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
Q8CEQ0 UniProt NPD GO	CDKL1_MOUSE	Cyclin-dependent kinase-like 1 (EC 2.7.11.22)	0.61	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				352
Q00555 UniProt NPD GO	CFTR_SHEEP	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.61	-	end	11	Membrane; multi-pass membrane protein			1CKZ	1481
P07252 UniProt NPD GO	CBP1_YEAST	Cytochrome B pre-mRNA-processing protein 1	0.61	-	mit	0		extrinsic to mitochondrial inner membrane [IDA] mitochondrion [IDA]			654
Q6E3F2 UniProt NPD GO	CPB2_CAERE	Cytoplasmic polyadenylation element-binding protein 2	0.61	-	nuc	0					571
Q6CUD4 UniProt NPD GO	DUO1_KLULA	DASH complex subunit DUO1 (Outer kinetochore protein DUO1)	0.61	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				208
O54786 UniProt NPD GO	DFFA_MOUSE	DNA fragmentation factor subunit alpha (DNA fragmentation factor 45 kDa subunit) (DFF-45) (Inhibitor ...	0.61	-	nuc	0	Cytoplasm (By similarity)			1F2R	331
P40469 UniProt NPD GO	MET18_YEAST	DNA repair/transcription protein MET18/MMS19	0.61	-	cyt	0	Nucleus	nucleoplasm [IMP]			1032
Q6DIH3 UniProt NPD GO	MCM2_XENTR	DNA replication licensing factor mcm2 (Minichromosome maintenance protein 2)	0.61	-	cyt	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	chromatin [ISS] MCM complex [ISS]			884
Q9JKB3 UniProt NPD GO	DBPA_MOUSE	DNA-binding protein A (Cold shock domain-containing protein A) (Y-box protein 3)	0.61	-	nuc	0	Cytoplasm. Nucleus (By similarity)	nucleus [IDA]			361
Q9UPW6 UniProt NPD GO	SATB2_HUMAN	DNA-binding protein SATB2 (Special AT-rich sequence-binding protein 2)	0.61	-	nuc	0	Nucleus (By similarity)		608148	2CSF	733
P17545 UniProt NPD GO	RPB1_TRYBB	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6)	0.61	-	nuc	0	Nucleus				1766
P17546 UniProt NPD GO	RPB2_TRYBB	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6)	0.61	-	nuc	0	Nucleus				1766
Q755B3 UniProt NPD GO	RPB9_ASHGO	DNA-directed RNA polymerase II subunit 9 (EC 2.7.7.6)	0.61	-	nuc	1	Nucleus (By similarity)				122
Q6L3A6 UniProt NPD GO	RPOC1_SACHY	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.61	-	cyt	0	Plastid; chloroplast				683
Q6ENX2 UniProt NPD GO	RPOC1_SACOF	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.61	-	cyt	0	Plastid; chloroplast				683
P84634 UniProt NPD GO	DCL4_ARATH	Dicer-like protein 4 (EC 3.1.26.-)	0.61	-	cyt	0	Nucleus				1589
Q5PYH5 UniProt NPD GO	DLG1L_BRARE	Discs large homolog 1-like protein (Synapse-associated protein 97B) (SAP-97B)	0.61	-	mit	0	Membrane; peripheral membrane protein (By similarity)	basolateral plasma membrane [ISS] intercellular junction [ISS] plasma membrane [ISS]			827
Q63622 UniProt NPD GO	DLG2_RAT	Discs large homolog 2 (Postsynaptic density protein PSD-93) (Channel-associated protein of synapse-1 ...	0.61	-	nuc	0	Membrane; lipid-anchor. Concentrated in soma and postsynaptic density of a subset of neurons	membrane fraction [IMP]			852
Q9NXW2 UniProt NPD GO	DNJBC_HUMAN	DnaJ homolog subfamily B member 12	0.61	-	nuc	1	Membrane; single-pass membrane protein (Potential)		608376	2CTP	375
Q9UKB3 UniProt NPD GO	DJC12_HUMAN	DnaJ homolog subfamily C member 12 (J domain-containing protein 1)	0.61	-	nuc	0			606060	2CTQ	198
Q7L591 UniProt NPD GO	DOK3_HUMAN	Docking protein 3 (Downstream of tyrosine kinase 3)	0.61	-	nuc	0	Cytoplasm (By similarity)				496
Q9BYI3 UniProt NPD GO	DRC1A_HUMAN	Down-regulated by CTNNB1 protein A	0.61	-	nuc	0	Cytoplasm. Mainly				521
Q91Z46 UniProt NPD GO	DUS7_MOUSE	Dual specificity protein phosphatase 7 (EC 3.1.3.48) (EC 3.1.3.16) (Fragment)	0.61	-	nuc	0	Cytoplasm (By similarity)				358
Q9UJW0 UniProt NPD GO	DCTN4_HUMAN	Dynactin subunit 4 (Dynactin subunit p62)	0.61	-	nuc	0	Cytoplasm. Centrosome. Has a punctate cytoplasmic distribution as well as centrosomal distribution t ...	centrosome [TAS] cytoplasm [TAS] nucleus [TAS]			460
Q5R7U7 UniProt NPD GO	DCTN4_PONPY	Dynactin subunit 4 (Dynactin subunit p62)	0.61	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Has a punctate cytoplasmic distribution as we ...				460
