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
P23088 UniProt NPD GO	HVCM_HETFR	Ig heavy chain C region, membrane-bound form (Clone 3050)	0.15	-	nuc	0					461
P18531 UniProt NPD GO	HV60_MOUSE	Ig heavy chain V region M315 precursor	0.15	-	exc	0				1EZV	116
P01628 UniProt NPD GO	KV2C_MOUSE	Ig kappa chain V-II region MOPC 511	0.15	-	nuc	0					113
P01674 UniProt NPD GO	KV3V_MOUSE	Ig kappa chain V-III region PC 2154	0.15	-	mit	0					108
P01668 UniProt NPD GO	KV3P_MOUSE	Ig kappa chain V-III region PC 7210	0.15	-	nuc	0					110
P01705 UniProt NPD GO	LV2B_HUMAN	Ig lambda chain V-II region NEI	0.15	-	nuc	0		extracellular region [NAS]			111
P01717 UniProt NPD GO	LV4C_HUMAN	Ig lambda chain V-IV region Hil	0.15	-	nuc	0		extracellular region [NAS]			107
P06318 UniProt NPD GO	LV6D_HUMAN	Ig lambda chain V-VI region WLT	0.15	-	nuc	0		extracellular region [NAS]			111
P01845 UniProt NPD GO	LAC3_MOUSE	Ig lambda-3 chain C region	0.15	-	nuc	0					104
P13525 UniProt NPD GO	MA8J_SCHJA	Immunogenic miracidial antigen 8I'	0.15	-	mit	0					139
Q6FMZ2 UniProt NPD GO	TIM21_CANGA	Import inner membrane translocase subunit TIM21, mitochondrial precursor	0.15	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				215
P21620 UniProt NPD GO	IMDH_LEIDO	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) (IMP dehydrogenase) (IMPDH) (IMPD)	0.15	-	cyt	0					514
P50096 UniProt NPD GO	IMDH1_MOUSE	Inosine-5'-monophosphate dehydrogenase 1 (EC 1.1.1.205) (IMP dehydrogenase 1) (IMPDH-I) (IMPD 1)	0.15	-	cyt	0					514
Q84Y01 UniProt NPD GO	ITPK1_MAIZE	Inositol-tetrakisphosphate 1-kinase 1 (EC 2.7.1.134) (Inositol-triphosphate 5/6-kinase 1) (EC 2.7.1. ...	0.15	-	cyt	0					342
Q6UWQ7 UniProt NPD GO	IGFL2_HUMAN	Insulin growth factor-like family member 2 precursor	0.15	-	exc	0	Secreted protein (Potential)				119
P17647 UniProt NPD GO	IGF1_CAVPO	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.15	-	exc	0	Secreted protein				130
Q6GUL6 UniProt NPD GO	IGF1_PANTA	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.15	-	nuc	0	Secreted protein				153
P10763 UniProt NPD GO	IGF1_SHEEP	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.15	-	nuc	0	Secreted protein				154
Q9P2C4 UniProt NPD GO	GP178_HUMAN	Integral membrane protein GPR178	0.15	-	end	9	Membrane; multi-pass membrane protein (Potential)				612
P10667 UniProt NPD GO	MUA1_XENLA	Integumentary mucin A.1 precursor (FIM-A.1) (Preprospasmolysin)	0.15	-	exc	0	Secreted protein				400
Q5NKV2 UniProt NPD GO	ICAM2_PANTR	Intercellular adhesion molecule 2 precursor (ICAM-2) (CD102 antigen)	0.15	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				275
P33896 UniProt NPD GO	INAR1_MOUSE	Interferon-alpha/beta receptor alpha chain precursor (IFN-alpha-REC)	0.15	-	end	1 *	Membrane; single-pass type I membrane protein				590
Q9BEH0 UniProt NPD GO	IL1RA_CANFA	Interleukin-1 receptor antagonist protein precursor (IL-1ra) (IRAP) (IL1 inhibitor) (IL-1RN)	0.15	-	end	0	Secreted protein				176
Q9JHK7 UniProt NPD GO	IL10_MARMO	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.15	-	end	0	Secreted protein	extracellular region [ISS]			178
O97798 UniProt NPD GO	IL10_TRIVU	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.15	-	vac	0	Secreted protein				174
P68221 UniProt NPD GO	IL12B_CAPHI	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.15	-	exc	1 *	Secreted protein				327
P68220 UniProt NPD GO	IL12B_SHEEP	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.15	-	exc	1 *	Secreted protein				327
