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
Q7H6J1 UniProt NPD GO	RPOA_HORJU	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.48	-	cyt	0	Plastid; chloroplast				339
Q7H6J0 UniProt NPD GO	RPOA_HORMA	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.48	-	cyt	0	Plastid; chloroplast				339
Q7H6F6 UniProt NPD GO	RPOA_PSAJU	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.48	-	cyt	0	Plastid; chloroplast				339
Q7YJX8 UniProt NPD GO	RPOB_CALFE	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.48	-	cyt	0	Plastid; chloroplast				1060
Q49L06 UniProt NPD GO	RPOB_EUCGG	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.48	-	nuc	0	Plastid; chloroplast				1072
Q9BBS9 UniProt NPD GO	RPOB_LOTJA	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.48	-	nuc	0	Plastid; chloroplast				1070
Q9MTM4 UniProt NPD GO	RPOC1_OENHO	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.48	-	cyt	0	Plastid; chloroplast				679
P28309 UniProt NPD GO	DEF2_MOUSE	Defensin-related cryptdin 2 precursor	0.48	-	exc	0	Secreted protein				93
P50705 UniProt NPD GO	DEF7_MOUSE	Defensin-related cryptdin 7 precursor	0.48	-	exc	0	Secreted protein				93
O57409 UniProt NPD GO	DLLB_BRARE	Delta-like protein B precursor (DeltaB protein)	0.48	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				615
Q9Y6T7 UniProt NPD GO	DGKB_HUMAN	Diacylglycerol kinase beta (EC 2.7.1.107) (Diglyceride kinase beta) (DGK-beta) (DAG kinase beta) (90 ...	0.48	+	cyt	0	Cytoplasm (By similarity)		604070		804
Q86XP1 UniProt NPD GO	DGKH_HUMAN	Diacylglycerol kinase eta (EC 2.7.1.107) (Diglyceride kinase eta) (DGK-eta) (DAG kinase eta)	0.48	-	nuc	0	Cytoplasm. Translocated from the cytoplasm to endosomes in response to stress stimuli. Isoform 2 is ...		604071		1220
Q64398 UniProt NPD GO	DGKH_MESAU	Diacylglycerol kinase eta (EC 2.7.1.107) (Diglyceride kinase eta) (DGK-eta) (DAG kinase eta) (130 kD ...	0.48	-	nuc	0	Cytoplasm. Translocated from the cytoplasm to endosomes in response to stress stimuli (By similarity ...				1154
Q4PA25 UniProt NPD GO	DPH1_USTMA	Diphthamide biosynthesis protein 1	0.48	-	nuc	0	Cytoplasm (By similarity)				609
Q99M87 UniProt NPD GO	DNJA3_MOUSE	DnaJ homolog subfamily A member 3, mitochondrial precursor (Tumorous imaginal discs protein Tid56 ho ...	0.48	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	cytosol [IDA] mitochondrion [IDA] nucleus [IDA]			480
O75953 UniProt NPD GO	DNJB5_HUMAN	DnaJ homolog subfamily B member 5 (Heat shock protein Hsp40-3) (Heat shock protein cognate 40) (Hsc4 ...	0.48	-	cyt	0					348
O60496 UniProt NPD GO	DOK2_HUMAN	Docking protein 2 (Downstream of tyrosine kinase 2) (p56(dok-2))	0.48	-	nuc	0			604997		412
O70469 UniProt NPD GO	DOK2_MOUSE	Docking protein 2 (Downstream of tyrosine kinase 2) (p56(dok-2)) (Dok-related protein) (Dok-R) (IL-f ...	0.48	-	nuc	0					412
Q99KE3 UniProt NPD GO	DOK4_MOUSE	Docking protein 4 (Downstream of tyrosine kinase 4)	0.48	-	nuc	0					325
Q9FNX5 UniProt NPD GO	DRP1E_ARATH	Dynamin-related protein 1E (Dynamin-like protein E) (Dynamin-like protein 4) (Dynamin-like protein D ...	0.48	-	cyt	0	Cytoplasm. Microtubule-associated				624
Q62165 UniProt NPD GO	DAG1_MOUSE	Dystroglycan precursor (Dystrophin-associated glycoprotein 1) [Contains: Alpha-dystroglycan (Alpha-D ...	0.48	-	nuc	1	Alpha-dystroglycan: Secreted protein; extracellular space. Beta-dystroglycan: Cell membrane; single- ...	dystroglycan complex [IDA] insoluble fraction [IDA] plasma membrane [IDA]		1U2C	893
Q28685 UniProt NPD GO	DAG1_RABIT	Dystroglycan precursor (Dystrophin-associated glycoprotein 1) [Contains: Alpha-dystroglycan (Alpha-D ...	0.48	-	exc	1	Alpha-dystroglycan: Secreted protein; extracellular space. Beta-dystroglycan: Cell membrane; single- ...				895
Q5JVL4 UniProt NPD GO	EFHC1_HUMAN	EF-hand domain-containing protein 1	0.48	-	nuc	0		axoneme [ISS] cell soma [ISS]	608815		640
Q8R2E9 UniProt NPD GO	ERO1B_MOUSE	ERO1-like protein beta precursor (EC 1.8.4.-) (ERO1-Lbeta) (Oxidoreductin-1-Lbeta) (Endoplasmic oxid ...	0.48	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				467
Q9LV01 UniProt NPD GO	ETOL2_ARATH	ETO1-like protein 2 (Ethylene overproducer 1-like protein 2)	0.48	-	cyt	0					925
