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
P93960 UniProt NPD GO	RPOA_PSARU	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	cyt	0	Plastid; chloroplast				339
Q7H6G1 UniProt NPD GO	RPOA_PSEPI	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	cyt	0	Plastid; chloroplast				339
Q6YLW2 UniProt NPD GO	RPOA_SECCE	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	cyt	0	Plastid; chloroplast				339
P93964 UniProt NPD GO	RPOA_SECST	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	cyt	0	Plastid; chloroplast				339
Q2PMQ3 UniProt NPD GO	RPOA_SOYBN	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	+	mit	0	Plastid; chloroplast				333
Q7GED0 UniProt NPD GO	RPOA_TAECM	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	cyt	0	Plastid; chloroplast				339
P12073 UniProt NPD GO	RPOA_WHEAT	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	cyt	0	Plastid; chloroplast				339
Q5QA72 UniProt NPD GO	RPOB_ACOGR	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.47	-	cyt	0	Plastid; chloroplast				1071
Q4VZP1 UniProt NPD GO	RPOB_CUCSA	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.47	-	nuc	0	Plastid; chloroplast				1071
P11703 UniProt NPD GO	RPOB_SPIOL	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.47	-	cyt	0	Plastid; chloroplast				1070
Q8S8Y0 UniProt NPD GO	RPOC1_ATRBE	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.47	-	cyt	0	Plastid; chloroplast				681
Q3C1G8 UniProt NPD GO	RPOC1_NICSY	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.47	-	cyt	0	Plastid; chloroplast				681
P23581 UniProt NPD GO	RPOC2_EUGGR	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.47	-	nuc	0	Plastid; chloroplast				830
P20434 UniProt NPD GO	RPB5_YEAST	DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide (EC 2.7.7.6) (ABC27)	0.47	-	nuc	0	Nucleus	DNA-directed RNA polymerase I complex [TAS] DNA-directed RNA polymerase II, core complex [TAS] DNA-directed RNA polymerase III complex [TAS]		2B8K	215
Q9CXE6 UniProt NPD GO	XRCC3_MOUSE	DNA-repair protein XRCC3 (X-ray repair cross-complementing protein 3)	0.47	-	cyt	0	Nucleus (Probable)				349
Q12220 UniProt NPD GO	DIP2_YEAST	DOM34-interacting protein 2 (U3 small nucleolar RNA-associated protein 12) (U3 snoRNA-associated pro ...	0.47	-	cyt	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [IPI]			943
Q2KIW3 UniProt NPD GO	DYDC2_BOVIN	DPY30 domain-containing protein 2	0.47	-	nuc	0					194
Q75WG5 UniProt NPD GO	TXDT9_MACGS	Delta-atracotoxin-9 precursor	0.47	-	nuc	0	Secreted protein				70
Q9NR61 UniProt NPD GO	DLL4_HUMAN	Delta-like protein 4 precursor (Drosophila Delta homolog 4)	0.47	-	exc	1	Membrane; single-pass type I membrane protein (Probable)		605185		685
Q9JI71 UniProt NPD GO	DLL4_MOUSE	Delta-like protein 4 precursor (Drosophila Delta homolog 4)	0.47	-	exc	1	Membrane; single-pass type I membrane protein (Probable)				686
Q9IAT6 UniProt NPD GO	DLLC_BRARE	Delta-like protein C precursor (DeltaC protein) (delC)	0.47	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				664
Q8UWJ4 UniProt NPD GO	DLLD_BRARE	Delta-like protein D precursor (DeltaD protein) (After eight protein)	0.47	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)	cytoplasm [IGI] plasma membrane [IDA]			717
P27707 UniProt NPD GO	DCK_HUMAN	Deoxycytidine kinase (EC 2.7.1.74) (dCK)	0.47	-	cyt	0	Nucleus		125450	2A7Q	260
Q9QY48 UniProt NPD GO	DNS2B_MOUSE	Deoxyribonuclease-2-beta precursor (EC 3.1.22.1) (Deoxyribonuclease II beta) (DNase II beta) (DNase2 ...	0.47	-	exc	0	Lysosome (Probable)	cytoplasm [IDA] extracellular region [IDA]			354
O13836 UniProt NPD GO	DIN1_SCHPO	Dhp1-interacting protein 1	0.47	-	nuc	0					352
P31016 UniProt NPD GO	DLG4_RAT	Discs large homolog 4 (Postsynaptic density protein 95) (PSD-95) (Synapse-associated protein 90) (SA ...	0.47	-	nuc	0	Cell membrane; peripheral membrane protein. High levels in postsynaptic density of neurons in the fo ...	postsynaptic membrane [IDA] synapse [IDA] synaptosome [IDA]		1TQ3	724
Q2NL21 UniProt NPD GO	DCJ11_BOVIN	DnaJ homolog subfamily C member 11	0.47	-	cyt	0					559
