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
Q9YHA0 UniProt NPD GO	EYA1_CHICK	Eyes absent homolog 1 (EC 3.1.3.48) (Fragment)	0.05	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				119
Q6FN48 UniProt NPD GO	CAPZA_CANGA	F-actin capping protein subunit alpha	0.05	-	cyt	0					262
Q8NCQ5 UniProt NPD GO	FBX15_HUMAN	F-box only protein 15	0.05	-	mit	0			609093		434
O74381 UniProt NPD GO	POF9_SCHPO	F-box protein pof9	0.05	-	cyt	0					467
Q12284 UniProt NPD GO	ERV2_YEAST	FAD-linked sulfhydryl oxidase ERV2 (EC 1.8.3.-)	0.05	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein; lumena ...	microsome [IDA]		1JRA	196
Q5AXD5 UniProt NPD GO	FKB1B_EMENI	FK506-binding protein 1B (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rapamyc ...	0.05	-	cyt	0					120
P68107 UniProt NPD GO	FKB1B_BOVIN	FK506-binding protein 1B (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase 1B) (PPIase 1B) (Rotamase ...	0.05	-	cyt	0	Cytoplasm	cytoplasm [NAS]			107
Q9Z2I2 UniProt NPD GO	FKB1B_MOUSE	FK506-binding protein 1B (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase 1B) (PPIase 1B) (Rotamase ...	0.05	-	cyt	0					107
Q8HYX6 UniProt NPD GO	FKB1B_RABIT	FK506-binding protein 1B (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase 1B) (PPIase 1B) (Rotamase ...	0.05	-	cyt	0					107
P97534 UniProt NPD GO	FKB1B_RAT	FK506-binding protein 1B (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase 1B) (PPIase 1B) (Rotamase ...	0.05	-	cyt	0					107
P68106 UniProt NPD GO	FKB1B_HUMAN	FK506-binding protein 1B (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase 1B) (PPIase 1B) (Rotamase ...	0.05	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]	600620	1C9H	107
Q6FSC1 UniProt NPD GO	FKBP2_CANGA	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.05	-	nuc	0	Endoplasmic reticulum (By similarity)				136
P41487 UniProt NPD GO	FAR4_HOMAM	FMRFamide-like neuropeptide 4 (FLI 4) (F1)	0.05	-		0	Secreted protein				8
P43171 UniProt NPD GO	FAR7_ASCSU	FMRFamide-like neuropeptide AF7	0.05	-		0	Secreted protein				8
P83277 UniProt NPD GO	FAR4_MACRS	FMRFamide-like neuropeptide FLP4 (APALRLRF-amide)	0.05	-		0	Secreted protein				8
P41853 UniProt NPD GO	FARP_ARTTR	FMRFamide-like neuropeptide RYIRF-amide	0.05	-		0					5
Q9D2W0 UniProt NPD GO	FXYD4_MOUSE	FXYD domain-containing ion transport regulator 4 precursor (Channel-inducing factor) (CHIF)	0.05	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				88
P83594 UniProt NPD GO	IFXA_BAUUN	Factor Xa inhibitor BuXI	0.05	-	cyt	0	Secreted protein				172
Q9LZX4 UniProt NPD GO	FLA10_ARATH	Fasciclin-like arabinogalactan protein 10 precursor	0.05	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			422
Q05634 UniProt NPD GO	FASC_STRPU	Fascin	0.05	-	cyt	0					495
P08757 UniProt NPD GO	FAS_CAPHI	Fatty acid synthase (EC 2.3.1.85) (Fragment)	0.05	-	cyt	0					35
O42494 UniProt NPD GO	FABP_FUGRU	Fatty acid-binding protein	0.05	-	cyt	0	Cytoplasm (Potential)				125
Q20222 UniProt NPD GO	FABP3_CAEEL	Fatty acid-binding protein homolog 3 precursor (Lipid-binding protein 3)	0.05	-	vac	0	Secreted protein. From muscle into the perienteric fluid				165
P51648 UniProt NPD GO	AL3A2_HUMAN	Fatty aldehyde dehydrogenase (EC 1.2.1.3) (Aldehyde dehydrogenase, microsomal) (Aldehyde dehydrogena ...	0.05	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein; cytoplasmic sid ...		609523		485
P20307 UniProt NPD GO	KRFD_CHICK	Feather keratin III (Keratin gene D protein) (F-ker)	0.05	-	nuc	0					97
P15789 UniProt NPD GO	FER2_CYACA	Ferredoxin	0.05	-	cyt	0	Plastid; chloroplast				97