O94429 UniProt NPD GO	EFG2_SCHPO	Elongation factor G 2, mitochondrial precursor (mEF-G-2)	0.48	-	mit	0	Mitochondrion (By similarity)				813
Q701P2 UniProt NPD GO	KO1_GIBIN	Ent-kaurene oxidase (EC 1.14.13.78) (Cytochrome P450-4) (Cytochrome P450 503A1)	0.48	-	cyt	0					525
O35290 UniProt NPD GO	ECP3_MOUSE	Eosinophil cationic-type ribonuclease 3 precursor (MR-3)	0.48	-	nuc	0					156
Q60750 UniProt NPD GO	EPHA1_MOUSE	Ephrin type-A receptor 1 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor ESK)	0.48	-	end	1 *	Membrane; single-pass type I membrane protein			1X5A	977
P15976 UniProt NPD GO	GATA1_HUMAN	Erythroid transcription factor (GATA-binding factor 1) (GATA-1) (Eryf1) (GF-1) (NF-E1 DNA-binding pr ...	0.48	+	nuc	0	Nucleus	nucleus [TAS]	305371		413
Q9HGI8 UniProt NPD GO	ERF2_KLULA	Eukaryotic peptide chain release factor GTP-binding subunit (ERF2) (Translation release factor 3) (P ...	0.48	-	nuc	0	Cytoplasm (Probable)				700
Q5R8D1 UniProt NPD GO	IF31_PONPY	Eukaryotic translation initiation factor 3 subunit 1 (eIF-3 alpha)	0.48	-	cyt	0					259
Q6BT51 UniProt NPD GO	EXO70_DEBHA	Exocyst complex protein EXO70	0.48	-	nuc	0	Bud (By similarity). Bud neck (By similarity)				613
Q58DB6 UniProt NPD GO	EYA2_BOVIN	Eyes absent homolog 2 (EC 3.1.3.48)	0.48	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				537
O14745 UniProt NPD GO	NHERF_HUMAN	Ezrin-radixin-moesin-binding phosphoprotein 50 (EBP50) (Na(+)/H(+) exchange regulatory cofactor NHE- ...	0.48	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein. Colocalizes with actin in microvilli-rich ap ...	actin cytoskeleton [TAS]	604990	1SGH	357
Q5NBU5 UniProt NPD GO	FBX39_MOUSE	F-box only protein 39	0.48	-	cyt	0					443
Q66H10 UniProt NPD GO	FBX39_RAT	F-box only protein 39	0.48	-	cyt	0					443
Q8C7B6 UniProt NPD GO	FXL22_MOUSE	F-box/LRR-repeat protein 22 (F-box and leucine-rich repeat protein 22)	0.48	-	nuc	0					236
Q8N3Y1 UniProt NPD GO	FBXW8_HUMAN	F-box/WD repeat protein 8 (F-box and WD-40 domain protein 8) (F-box only protein 29)	0.48	+	cyt	0			609073		598
Q07895 UniProt NPD GO	YL001_YEAST	FAS1 domain-containing protein YLR001C precursor	0.48	-	end	1	Vacuole; vacuolar membrane; type I single-pass membrane protein (Potential)	mitochondrion [IDA] vacuolar membrane (sensu Fungi) [IDA]			862
Q59VR3 UniProt NPD GO	FKBP3_CANAL	FK506-binding protein 3 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.48	-	nuc	0	Nucleus; nucleolus (By similarity)				426
P59647 UniProt NPD GO	FXYD5_RAT	FXYD domain-containing ion transport regulator 5 precursor	0.48	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				178
P14448 UniProt NPD GO	FIBA_CHICK	Fibrinogen alpha chain precursor [Contains: Fibrinopeptide A]	0.48	-	nuc	0	Secreted protein			1M1J	741
P02674 UniProt NPD GO	FIBA1_PETMA	Fibrinogen alpha-1 chain precursor [Contains: Fibrinopeptide A] (Fragment)	0.48	-	nuc	0	Secreted protein			1N73	966
P51887 UniProt NPD GO	FMOD_CHICK	Fibromodulin precursor (FM) (Keratan sulfate proteoglycan fibromodulin) (KSPG fibromodulin)	0.48	-	exc	0	Secreted protein; extracellular space; extracellular matrix				380
Q99853 UniProt NPD GO	FOXB1_HUMAN	Forkhead box protein B1 (Transcription factor FKH-5)	0.48	+	nuc	0	Nucleus (By similarity)				324
O43638 UniProt NPD GO	FREA_HUMAN	Forkhead-related transcription factor 10 (FREAC-10) (Forkhead-like 18 protein)	0.48	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	602939		330
O75459 UniProt NPD GO	GAGB1_HUMAN	G antigen family B member 1 (Prostate-associated gene 1 protein) (PAGE-1) (GAGE-9) (AL5)	0.48	-	mit	0			300288		146
Q9GZZ7 UniProt NPD GO	GFRA4_HUMAN	GDNF family receptor alpha-4 precursor (GFR-alpha-4) (Persephin receptor)	0.48	-	exc	0	Isoform GFRalpha4a, isoform GFRalpha4b: Cell membrane; lipid-anchor; GPI-anchor. Isoform GFRalpha4c: ...				299
P55041 UniProt NPD GO	GEM_MOUSE	GTP-binding protein GEM (GTP-binding mitogen-induced T-cell protein) (RAS-like protein KIR)	0.48	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side				295

You are viewing entries 26201 to 26250 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.