P21575 UniProt NPD GO	DYN1_RAT	Dynamin-1 (EC 3.6.5.5) (D100) (Dynamin, brain) (B-dynamin)	0.61	-	nuc	0	Cytoplasm. Microtubule-associated			2AKA	851
O35303 UniProt NPD GO	DNM1L_RAT	Dynamin-1-like protein (EC 3.6.5.5) (Dynamin-like protein)	0.61	-	nuc	0	Cytoplasm; cytosol (By similarity). Mainly. Intracellular membrane; peripheral membrane protein (By ...				755
Q16959 UniProt NPD GO	DYI2_ANTCR	Dynein intermediate chain 2, ciliary	0.61	-	nuc	0					702
Q62940 UniProt NPD GO	NEDD4_RAT	E3 ubiquitin-protein ligase NEDD4 (EC 6.3.2.-)	0.61	-	cyt	0	Cytoplasm			1I5H	887
O00321 UniProt NPD GO	ETV2_HUMAN	ETS translocation variant 2 (Ets-related protein 71)	0.61	+	nuc	0	Nucleus		609358		341
Q9UKW6 UniProt NPD GO	ELF5_HUMAN	ETS-related transcription factor Elf-5 (E74-like factor 5) (Epithelium-specific Ets transcription fa ...	0.61	-	mit	0			605169		265
O95936 UniProt NPD GO	EOMES_HUMAN	Eomesodermin homolog	0.61	+	nuc	0	Nucleus (Potential)		604615		686
O61460 UniProt NPD GO	VAB1_CAEEL	Ephrin receptor 1 precursor (EC 2.7.10.1) (Tyrosine-protein kinase Eph receptor) (Variable abnormal ...	0.61	-	exc	2	Membrane; single-pass type I membrane protein	axon [IDA] integral to membrane [ISS]			1122
P00533 UniProt NPD GO	EGFR_HUMAN	Epidermal growth factor receptor precursor (EC 2.7.10.1) (Receptor tyrosine-protein kinase ErbB-1)	0.61	-	exc	2	Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein	cytoplasm [IDA] endosome [IDA] extracellular space [NAS] nucleus [IDA] plasma membrane [IDA]	131550	2GS7	1210
Q40476 UniProt NPD GO	ERF1_TOBAC	Ethylene-responsive transcription factor 1 (Ethylene-responsive element-binding factor 1) (EREBP-1) ...	0.61	+	nuc	0	Nucleus (Probable)				236
O80341 UniProt NPD GO	ERF5_ARATH	Ethylene-responsive transcription factor 5 (Ethylene-responsive element-binding factor 5) (EREBP-5) ...	0.61	-	nuc	0	Nucleus (Probable)				300
Q9HGI7 UniProt NPD GO	ERF2_CANMA	Eukaryotic peptide chain release factor GTP-binding subunit (ERF2) (Translation release factor 3) (P ...	0.61	-	nuc	0	Cytoplasm (Probable)				712
Q5ZJ43 UniProt NPD GO	EXOC8_CHICK	Exocyst complex component 8	0.61	-	nuc	0	Cytoplasm (By similarity)				708
Q6MFS1 UniProt NPD GO	EXO70_NEUCR	Exocyst complex protein EXO70	0.61	-	nuc	0	Bud (By similarity). Bud neck (By similarity)				653
Q9JHI7 UniProt NPD GO	EXOS9_MOUSE	Exosome complex exonuclease RRP45 (EC 3.1.13.-) (Exosome component 9) (Polymyositis/scleroderma auto ...	0.61	+	cyt	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)	nucleolus [TAS]			438
Q802D3 UniProt NPD GO	XPO4_BRARE	Exportin-4	0.61	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				1150
Q8QHJ8 UniProt NPD GO	XPO6_BRARE	Exportin-6 (Exp6)	0.61	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Shuttles between the nucleus and the cytoplasm ( ...				1128
P41180 UniProt NPD GO	CASR_HUMAN	Extracellular calcium-sensing receptor precursor (CaSR) (Parathyroid Cell calcium-sensing receptor)	0.61	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	601199		1078
Q8TB52 UniProt NPD GO	FBX30_HUMAN	F-box only protein 30	0.61	-	nuc	0			609101		745
Q7X923 UniProt NPD GO	SPT16_ORYSA	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16)	0.61	+	nuc	0	Nucleus (By similarity)				1056
Q2UBF1 UniProt NPD GO	SPT16_ASPOR	FACT complex subunit spt16 (Facilitates chromatin transcription complex subunit spt16)	0.61	+	mit	0	Nucleus (By similarity)				1042
Q7Z6J4 UniProt NPD GO	FGD2_HUMAN	FYVE, RhoGEF and PH domain-containing protein 2 (Zinc finger FYVE domain-containing protein 4)	0.61	-	nuc	0	Cytoplasm (Probable)	cytoplasm [ISS] Golgi apparatus [ISS] lamellipodium [ISS] ruffle [ISS]	605091		655
Q6QHK4 UniProt NPD GO	FIGLA_HUMAN	Factor in the germline alpha (Transcription factor FIGa) (FIGalpha)	0.61	-	nuc	0	Nucleus (Probable)		608697		219
Q9NPI8 UniProt NPD GO	FANCF_HUMAN	Fanconi anemia group F protein (Protein FACF)	0.61	-	cyt	0	Nucleus		603467		374
Q9N5M6 UniProt NPD GO	FBF1_CAEEL	Fem-3 mRNA-binding factor 1	0.61	-	nuc	0	Cytoplasm				614

You are viewing entries 18401 to 18450 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.