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
O14080 UniProt NPD GO	YEAF_SCHPO	Hypothetical protein UNK4,15 in chromosome I	0.29	-	mit	0					208
Q08890 UniProt NPD GO	IDS_MOUSE	Iduronate 2-sulfatase precursor (EC 3.1.6.13) (Alpha-L-iduronate sulfate sulfatase)	0.29	-	nuc	1	Lysosome				563
P01607 UniProt NPD GO	KV1O_HUMAN	Ig kappa chain V-I region Rei	0.29	-	nuc	0		extracellular region [NAS]		1REI	108
P06309 UniProt NPD GO	KV2E_HUMAN	Ig kappa chain V-II region GM607 precursor (Fragment)	0.29	-	nuc	0		extracellular region [NAS]			117
P01621 UniProt NPD GO	KV3C_HUMAN	Ig kappa chain V-III region NG9 precursor (Fragment)	0.29	-	nuc	0		extracellular region [NAS]			100
P01643 UniProt NPD GO	KV5J_MOUSE	Ig kappa chain V-V region MOPC 173	0.29	-	nuc	0					108
P20768 UniProt NPD GO	MUC_SUNMU	Ig mu chain C region	0.29	-	exc	0					457
Q6CDV7 UniProt NPD GO	TIM50_YARLI	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.29	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				466
P38440 UniProt NPD GO	INHA_SHEEP	Inhibin alpha chain precursor (Fragment)	0.29	-	nuc	0	Secreted protein (By similarity)	extracellular region [ISS]			265
P09529 UniProt NPD GO	INHBB_HUMAN	Inhibin beta B chain precursor (Activin beta-B chain)	0.29	-	end	0	Secreted protein	extracellular region [TAS]	147390		407
P0C0T1 UniProt NPD GO	ITPK1_BOVIN	Inositol-tetrakisphosphate 1-kinase (EC 2.7.1.134) (Inositol-triphosphate 5/6-kinase) (EC 2.7.1.-) ( ...	0.29	-	cyt	0					419
P84775 UniProt NPD GO	IGF1B_XENLA	Insulin-like growth factor I-B precursor (IGF-IB) (IGF-I'') (Somatomedin) (Fragment)	0.29	-	nuc	0					44
P24591 UniProt NPD GO	IBP1_BOVIN	Insulin-like growth factor-binding protein 1 precursor (IGFBP-1) (IBP-1) (IGF-binding protein 1)	0.29	-	nuc	0	Secreted protein				263
Q9NQX7 UniProt NPD GO	ITM2C_HUMAN	Integral membrane protein 2C (Transmembrane protein BRI3) (Cerebral protein 14) [Contains: CT-BRI3]	0.29	-	mit	1	Membrane; single-pass type II membrane protein (Potential)		609554		267
Q4R540 UniProt NPD GO	ITM2C_MACFA	Integral membrane protein 2C [Contains: CT-BRI3]	0.29	-	mit	1	Membrane; single-pass type II membrane protein (Potential)				267
P53711 UniProt NPD GO	ITA2B_PAPCY	Integrin alpha-IIb (Platelet membrane glycoprotein IIb) (GPalpha IIb) (GPIIb) (CD41 antigen) [Contai ...	0.29	-	cyt	1	Membrane; single-pass type I membrane protein				604
Q462R2 UniProt NPD GO	ITBP2_PIG	Integrin beta-1-binding protein 2 (Melusin)	0.29	-	nuc	0					346
Q5NKV6 UniProt NPD GO	ICAM1_MACMU	Intercellular adhesion molecule 1 precursor (ICAM-1)	0.29	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				532
O77812 UniProt NPD GO	IFNB_MACFA	Interferon beta precursor (IFN-beta)	0.29	-	exc	1 *	Secreted protein				187
Q9QZ85 UniProt NPD GO	IIGP1_MOUSE	Interferon-inducible GTPase (EC 3.6.5.-)	0.29	-	nuc	0	Cytoplasm. Nucleus; nuclear envelope; peripheral membrane protein. Endoplasmic reticulum; endoplasmi ...			1TQD	413
P14719 UniProt NPD GO	ILRL1_MOUSE	Interleukin-1 receptor-like 1 precursor (ST2 protein) (T1 protein) (Lymphocyte antigen 84)	0.29	-	mit	1	Cell membrane; single-pass type I membrane protein. Isoform B: Secreted protein				567
O09030 UniProt NPD GO	I13R1_MOUSE	Interleukin-13 receptor alpha-1 chain precursor (IL-13R-alpha-1) (IL-13RA-1) (Interleukin-13-binding ...	0.29	-	end	1	Membrane; single-pass type I membrane protein				424
Q9NRM6 UniProt NPD GO	I17RB_HUMAN	Interleukin-17 receptor B precursor (IL-17 receptor B) (IL-17RB) (Interleukin-17B receptor) (IL-17B ...	0.29	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein	integral to plasma membrane [TAS] membrane [NAS]	605458		502
Q7TNI4 UniProt NPD GO	I22RA_RAT	Interleukin-22 receptor alpha-2 chain precursor (IL-22R-alpha-2) (Interleukin 22-binding protein) (I ...	0.29	-	exc	0	Secreted protein (By similarity)				229