Q9TU73 UniProt NPD GO	IL18_BOVIN	Interleukin-18 precursor (IL-18) (Interferon-gamma-inducing factor) (IFN-gamma-inducing factor) (Int ...	0.15	-	nuc	0	Secreted protein				193
P42202 UniProt NPD GO	IL4_HORSE	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.15	-	exc	0	Secreted protein				134
Q6BSK8 UniProt NPD GO	MIA40_DEBHA	Intermembrane space import and assembly protein 40, mitochondrial precursor (Mitochondrial import in ...	0.15	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...				249
Q9XSZ5 UniProt NPD GO	MMP1_HORSE	Interstitial collagenase precursor (EC 3.4.24.7) (Matrix metalloproteinase-1) (MMP-1)	0.15	-	exc	0					469
O60928 UniProt NPD GO	IRK13_HUMAN	Inward rectifier potassium channel 13 (Potassium channel, inwardly rectifying subfamily J member 13) ...	0.15	-	mit	2	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [NAS]	603208		360
P63252 UniProt NPD GO	IRK2_HUMAN	Inward rectifier potassium channel 2 (Potassium channel, inwardly rectifying subfamily J member 2) ( ...	0.15	-	mit	2	Membrane; multi-pass membrane protein		609622		427
P63253 UniProt NPD GO	IRK2_MACMU	Inward rectifier potassium channel 2 (Potassium channel, inwardly rectifying subfamily J member 2) ( ...	0.15	-	mit	2	Membrane; multi-pass membrane protein				427
Q64273 UniProt NPD GO	IRK2_RAT	Inward rectifier potassium channel 2 (Potassium channel, inwardly rectifying subfamily J member 2) ( ...	0.15	-	mit	2	Membrane; multi-pass membrane protein				427
Q9EQX4 UniProt NPD GO	IBA2_MOUSE	Ionized calcium-binding adapter molecule 2	0.15	-	nuc	0					150
P41555 UniProt NPD GO	ACEA_YARLI	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.15	-	pox	0	Glyoxysome				540
Q27707 UniProt NPD GO	SYI_ANTLO	Isoleucyl-tRNA synthetase (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS) (Fragment)	0.15	-	cyt	0					628
O13317 UniProt NPD GO	TRI11_FUSSP	Isotrichodermin C-15 hydroxylase (EC 1.14.-.-) (Cytochrome P450 65A1)	0.15	-	mit	1 *					492
Q25489 UniProt NPD GO	HYEP_MANSE	Juvenile hormone epoxide hydrolase (EC 3.3.2.3) (Juvenile hormone-specific epoxide hydrolase) (JHEH) ...	0.15	-	end	1 *	Microsome; microsomal membrane; single-pass membrane protein				462
O75525 UniProt NPD GO	KHDR3_HUMAN	KH domain-containing, RNA-binding, signal transduction-associated protein 3 (Sam68-like mammalian pr ...	0.15	-	nuc	0	Nucleus. Localized in a compartment adjacent to the nucleolus, but distinct from the peri-nucleolar ...	nucleus [TAS]			346
Q8AY55 UniProt NPD GO	NXKB_BUNCA	Kappa 1b-bungarotoxin precursor	0.15	-	nuc	0	Secreted protein (By similarity)				87
Q95224 UniProt NPD GO	CASK_OVIDA	Kappa-casein (Fragment)	0.15	-	nuc	0	Secreted protein				124
Q80YG3 UniProt NPD GO	KLDC1_MOUSE	Kelch domain-containing protein 1	0.15	-	cyt	0					406
O94889 UniProt NPD GO	KLH18_HUMAN	Kelch-like protein 18	0.15	-	cyt	0					509
P04262 UniProt NPD GO	K2CB_BOVIN	Keratin, type II cytoskeletal 68 kDa, component IB (Fragment)	0.15	-	nuc	0					166
P26372 UniProt NPD GO	KRUC_SHEEP	Keratin, ultra high-sulfur matrix protein (UHS keratin)	0.15	-	nuc	0					182
Q3LHN2 UniProt NPD GO	KR192_HUMAN	Keratin-associated protein 19-2	0.15	-	nuc	0					52
Q701N4 UniProt NPD GO	KRA52_HUMAN	Keratin-associated protein 5-2 (Keratin-associated protein 5.2) (Ultrahigh sulfur keratin-associated ...	0.15	-	nuc	0					177
P69300 UniProt NPD GO	KM11_TRYBB	Kinetoplastid membrane protein 11 (KMP-11)	0.15	-	nuc	0	Cytoplasm. Associated with microtubules				92

You are viewing entries 57101 to 57150 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.