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
P42564 UniProt NPD GO	FAR5_HIRME	FMRFamide-like neuropeptide GGKYMRF-amide	0.03	-		0	Secreted protein				7
P41966 UniProt NPD GO	FARP_MONEX	FMRFamide-like neuropeptide GNFFRF-amide	0.03	-		0	Secreted protein				6
P42563 UniProt NPD GO	FAR4_HIRME	FMRFamide-like neuropeptide YMRF-amide	0.03	-		0	Secreted protein				4
Q9NVQ4 UniProt NPD GO	FAIM1_HUMAN	Fas apoptotic inhibitory molecule 1	0.03	-	cyt	0					179
Q9WUD8 UniProt NPD GO	FAIM1_MOUSE	Fas apoptotic inhibitory molecule 1	0.03	-	cyt	0					179
Q8K097 UniProt NPD GO	FAIM2_MOUSE	Fas apoptotic inhibitory molecule 2 (Lifeguard protein)	0.03	-	end	7	Cell membrane; multi-pass membrane protein (By similarity). Postsynaptic membrane (By similarity)				317
O88407 UniProt NPD GO	FAIM2_RAT	Fas apoptotic inhibitory molecule 2 (Lifeguard protein) (Neural membrane protein 35)	0.03	-	end	7	Cell membrane; multi-pass membrane protein. Postsynaptic membrane				316
Q9BWQ8 UniProt NPD GO	FAIM2_HUMAN	Fas apoptotic inhibitory molecule 2 (Lifeguard protein) (Transmembrane BAX inhibitor motif-containin ...	0.03	-	end	7	Cell membrane; multi-pass membrane protein (By similarity). Postsynaptic membrane (By similarity)		604306		316
O45035 UniProt NPD GO	FABP_SCHJA	Fatty acid-binding protein (Sj-FABPc) (Sj14FABP)	0.03	-	cyt	0	Cytoplasm				132
Q20224 UniProt NPD GO	FABP2_CAEEL	Fatty acid-binding protein homolog 2 precursor (Lipid-binding protein 2)	0.03	-	exc	0	Secreted protein. From muscle into the perienteric fluid				161
O97788 UniProt NPD GO	FABPA_PIG	Fatty acid-binding protein, adipocyte (AFABP) (Adipocyte lipid-binding protein) (ALBP) (A-FABP) (AP2 ...	0.03	-	cyt	0	Cytoplasm (Potential)				131
P55053 UniProt NPD GO	FABPE_RAT	Fatty acid-binding protein, epidermal (E-FABP) (Cutaneous fatty acid-binding protein) (C-FABP) (DA11 ...	0.03	-	cyt	0	Cytoplasm				134
Q90239 UniProt NPD GO	FABPL_ANOPU	Fatty acid-binding protein, liver (L-FABP) (Liver basic FABP) (LB-FABP)	0.03	-	cyt	0	Cytoplasm				125
P80856 UniProt NPD GO	FABPL_RHASA	Fatty acid-binding protein, liver (L-FABP) (Liver basic FABP) (LB-FABP)	0.03	-	cyt	0	Cytoplasm				125
P83409 UniProt NPD GO	FABPL_BUFAR	Fatty acid-binding protein, liver (L-FABP) (Liver basic FABP) (Lb-FABP)	0.03	-	cyt	0	Cytoplasm			1P6P	125
Q60HH8 UniProt NPD GO	AL3A2_MACFA	Fatty aldehyde dehydrogenase (EC 1.2.1.3) (Aldehyde dehydrogenase, microsomal) (Aldehyde dehydrogena ...	0.03	-	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein; cytoplasmic sid ...				485
P34383 UniProt NPD GO	FAR2_CAEEL	Fatty-acid and retinol-binding protein 2 precursor	0.03	-	exc	0	Secreted protein (By similarity)				182
Q9N1F2 UniProt NPD GO	FLVC1_FELCA	Feline leukemia virus subgroup C receptor-related protein 1	0.03	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				560
Q9Y5Y0 UniProt NPD GO	FLVC1_HUMAN	Feline leukemia virus subgroup C receptor-related protein 1 (Feline leukemia virus subgroup C recept ...	0.03	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS]	609144		555
P22341 UniProt NPD GO	FER_EUGVI	Ferredoxin	0.03	-	nuc	0	Plastid; chloroplast				96
P07484 UniProt NPD GO	FER_RHOPL	Ferredoxin	0.03	-	cyt	0	Plastid; chloroplast				97
P00238 UniProt NPD GO	FER_SCEQU	Ferredoxin	0.03	-	cyt	0	Plastid; chloroplast				96
P04669 UniProt NPD GO	FER_SILPR	Ferredoxin, chloroplast precursor	0.03	-	mit	0	Plastid; chloroplast				146
P41345 UniProt NPD GO	FENR2_ORYSA	Ferredoxin--NADP reductase, root isozyme, chloroplast precursor (EC 1.18.1.2) (FNR)	0.03	-	nuc	0	Plastid; chloroplast; chloroplast stroma. Stromal side of the thylakoid membrane in the vicinity of ...				378
P00221 UniProt NPD GO	FER1_SPIOL	Ferredoxin-1, chloroplast precursor (Ferredoxin I) (Fd I)	0.03	-	mit	0	Plastid; chloroplast			1A70	147
