) (CDw210a antigen)	0.31	-	end	1	Membrane; single-pass type I membrane protein				575
Q60I29 UniProt NPD GO	IL17_PIG	Interleukin-17A precursor (IL-17A) (IL-17)	0.31	-	exc	1 *	Secreted protein (By similarity)				153
Q9P0M4 UniProt NPD GO	IL17C_HUMAN	Interleukin-17C precursor (IL-17C) (Cytokine CX2)	0.31	-	nuc	0	Secreted protein	extracellular space [TAS] soluble fraction [TAS]	604628		197
Q7JFM2 UniProt NPD GO	IL2_AOTLE	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.31	-	exc	0	Secreted protein (By similarity)	extracellular space [ISS]			154
Q7JFM5 UniProt NPD GO	IL2_AOTNA	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.31	-	exc	0	Secreted protein (By similarity)	extracellular space [ISS]			154
Q7JFM3 UniProt NPD GO	IL2_AOTNI	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.31	-	exc	0	Secreted protein (By similarity)	extracellular space [ISS]			154
Q7JFM4 UniProt NPD GO	IL2_AOTVO	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.31	-	exc	0	Secreted protein (By similarity)				154
P60569 UniProt NPD GO	IL2_HYLLA	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.31	-	exc	0	Secreted protein	extracellular space [ISS]			153
Q9XS38 UniProt NPD GO	IL2_PAPHA	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.31	-	exc	0	Secreted protein (By similarity)				154
Q8MKH2 UniProt NPD GO	IL2_SAISC	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.31	-	exc	0	Secreted protein	extracellular space [ISS]			154
P60568 UniProt NPD GO	IL2_HUMAN	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF) (Aldesleukin)	0.31	-	exc	0	Secreted protein	extracellular space [TAS]	147680	3INK	153
Q8IZJ0 UniProt NPD GO	IL28A_HUMAN	Interleukin-28A precursor (IL-28A) (Interferon lambda-2) (IFN-lambda-2) (Cytokine ZCYTO20)	0.31	-	nuc	1 *	Secreted protein		607401		200
P51492 UniProt NPD GO	IL4_MACMU	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.31	-	exc	0	Secreted protein	extracellular space [ISS]			153
P26892 UniProt NPD GO	IL6_BOVIN	Interleukin-6 precursor (IL-6)	0.31	-	exc	1 *	Secreted protein				208
Q6V919 UniProt NPD GO	IL6_BUBBU	Interleukin-6 precursor (IL-6)	0.31	-	exc	1 *	Secreted protein				208
Q865W7 UniProt NPD GO	IL6_CAMBA	Interleukin-6 precursor (IL-6)	0.31	-	exc	1 *	Secreted protein				211
P20607 UniProt NPD GO	IL6_RAT	Interleukin-6 precursor (IL-6)	0.31	-	exc	0	Secreted protein				211
Q4WGL2 UniProt NPD GO	MIA40_ASPFU	Intermembrane space import and assembly protein 40, mitochondrial precursor (Mitochondrial import in ...	0.31	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...				297
Q5KGA4 UniProt NPD GO	MIA40_CRYNE	Intermembrane space import and assembly protein 40, mitochondrial precursor (Mitochondrial import in ...	0.31	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...				242
O13651 UniProt NPD GO	SYIC_SCHPO	Isoleucyl-tRNA synthetase, cytoplasmic (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS)	0.31	+	nuc	0	Cytoplasm (Potential)				1064
Q6BXJ4 UniProt NPD GO	JHD1_DEBHA	JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-)	0.31	-	nuc	0	Nucleus (By similarity)				514
P14690 UniProt NPD GO	KAF1_SORBI	Kafirin PGK1 precursor	0.31	-	exc	1 *					269
Q9H2R5 UniProt NPD GO	KLK15_HUMAN	Kallikrein-15 precursor (EC 3.4.21.-) (ACO protease)	0.31	-	exc	0	Secreted protein (Probable)	extracellular region [NAS]			256
Q8BJ66 UniProt NPD GO	KAZD1_MOUSE	Kazal-type serine protease inhibitor domain-containing protein 1 precursor (IGFBP-related protein 10 ...	0.31	-	exc	1 *	Secreted protein (Probable)				313
Q6NRH0 UniProt NPD GO	KLH12_XENLA	Kelch-like protein 12	0.31	-	cyt	0					564
Q5ZJU2 UniProt NPD GO	KHL15_CHICK	Kelch-like protein 15	0.31	-	cyt	0					488
P13645 UniProt NPD GO	K1C10_HUMAN	Keratin, type I cytoskeletal 10 (Cytokeratin-10) (CK-10) (Keratin-10) (K10)	0.31	-	nuc	0		intermediate filament [TAS]	607602		593
Q6PVZ1 UniProt NPD GO	K1C14_CHICK	Keratin, type I cytoskeletal 14 (Cytokeratin-14) (CK-14) (Keratin-14) (K14)	0.31	-	cyt	0		keratin filament [IDA]			467
O62702 UniProt NPD GO	KERA_BOVIN	Keratocan precursor (KTN) (Keratan sulfate proteoglycan keratocan) (KSPG keratocan) (Corneal keratan ...	0.31	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				352
P43630 UniProt NPD GO	KI3L2_HUMAN	Killer cell immunoglobulin-like receptor 3DL2 precursor (MHC class I NK cell receptor) (Natural kill ...	0.31	-	exc	1 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	604947		455
Q9UIL4 UniProt NPD GO	KIF25_HUMAN	Kinesin-like protein KIF25 (Kinesin-like protein 3)	0.31	-	nuc	0		kinesin complex [TAS]	603815		384
Q95M19 UniProt NPD GO	SCF_CAPHI	Kit ligand precursor (C-kit ligand) (Stem cell factor) (SCF) (Mast cell growth factor) (MGF)	0.31	-	exc	1 *	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				274
Q29030 UniProt NPD GO	SCF_PIG	Kit ligand precursor (C-kit ligand) (Stem cell factor) (SCF) (Mast cell growth factor) (MGF)	0.31	-	end	1 *	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				274
Q8K1S7 UniProt NPD GO	KREM2_MOUSE	Kremen protein 2 precursor (Kringle-containing protein marking the eye and the nose) (Kringle domain ...	0.31	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				461
Q9EPW2 UniProt NPD GO	KLF15_MOUSE	Krueppel-like factor 15 (Cardiovascular Krueppel-like factor)	0.31	-	nuc	0	Nucleus	nucleus [IDA]			415
P58334 UniProt NPD GO	KLF16_MOUSE	Krueppel-like factor 16 (Transcription factor BTEB4) (Basic transcription element-binding protein 4) ...	0.31	-	nuc	0	Nucleus				251
Q4R1H1 UniProt NPD GO	TYRP2_PIG	L-dopachrome tautomerase precursor (EC 5.3.3.12) (DT) (DCT) (L-dopachrome delta-isomerase) (Tyrosina ...	0.31	-	end	1	Melanosome; melanosomal membrane; single-pass type I membrane protein (By similarity)	cytosol [ISS] melanosome [ISS] microsome [ISS]			519
Q95235 UniProt NPD GO	LYAM1_PONPY	L-selectin precursor (Lymph node homing receptor) (Leukocyte adhesion molecule 1) (LAM-1) (Leukocyte ...	0.31	-	nuc	1	Membrane; single-pass type I membrane protein				372

You are viewing entries 39551 to 39600 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.