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
Q5ZJ06 UniProt NPD GO	IAG2_CHICK	Implantation-associated protein homolog precursor	0.25	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				328
O35777 UniProt NPD GO	IAG2_RAT	Implantation-associated protein precursor (IAP)	0.25	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)	oligosaccharyl transferase complex [ISS]			335
Q5S7T7 UniProt NPD GO	TIM50_PHYIN	Import inner membrane translocase subunit TIM50, mitochondrial precursor (NIF domain protein 3)	0.25	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				409
P32337 UniProt NPD GO	IMB3_YEAST	Importin beta-3 subunit (Karyopherin beta-3 subunit) (Protein secretion enhancer 1)	0.25	-	end	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			1089
Q98862 UniProt NPD GO	IHH_BRARE	Indian hedgehog B protein precursor (IHHB) (Echidna hedgehog protein) (EHH) [Contains: Indian hedgeh ...	0.25	-	mit	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				412
Q04997 UniProt NPD GO	INHA_MOUSE	Inhibin alpha chain precursor	0.25	-	end	0	Secreted protein	extracellular region [ISS]			366
P42917 UniProt NPD GO	INHBB_BOVIN	Inhibin beta B chain precursor (Activin beta-B chain)	0.25	-	end	0	Secreted protein (By similarity)	extracellular region [ISS]			408
Q04999 UniProt NPD GO	INHBB_MOUSE	Inhibin beta B chain precursor (Activin beta-B chain) (Fragment)	0.25	-	cyt	0	Secreted protein	extracellular region [ISS]			367
P14616 UniProt NPD GO	INSRR_HUMAN	Insulin receptor-related protein precursor (EC 2.7.10.1) (IRR) (IR-related receptor) [Contains: Insu ...	0.25	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	147671		1297
P51460 UniProt NPD GO	INSL3_HUMAN	Insulin-like 3 precursor (Leydig insulin-like peptide) (Ley-I-L) (Relaxin-like factor) [Contains: In ...	0.25	-	mit	0	Secreted protein	extracellular region [TAS] soluble fraction [TAS]	219050		131
Q5FWM8 UniProt NPD GO	GP180_XENLA	Integral membrane protein GPR180 precursor	0.25	-	end	7	Membrane; multi-pass membrane protein (Potential)				435
P53712 UniProt NPD GO	ITB1_BOVIN	Integrin beta-1 precursor (Fibronectin receptor subunit beta) (Integrin VLA-4 subunit beta) (CD29 an ...	0.25	-	end	1	Membrane; single-pass type I membrane protein				798
P35330 UniProt NPD GO	ICAM2_MOUSE	Intercellular adhesion molecule 2 precursor (ICAM-2) (CD102 antigen) (Lymphocyte function-associated ...	0.25	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [IDA] uropod [IDA]		1J19	277
Q28589 UniProt NPD GO	INAR1_SHEEP	Interferon-alpha/beta receptor alpha chain precursor (IFN-alpha-REC) (Interferon alpha/beta receptor ...	0.25	-	nuc	1	Membrane; single-pass type I membrane protein				560
P80217 UniProt NPD GO	IN35_HUMAN	Interferon-induced 35 kDa protein (IFP 35)	0.25	-	cyt	0	Nucleus. Nuclear following IFN treatment	nucleus [IDA]	600735		285
Q28386 UniProt NPD GO	IL1B_HORSE	Interleukin-1 beta precursor (IL-1 beta)	0.25	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				268
P51746 UniProt NPD GO	IL10_CEREL	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.25	-	exc	0	Secreted protein	extracellular region [NAS]			179
Q14626 UniProt NPD GO	I11RA_HUMAN	Interleukin-11 receptor alpha chain precursor (IL-11R-alpha) (IL-11RA)	0.25	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	600939		422
Q9XT83 UniProt NPD GO	IL2_HALGR	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.25	-	exc	0	Secreted protein (By similarity)				155
O62641 UniProt NPD GO	IL2_MIRAN	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.25	-	exc	0	Secreted protein				154
Q06435 UniProt NPD GO	IL3_SHEEP	Interleukin-3 precursor (IL-3) (Multipotential colony-stimulating factor) (Hematopoietic growth fact ...	0.25	-	exc	0	Secreted protein	extracellular space [ISS]			146
P30368 UniProt NPD GO	IL4_SHEEP	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.25	-	exc	0	Secreted protein				135
O08987 UniProt NPD GO	IL5_CAVPO	Interleukin-5 precursor (IL-5) (T-cell replacing factor) (TRF) (Eosinophil differentiation factor)	0.25	-	end	0	Secreted protein				135
Q62575 UniProt NPD GO	IL5_MERUN	Interleukin-5 precursor (IL-5) (T-cell replacing factor) (TRF) (Eosinophil differentiation factor)	0.25	-	exc	0	Secreted protein				132
