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
P34577 UniProt NPD GO	YNX4_CAEEL	Hypothetical protein T20G5.4 in chromosome III	0.23	-	mit	4 *					456
Q10027 UniProt NPD GO	YSXB_CAEEL	Hypothetical protein T28D9.11	0.23	-	nuc	0					64
Q10023 UniProt NPD GO	YSX4_CAEEL	Hypothetical protein T28D9.4	0.23	-	end	6	Membrane; multi-pass membrane protein (Potential)				468
O18303 UniProt NPD GO	YHS4_CAEEL	Hypothetical protein ZK849.4 in chromosome I	0.23	-	end	3 *					602
O14349 UniProt NPD GO	ISN1_SCHPO	IMP-specific 5'-nucleotidase 1 (EC 3.1.3.-)	0.23	-	mit	0					405
P01823 UniProt NPD GO	HV47_MOUSE	Ig heavy chain V region 36-60	0.23	-	nuc	0				1J1X	113
P01608 UniProt NPD GO	KV1P_HUMAN	Ig kappa chain V-I region Roy	0.23	-	nuc	0		extracellular region [NAS]			108
P01611 UniProt NPD GO	KV1S_HUMAN	Ig kappa chain V-I region Wes	0.23	-	nuc	0		extracellular region [NAS]			108
P01614 UniProt NPD GO	KV2A_HUMAN	Ig kappa chain V-II region Cum	0.23	-	nuc	0		extracellular region [NAS]			115
P01652 UniProt NPD GO	KV5S_MOUSE	Ig kappa chain V-V region J606	0.23	-	nuc	0					108
P01650 UniProt NPD GO	KV5Q_MOUSE	Ig kappa chain V-V region UPC 61	0.23	-	nuc	0					108
P01591 UniProt NPD GO	IGJ_HUMAN	Immunoglobulin J chain	0.23	-	nuc	0		extracellular region [NAS]	147790		137
Q7TNR6 UniProt NPD GO	IGS21_MOUSE	Immunoglobulin superfamily member 21 precursor	0.23	-	exc	0	Secreted protein (Potential)				468
Q5RE31 UniProt NPD GO	IAG2_PONPY	Implantation-associated protein precursor (IAP)	0.23	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				335
Q9H0U3 UniProt NPD GO	IAG2_HUMAN	Implantation-associated protein precursor (IAP) (Magnesium transporter protein 1) (MagT1)	0.23	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				335
Q7S8S5 UniProt NPD GO	TIM21_NEUCR	Import inner membrane translocase subunit tim-21, mitochondrial precursor	0.23	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				251
Q96P70 UniProt NPD GO	IPO9_HUMAN	Importin-9 (Imp9) (Ran-binding protein 9) (RanbP9)	0.23	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [IDA]			1040
Q15070 UniProt NPD GO	OXA1L_HUMAN	Inner membrane protein OXA1L, mitochondrial precursor (Oxidase assembly 1-like protein) (OXA1-like p ...	0.23	-	mit	4	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial electron transport chain [TAS]	601066		435
Q5CZK3 UniProt NPD GO	INSL3_PANTR	Insulin-like 3 precursor (Leydig insulin-like peptide) (Ley-I-L) (Relaxin-like factor) [Contains: In ...	0.23	-	mit	0	Secreted protein (By similarity)				131
P41694 UniProt NPD GO	IGF2_MUSVI	Insulin-like growth factor II precursor (IGF-II) (Fragment)	0.23	-	exc	0	Secreted protein				129
Q5R9A7 UniProt NPD GO	GP155_PONPY	Integral membrane protein GPR155	0.23	-	end	15 *	Membrane; multi-pass membrane protein				872
P53710 UniProt NPD GO	ITA2_BOVIN	Integrin alpha-2 precursor (Platelet membrane glycoprotein Ia) (GPIa) (Collagen receptor) (VLA-2 alp ...	0.23	-	nuc	1	Membrane; single-pass type I membrane protein				1170
Q06274 UniProt NPD GO	ITA5_XENLA	Integrin alpha-5 precursor (Fibronectin receptor subunit alpha) (Integrin alpha-F) (VLA-5) [Contains ...	0.23	-	end	2 *	Membrane; single-pass type I membrane protein				1050
P08514 UniProt NPD GO	ITA2B_HUMAN	Integrin alpha-IIb precursor (Platelet membrane glycoprotein IIb) (GPalpha IIb) (GPIIb) (CD41 antige ...	0.23	-	end	1 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	273800	1TYE	1039
P53714 UniProt NPD GO	ITB2_PIG	Integrin beta-2 precursor (Cell surface adhesion glycoproteins LFA-1/CR3/P150,95 subunit beta) (Comp ...	0.23	-	end	1	Membrane; single-pass type I membrane protein				769
Q92985 UniProt NPD GO	IRF7_HUMAN	Interferon regulatory factor 7 (IRF-7)	0.23	-	cyt	0	Nucleus. Cytoplasm. The phosphorylated and active form accumulates selectively in the nucleus	cytoplasm [TAS] nucleus [ISS]	605047		503