Q08258 UniProt NPD GO	GLTB_HORVU	Ferredoxin-dependent glutamate synthase (EC 1.4.7.1) (FD-GOGAT) (Fragment)	0.03	-	cyt	0	Plastid; chloroplast; chloroplast stroma				435
P53746 UniProt NPD GO	FRE4_YEAST	Ferric reductase transmembrane component 4 precursor (EC 1.16.1.7) (Ferric-chelate reductase 4)	0.03	-	end	5	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IMP]			719
Q8RX97 UniProt NPD GO	FRI1_TOBAC	Ferritin-1, chloroplast precursor (EC 1.16.3.1) (NtFer1)	0.03	-	nuc	0	Plastid; chloroplast (By similarity)				251
Q9SRL5 UniProt NPD GO	FRI2_ARATH	Ferritin-2, chloroplast precursor (EC 1.16.3.1)	0.03	-	nuc	0	Plastid; chloroplast (By similarity)				253
Q8H1T3 UniProt NPD GO	FRI2_TOBAC	Ferritin-2, chloroplast precursor (EC 1.16.3.1) (NtFer2)	0.03	-	exc	0	Plastid; chloroplast (By similarity)				259
Q94IC4 UniProt NPD GO	FRI2_SOYBN	Ferritin-2, chloroplast precursor (EC 1.16.3.1) (SFerH-2)	0.03	-	cyt	0	Plastid; chloroplast				257
P68120 UniProt NPD GO	FIBB_EQUAS	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.03	-		0	Secreted protein				19
P68121 UniProt NPD GO	FIBB_HORSE	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.03	-		0	Secreted protein				19
P19345 UniProt NPD GO	FIBB_MACFU	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.03	-		0	Secreted protein				9
P14479 UniProt NPD GO	FIBB_RANTA	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.03	-	cyt	0	Secreted protein				21
P12800 UniProt NPD GO	FIBG_CANFA	Fibrinogen gamma chain (Fragment)	0.03	-	nuc	0	Secreted protein				24
O95750 UniProt NPD GO	FGF19_HUMAN	Fibroblast growth factor 19 precursor (FGF-19)	0.03	-	exc	1 *	Secreted protein		603891	1PWA	216
P11403 UniProt NPD GO	FGF4_MOUSE	Fibroblast growth factor 4 precursor (FGF-4) (K-fibroblast growth factor) (HBGF-4)	0.03	-	exc	0					202
Q26427 UniProt NPD GO	FIBL_GALME	Fibroin light chain precursor (Fib-L) (L-fibroin) (PG-1)	0.03	-	end	0	Secreted protein				267
P07749 UniProt NPD GO	FCA1_TRYCR	Flagellar calcium-binding protein (FCABP) (1F8 protein) (P24) (29 kDa flagella protein) (F29) (24 kD ...	0.03	-	cyt	0	Flagellum				211
P52837 UniProt NPD GO	F4ST_FLACH	Flavonol 4'-sulfotransferase (EC 2.8.2.-) (F4-ST)	0.03	-	cyt	0	Cytoplasm				320
P32026 UniProt NPD GO	THGF_TOBAC	Flower-specific gamma-thionin precursor	0.03	-	exc	1 *	Cell wall (Potential). Vacuole (Potential). Possibly the cell wall or vacuole			1MR4	105
P38124 UniProt NPD GO	FLR1_YEAST	Fluconazole resistance protein 1	0.03	-	end	12	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [IDA]			548
Q9PS36 UniProt NPD GO	FSHB_RANCA	Follitropin beta chain (Follicle-stimulating hormone subunit beta) (FSH-beta) (FSH-B)	0.03	-	nuc	0	Secreted protein				107
Q9BDJ0 UniProt NPD GO	FSHB_PANTA	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B)	0.03	-	exc	0	Secreted protein				129
P01228 UniProt NPD GO	FSHB_PIG	Follitropin beta chain precursor (Follicle-stimulating hormone subunit beta) (FSH-beta) (FSH-B)	0.03	-	exc	0	Secreted protein				129
Q9SPK5 UniProt NPD GO	FTHS_ARATH	Formate--tetrahydrofolate ligase (EC 6.3.4.3) (Formyltetrahydrofolate synthetase) (10-formyletrahydr ...	0.03	-	cyt	0					634
P28723 UniProt NPD GO	FTHS_SPIOL	Formate--tetrahydrofolate ligase (EC 6.3.4.3) (Formyltetrahydrofolate synthetase) (10-formyletrahydr ...	0.03	-	cyt	0					636
Q13467 UniProt NPD GO	FZD5_HUMAN	Frizzled-5 precursor (Fz-5) (hFz5) (FzE5)	0.03	-	end	6	Cell membrane; multi-pass membrane protein (By similarity). Golgi apparatus; Golgi membrane; multi-p ...	integral to plasma membrane [TAS]	601723		585
Q9PTW1 UniProt NPD GO	FZD6_CHICK	Frizzled-6 (Fz-6) (cFz-6) (Fragment)	0.03	-	end	3	Membrane; multi-pass membrane protein				190

You are viewing entries 79901 to 79950 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.