P79339 UniProt NPD GO	IL4_MACFA	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.29	-	exc	0	Secreted protein	extracellular space [ISS]			153
Q9ESI9 UniProt NPD GO	IL5_SIGHI	Interleukin-5 precursor (IL-5) (T-cell replacing factor) (TRF) (Eosinophil differentiation factor)	0.29	-	exc	0	Secreted protein				132
P51494 UniProt NPD GO	IL6_MACMU	Interleukin-6 precursor (IL-6)	0.29	-	exc	1 *	Secreted protein	extracellular region [ISS] extracellular space [ISS]			212
Q15756 UniProt NPD GO	IRKI_HUMAN	Inward rectifying K(+) channel negative regulator Kir2.2v	0.29	-	end	3	Membrane; multi-pass membrane protein		602323		432
Q6PHW0 UniProt NPD GO	IYD1_HUMAN	Iodotyrosine dehalogenase 1 precursor (EC 1.-.-.-) (IYD-1)	0.29	-	nuc	1 *	Membrane; single-pass membrane protein				289
Q9XIK3 UniProt NPD GO	ISCAP_ARATH	Iron-sulfur assembly protein IscA, chloroplast precursor (Protein Scaffold protein AtCpIscA)	0.29	-	mit	0	Plastid; chloroplast; chloroplast stroma				180
Q9U6V6 UniProt NPD GO	JDP_MANSE	J domain-containing protein	0.29	-	nuc	0					170
Q9CR30 UniProt NPD GO	JOS2_MOUSE	Josephin-2 (Josephin domain-containing protein 2)	0.29	-	cyt	0					188
Q29137 UniProt NPD GO	CASK_TRAJA	Kappa-casein precursor (Fragment)	0.29	-	nuc	0	Secreted protein				171
P02668 UniProt NPD GO	CASK_BOVIN	Kappa-casein precursor [Contains: Casoxin C; Casoxin 6; Casoxin A; Casoxin B; Casoplatelin]	0.29	-	exc	0	Secreted protein				190
Q91XA8 UniProt NPD GO	KLD8A_MOUSE	Kelch domain-containing protein 8A	0.29	-	cyt	0					350
Q8IY47 UniProt NPD GO	KBTB2_HUMAN	Kelch repeat and BTB domain-containing protein 2 (BTB and kelch domain-containing protein 1)	0.29	-	cyt	0					623
Q8BHI4 UniProt NPD GO	KBTB3_MOUSE	Kelch repeat and BTB domain-containing protein 3 (BTB and kelch domain-containing protein 3)	0.29	-	cyt	0					607
Q9NVR0 UniProt NPD GO	KLH11_HUMAN	Kelch-like protein 11 precursor	0.29	-	cyt	0	Secreted protein (Potential)				708
P05785 UniProt NPD GO	K1C14_BOVIN	Keratin, type I cytoskeletal 14 (Cytokeratin-14) (CK-14) (Keratin-14) (K14) (Cytokeratin-7) (Cytoker ...	0.29	-	nuc	0					93
Q3LI76 UniProt NPD GO	KR151_HUMAN	Keratin-associated protein 15-1	0.29	-	nuc	0					137
P26371 UniProt NPD GO	KRA59_HUMAN	Keratin-associated protein 5-9 (Keratin-associated protein 5.9) (Ultrahigh sulfur keratin-associated ...	0.29	-	nuc	0			148021		169
Q28132 UniProt NPD GO	SCF_BOVIN	Kit ligand precursor (C-kit ligand) (Stem cell factor) (SCF) (Mast cell growth factor) (MGF)	0.29	-	exc	1 *	Isoform 1, isoform 2: Cell membrane; single-pass type I membrane protein (By similarity). Processed ...				274
Q95MD2 UniProt NPD GO	SCF_HORSE	Kit ligand precursor (C-kit ligand) (Stem cell factor) (SCF) (Mast cell growth factor) (MGF)	0.29	-	nuc	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				274
P98131 UniProt NPD GO	LYAM1_BOVIN	L-selectin precursor (Lymph node homing receptor) (Leukocyte adhesion molecule 1) (LAM-1) (Leukocyte ...	0.29	+	cyt	1 *	Membrane; single-pass type I membrane protein				370
P50464 UniProt NPD GO	UNC97_CAEEL	LIM protein unc-97 (Uncoordinated protein 97) (PINCH homolog)	0.29	-	cyt	0	Cell membrane; cell-cell junction; adherens junction. Nucleus	adherens junction [IDA] nucleus [IDA]			348
Q9M886 UniProt NPD GO	LBD41_ARATH	LOB domain-containing protein 41	0.29	-	nuc	0					263
Q9CA30 UniProt NPD GO	LBD42_ARATH	LOB domain-containing protein 42	0.29	-	nuc	0					233
P59761 UniProt NPD GO	LGEN_BOVIN	Lactogenin (EC 3.1.27.-) (Fragments)	0.29	-	nuc	0	Secreted protein				73
P13934 UniProt NPD GO	LEA76_BRANA	Late embryogenesis abundant protein 76 (LEA 76)	0.29	-	nuc	0					280
P20462 UniProt NPD GO	LLPA_MACEU	Late lactation protein A precursor (LLP-A)	0.29	-	exc	0	Secreted protein				176

You are viewing entries 41401 to 41450 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.