P43480 UniProt NPD GO	IL10_BOVIN	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.23	-	exc	0	Secreted protein	extracellular region [ISS]			178
P22301 UniProt NPD GO	IL10_HUMAN	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.23	-	exc	0	Secreted protein	extracellular region [NAS]	124092	2ILK	178
Q61190 UniProt NPD GO	I10R2_MOUSE	Interleukin-10 receptor beta chain precursor (IL-10R-B) (IL-10R2) (Cytokine receptor family 2 member ...	0.23	-	end	1 *	Membrane; single-pass type I membrane protein				349
P97636 UniProt NPD GO	IL18_RAT	Interleukin-18 precursor (IL-18) (Interferon-gamma-inducing factor) (IFN-gamma-inducing factor) (Int ...	0.23	-	cyt	0	Secreted protein	extracellular region [ISS]			194
Q6PHB0 UniProt NPD GO	I20RA_MOUSE	Interleukin-20 receptor alpha chain precursor (IL-20R-alpha) (IL-20R1)	0.23	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				546
Q28819 UniProt NPD GO	IL6_PHOVI	Interleukin-6 precursor (IL-6) (Fragment)	0.23	-	exc	0	Secreted protein				209
P08505 UniProt NPD GO	IL6_MOUSE	Interleukin-6 precursor (IL-6) (Interleukin HP-1) (B-cell hybridoma growth factor)	0.23	-	exc	0	Secreted protein				211
P15248 UniProt NPD GO	IL9_HUMAN	Interleukin-9 precursor (IL-9) (T-cell growth factor P40) (P40 cytokine)	0.23	-	exc	0	Secreted protein		146931		144
P19111 UniProt NPD GO	PPBI_BOVIN	Intestinal alkaline phosphatase precursor (EC 3.1.3.1) (IAP)	0.23	-	end	0	Cell membrane; lipid-anchor; GPI-anchor				533
P12969 UniProt NPD GO	IAPP_RAT	Islet amyloid polypeptide precursor (Diabetes-associated peptide) (DAP) (Amylin)	0.23	-	exc	0	Secreted protein	secretory granule [TAS]			93
P28299 UniProt NPD GO	ACEA_NEUCR	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.23	-	cyt	0	Glyoxysome				548
Q9AR07 UniProt NPD GO	JMT_ARATH	Jasmonate O-methyltransferase (EC 2.1.1.141) (S-adenosyl-L-methionine:jasmonic acid carboxyl methylt ...	0.23	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Partially (By similarity)				389
P69769 UniProt NPD GO	CXK3K_CONRA	Kappa-M-conotoxin RIIIK precursor (Kappa-M-RIIIK) (Conotoxin R3.1)	0.23	-	exc	0	Secreted protein (By similarity)				75
Q28794 UniProt NPD GO	CASK_TAYTA	Kappa-casein (Fragment)	0.23	-	nuc	0	Secreted protein				146
P02670 UniProt NPD GO	CASK_CAPHI	Kappa-casein precursor (Kappa-CN)	0.23	-	exc	0	Secreted protein				192
Q6DEL7 UniProt NPD GO	KHL15_BRARE	Kelch-like protein 15	0.23	-	cyt	0					604
P02445 UniProt NPD GO	KRA34_SHEEP	Keratin, high sulfur matrix protein, IIIB4	0.23	-	nuc	0					98
P04263 UniProt NPD GO	K2CA_BOVIN	Keratin, type II cytoskeletal 68 kDa, component IA (Fragment)	0.23	-	nuc	0					182
Q06220 UniProt NPD GO	SCF_CANFA	Kit ligand precursor (C-kit ligand) (Stem cell factor) (SCF) (Mast cell growth factor) (MGF)	0.23	-	nuc	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein. Also exists as ...				274
P79169 UniProt NPD GO	SCF_FELCA	Kit ligand precursor (C-kit ligand) (Stem cell factor) (SCF) (Mast cell growth factor) (MGF)	0.23	-	nuc	1	Isoform 1, isoform 2: Cell membrane; single-pass type I membrane protein (By similarity). Processed ...				274
O74298 UniProt NPD GO	LYS2_PENCH	L-aminoadipate-semialdehyde dehydrogenase large subunit (EC 1.2.1.31) (Alpha-aminoadipate reductase) ...	0.23	-	mit	0					1409
Q9TUM0 UniProt NPD GO	TRFL_CAMDR	Lactotransferrin precursor (EC 3.4.21.-) (Lactoferrin)	0.23	-	exc	0	Secreted protein			1I6Q	708
Q14739 UniProt NPD GO	LBR_HUMAN	Lamin-B receptor (Integral nuclear envelope inner membrane protein) (LMN2R)	0.23	-	end	8	Nucleus; nuclear inner membrane; multi-pass membrane protein	integral to membrane [IDA] integral to nuclear inner membrane [TAS]	600024		615
Q95V77 UniProt NPD GO	LEA1_APHAV	Late embryogenesis abundant protein 1 (Aavlea1)	0.23	-	nuc	0					143

You are viewing entries 47501 to 47550 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.