P05113 UniProt NPD GO	IL5_HUMAN	Interleukin-5 precursor (IL-5) (T-cell replacing factor) (TRF) (Eosinophil differentiation factor) ( ...	0.25	-	exc	0	Secreted protein	extracellular space [TAS]	147850	1HUL	134
Q6CSA1 UniProt NPD GO	MIA40_KLULA	Intermembrane space import and assembly protein 40, mitochondrial precursor (Mitochondrial import in ...	0.25	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...				406
Q5REW1 UniProt NPD GO	IYD1_PONPY	Iodotyrosine dehalogenase 1 precursor (EC 1.-.-.-) (IYD-1)	0.25	-	nuc	2 *	Membrane; single-pass membrane protein (By similarity)				289
P17716 UniProt NPD GO	IAPP_CANFA	Islet amyloid polypeptide precursor (Amylin)	0.25	-	nuc	0	Secreted protein				89
Q9BXS1 UniProt NPD GO	IDI2_HUMAN	Isopentenyl-diphosphate delta-isomerase 2 (EC 5.3.3.2) (IPP isomerase 2) (Isopentenyl pyrophosphate ...	0.25	-	cyt	0	Peroxisome (By similarity)				227
Q28417 UniProt NPD GO	CASK_GIRCA	Kappa-casein (Fragment)	0.25	-	mit	0	Secreted protein				153
P50423 UniProt NPD GO	CASK_OREAM	Kappa-casein precursor	0.25	-	exc	0	Secreted protein				192
P50424 UniProt NPD GO	CASK_RUPRU	Kappa-casein precursor	0.25	-	exc	0	Secreted protein				192
P02669 UniProt NPD GO	CASK_SHEEP	Kappa-casein precursor	0.25	-	exc	0	Secreted protein				192
Q8VCX6 UniProt NPD GO	KPTN_MOUSE	Kaptin	0.25	-	cyt	0	Cytoplasm (By similarity). Cytoplasm; perinuclear region (By similarity). Perinuclear at the tips of ...				430
Q9UJP4 UniProt NPD GO	KLH21_HUMAN	Kelch-like protein 21	0.25	-	mit	0					539
P60328 UniProt NPD GO	KR123_HUMAN	Keratin-associated protein 12-3 (Keratin-associated protein 12.3) (High sulfur keratin-associated pr ...	0.25	-	mit	0					96
Q9UIH9 UniProt NPD GO	KLF15_HUMAN	Krueppel-like factor 15 (Kidney-enriched krueppel-like factor)	0.25	-	nuc	0	Nucleus		606465		416
O43291 UniProt NPD GO	SPIT2_HUMAN	Kunitz-type protease inhibitor 2 precursor (Hepatocyte growth factor activator inhibitor type 2) (HA ...	0.25	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)	extracellular region [TAS] integral to membrane [TAS] soluble fraction [TAS]	605124		252
O93364 UniProt NPD GO	OXLA_CROAD	L-amino-acid oxidase precursor (EC 1.4.3.2) (LAO) (LAAO) (Apoxin I)	0.25	-	end	0	Secreted protein				516
Q5F425 UniProt NPD GO	LIN7C_CHICK	LIN-7 homolog C (LIN-7C)	0.25	-	cyt	0	Cell membrane; peripheral membrane protein. Cell membrane; cell-cell junction; peripheral membrane p ...				197
Q5RAA5 UniProt NPD GO	LIN7C_PONPY	LIN-7 homolog C (LIN-7C)	0.25	-	cyt	0	Cell membrane; peripheral membrane protein. Cell membrane; cell-cell junction; peripheral membrane p ...				197
Q9NUP9 UniProt NPD GO	LIN7C_HUMAN	LIN-7 homolog C (LIN-7C) (Mammalian LIN-seven protein 3) (MALS-3) (Vertebrate LIN 7 homolog 3) (Veli ...	0.25	-	cyt	0	Cell membrane; peripheral membrane protein. Cell membrane; cell-cell junction; peripheral membrane p ...				197
Q792I0 UniProt NPD GO	LIN7C_RAT	LIN-7 homolog C (LIN-7C) (Mammalian LIN-seven protein 3) (MALS-3) (Vertebrate LIN 7 homolog 3) (Veli ...	0.25	-	cyt	0	Cell membrane; peripheral membrane protein. Cell membrane; cell-cell junction; peripheral membrane p ...	intercellular junction [IDA] synapse [IDA]			197
O88952 UniProt NPD GO	LIN7C_MOUSE	LIN-7 homolog C (LIN-7C) (mLin7C) (Mammalian LIN-seven protein 3) (MALS-3) (Vertebrate LIN 7 homolog ...	0.25	-	cyt	0	Cell membrane; peripheral membrane protein. Cell membrane; cell-cell junction; peripheral membrane p ...	synaptosome [IDA]			197
O81322 UniProt NPD GO	LBD31_ARATH	LOB domain-containing protein 31	0.25	-	nuc	0					215
Q26474 UniProt NPD GO	LACH_SCHAM	Lachesin precursor	0.25	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				349
Q5R7H4 UniProt NPD GO	LBR_PONPY	Lamin-B receptor (Integral nuclear envelope inner membrane protein)	0.25	-	end	8	Nucleus; nuclear inner membrane; multi-pass membrane protein (By similarity)				615
O93416 UniProt NPD GO	LEP_MELGA	Leptin (Obesity factor) (Fragment)	0.25	-	nuc	0	Secreted protein (Probable)				145
Q8CI70 UniProt NPD GO	LRC20_MOUSE	Leucine-rich repeat-containing protein 20	0.25	-	mit	0					184
Q9DAK8 UniProt NPD GO	LRC51_MOUSE	Leucine-rich repeat-containing protein 51	0.25	-	nuc	0					192

You are viewing entries 45351 to 45400 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.)

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