Q41014 UniProt NPD GO	FENR2_PEA	Ferredoxin--NADP reductase, root isozyme, chloroplast precursor (EC 1.18.1.2) (FNR)	0.05	-	cyt	0	Plastid; chloroplast; chloroplast stroma. Stromal side of the thylakoid membrane in the vicinity of ...				377
P16972 UniProt NPD GO	FER1_ARATH	Ferredoxin-1, chloroplast precursor	0.05	-	mit	0	Plastid; chloroplast				148
P11051 UniProt NPD GO	FER1_ORYSA	Ferredoxin-1, chloroplast precursor (Ferredoxin I) (Anti-disease protein 1)	0.05	-	mit	0	Plastid; chloroplast				139
P27788 UniProt NPD GO	FER3_MAIZE	Ferredoxin-3, chloroplast precursor (Ferredoxin III) (Fd III)	0.05	-	mit	0	Plastid; chloroplast				152
P19133 UniProt NPD GO	FRIL_PIG	Ferritin light chain (Ferritin L subunit) (Fragment)	0.05	-	nuc	0					78
Q9HE18 UniProt NPD GO	FAEB_PENFN	Feruloyl esterase B precursor (EC 3.1.1.73) (Ferulic acid esterase B) (FAEB) (Cinnamoyl esterase)	0.05	-	exc	1 *	Secreted protein	extracellular region [IDA]			353
P68213 UniProt NPD GO	FIBA_CANFA	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.05	-	cyt	0	Secreted protein				28
P68123 UniProt NPD GO	FIBB_CAMDR	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.05	-		0	Secreted protein				19
P68122 UniProt NPD GO	FIBB_LAMGL	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.05	-		0	Secreted protein				19
P68124 UniProt NPD GO	FIBB_LAMVI	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.05	-		0	Secreted protein				19
P14475 UniProt NPD GO	FIBB_MUNMU	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.05	-	nuc	0	Secreted protein				21
P21828 UniProt NPD GO	FIBL_BOMMO	Fibroin light chain precursor (Fib-L) (L-fibroin)	0.05	-	exc	0	Secreted protein				262
Q9ZWQ9 UniProt NPD GO	FLS_CITUN	Flavonol synthase/flavanone 3-hydroxylase (EC 1.14.11.23) (EC 1.14.11.9) (FLS) (CitFLS)	0.05	-	cyt	0	Cytoplasm (By similarity)				335
Q95J82 UniProt NPD GO	FSHB_MONDO	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B)	0.05	-	exc	0	Secreted protein				129
Q2PUH2 UniProt NPD GO	FSHB_PANTR	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B)	0.05	-	exc	0	Secreted protein				129
Q6SV86 UniProt NPD GO	FSHB_BUBBU	Follitropin beta chain precursor (Follicle-stimulating hormone subunit beta) (FSH-beta) (FSH-B)	0.05	-	exc	0	Secreted protein (By similarity)				129
Q8HY83 UniProt NPD GO	FSHB_CAPHI	Follitropin beta chain precursor (Follicle-stimulating hormone subunit beta) (FSH-beta) (FSH-B)	0.05	-	exc	0	Secreted protein (By similarity)				129
P01225 UniProt NPD GO	FSHB_HUMAN	Follitropin beta chain precursor (Follicle-stimulating hormone subunit beta) (FSH-beta) (FSH-B)	0.05	-	exc	0	Secreted protein	extracellular region [NAS] soluble fraction [TAS]	136530	1XWD	129
Q07103 UniProt NPD GO	FDH_NEUCR	Formate dehydrogenase (EC 1.2.1.2) (NAD-dependent formate dehydrogenase) (FDH)	0.05	-	nuc	0					375
Q07540 UniProt NPD GO	FRDA_YEAST	Frataxin homolog, mitochondrial precursor [Contains: Frataxin homolog intermediate form]	0.05	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA] mitochondrion [IDA]		2GA5	174
P18537 UniProt NPD GO	FRIZ_DROME	Frizzled precursor (Frizzled-1) (dFz1)	0.05	-	end	7	Membrane; multi-pass membrane protein	cell cortex [IDA] integral to plasma membrane [TAS] plasma membrane [IDA]			581
O57328 UniProt NPD GO	FZD1_CHICK	Frizzled-1 precursor (Fz-1) (cFz-1)	0.05	-	end	7	Membrane; multi-pass membrane protein				592
Q9EQD0 UniProt NPD GO	FZD5_MOUSE	Frizzled-5 precursor (Fz-5) (mFz5)	0.05	-	end	7	Cell membrane; multi-pass membrane protein. Golgi apparatus; Golgi membrane; multi-pass membrane pro ...				585
Q9H461 UniProt NPD GO	FZD8_HUMAN	Frizzled-8 precursor (Fz-8) (hFz8)	0.05	+	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS]	606146		694

You are viewing entries 74401 to 74450 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.