P70169 UniProt NPD GO	DOC2B_MOUSE	Double C2-like domain-containing protein beta (Doc2-beta)	0.47	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				412
P08480 UniProt NPD GO	IPSG_FELCA	Double-headed protease inhibitor, submandibular gland	0.47	-	nuc	0	Secreted protein				111
Q62418 UniProt NPD GO	DBNL_MOUSE	Drebrin-like protein (SH3 domain-containing protein 7) (Actin-binding protein 1)	0.47	-	nuc	0	Cytoskeleton. Cortical cytoskeleton. Associates with lamellipodial actin and membrane ruffles	cell cortex [IDA] cytoplasm [IDA] lamellipodium [IDA] ruffle [IDA]			436
Q9UJU6 UniProt NPD GO	DBNL_HUMAN	Drebrin-like protein (SH3 domain-containing protein 7) (Drebrin F) (Cervical SH3P7) (HPK1-interactin ...	0.47	-	nuc	0	Cytoskeleton. Cortical cytoskeleton. Associates with lamellipodial actin	cell cortex [ISS] cytoplasm [ISS] lamellipodium [ISS]		1X67	430
Q02750 UniProt NPD GO	MP2K1_HUMAN	Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) (MAP kinase kinase 1) (MAPK ...	0.47	-	cyt	0			176872	1S9J	392
P29678 UniProt NPD GO	MP2K1_RABIT	Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) (MAP kinase kinase 1) (MAPK ...	0.47	-	cyt	0					392
Q863A5 UniProt NPD GO	DYXC1_GORGO	Dyslexia susceptibility 1 candidate gene 1 protein homolog	0.47	-	nuc	0	Nucleus (By similarity)				420
Q00690 UniProt NPD GO	LYAM2_MOUSE	E-selectin precursor (Endothelial leukocyte adhesion molecule 1) (ELAM-1) (Leukocyte-endothelial cel ...	0.47	-	exc	1	Membrane; single-pass type I membrane protein				612
Q5ZHP7 UniProt NPD GO	EAF2_CHICK	ELL-associated factor 2	0.47	-	nuc	0	Nucleus (By similarity)				264
Q8WWZ3 UniProt NPD GO	EDAD_HUMAN	Ectodysplasin A receptor-associated adapter protein (EDAR-associated death domain protein) (Crinkled ...	0.47	-	nuc	0	Cytoplasm (Probable)	cytoplasm [ISS]	606603		215
P08712 UniProt NPD GO	ENPL_MESAU	Endoplasmin (Heat shock protein 90 kDa beta member 1) (94 kDa glucose-regulated protein) (GRP94) (Fr ...	0.47	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				400
P98072 UniProt NPD GO	ENTK_BOVIN	Enteropeptidase precursor (EC 3.4.21.9) (Enterokinase) [Contains: Enteropeptidase non-catalytic heav ...	0.47	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)			1EKB	1035
P04412 UniProt NPD GO	EGFR_DROME	Epidermal growth factor receptor precursor (EC 2.7.10.1) (Egfr) (Gurken receptor) (Protein torpedo) ...	0.47	+	exc	3 *	Membrane; single-pass type I membrane protein	plasma membrane [TAS]			1426
Q9BYJ1 UniProt NPD GO	LOXE3_HUMAN	Epidermis-type lipoxygenase 3 (EC 1.13.11.-) (e-LOX-3)	0.47	-	cyt	0			607206		711
Q8BMB3 UniProt NPD GO	IF4E3_MOUSE	Eukaryotic translation initiation factor 4E type 3 (eIF4E type 3) (eIF-4E type 3) (mRNA cap-binding ...	0.47	-	nuc	0					245
Q13541 UniProt NPD GO	4EBP1_HUMAN	Eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) (eIF4E-binding protein 1) (Ph ...	0.47	-	mit	0			602223	1WKW	117
Q9NPD3 UniProt NPD GO	EXOS4_HUMAN	Exosome complex exonuclease RRP41 (EC 3.1.13.-) (Ribosomal RNA-processing protein 41) (Exosome compo ...	0.47	+	cyt	0	Cytoplasm. Nucleus; nucleolus	cytoplasm [NAS] nucleolus [NAS]	606491		244
Q7XAK4 UniProt NPD GO	GID2_ORYSA	F-box protein GID2 (Gibberellin-insensitive dwarf protein 2) (Protein GIBBERELLIN INSENSITIVE DWARF2 ...	0.47	-	nuc	0	Nucleus				212
Q8C2S5 UniProt NPD GO	FBXL5_MOUSE	F-box/LRR-repeat protein 5 (F-box and leucine-rich repeat protein 5)	0.47	-	nuc	0					690
Q9UKA1 UniProt NPD GO	FBXL5_HUMAN	F-box/LRR-repeat protein 5 (F-box and leucine-rich repeat protein 5) (F-box protein FBL4/FBL5) (p45S ...	0.47	-	nuc	0		ubiquitin ligase complex [NAS]	605655		691
Q09990 UniProt NPD GO	LIN23_CAEEL	F-box/WD repeat protein lin-23 (Abnormal cell lineage protein 23)	0.47	-	cyt	0	Cytoplasm (Potential)	cytoplasm [NAS]			665
Q75N90 UniProt NPD GO	FBN3_HUMAN	Fibrillin-3 precursor	0.47	-	nuc	0	Secreted protein; extracellular space; extracellular matrix		608529		2809
P50609 UniProt NPD GO	FMOD_RAT	Fibromodulin precursor (FM) (Collagen-binding 59 kDa protein) (Keratan sulfate proteoglycan fibromod ...	0.47	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				376

You are viewing entries 26901 to 26950 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.